From sanges at biogem.it Thu Apr 1 04:27:06 2004 From: sanges at biogem.it (Remo Sanges) Date: Thu Apr 1 04:32:15 2004 Subject: [Bioperl-l] Singapore In-Reply-To: <200403310639.46455.richard@uwc.net> References: <200403310639.46455.richard@uwc.net> Message-ID: Hi Richard, you could try here: http://www.tll.org.sg/career/positions.asp Remo On Mar 30, 2004, at 8:39 PM, Richard Holland wrote: > Hi guys, > > Does anyone know anything about finding database/software/web > development > (bioinformatics-related or otherwise) work in Singapore? I'm finding it > rather hard to pin down any concrete information, and am wondering if I > should just go there and start knocking on doors rather than rely on > e-mail > to get my CV to the right people. > > I understand Elia Stupka used to work there so maybe he knows > something? I'm > already in touch with Mark Schreiber but obviously the more the > merrier. It's > turning out not to be the easiest of tasks. > > cheers, > Richard > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From abrusan at mpil-ploen.mpg.de Thu Apr 1 04:33:24 2004 From: abrusan at mpil-ploen.mpg.de (Gyoergy Abrusan) Date: Thu Apr 1 04:37:07 2004 Subject: [Bioperl-l] deleting string fragments? Message-ID: <406BE1E4.2040507@mpil-ploen.mpg.de> Dear All, I would like to ask whether there is a command that deletes a certain fragment of a sring. what I mean is: eg. I have stings like adfdfgfgg-dfgdfmgfgfgfg I would like to remove -dfg and print out only adfdfgfggdfmgfgfgfg Is there a commad (something similar to chop)that removes an arbitrary substring from a string (the place of the target sequences is alvays different)? eg.: open (OUT, ">RESULTS.txt") while(<>) { if ($_=~ /-dfg/g) {cut out -dfg ??? print OUT "$_";} else {print OUT "$_";} } close OUT; I would greatly appreciate any help. Thanking you in advance. Best, Gyorgy Abrusan From paulo.david at netvisao.pt Thu Apr 1 05:03:45 2004 From: paulo.david at netvisao.pt (Paulo Almeida) Date: Thu Apr 1 05:05:01 2004 Subject: [Bioperl-l] deleting string fragments? In-Reply-To: <406BE1E4.2040507@mpil-ploen.mpg.de> References: <406BE1E4.2040507@mpil-ploen.mpg.de> Message-ID: <406BE901.5080306@netvisao.pt> I think the easiest way is to use a substitution: while (<>){ s/-dfg//gi; print OUT; } 's/something/other/gi ' replaces 'something' with 'other'. The 'g' and 'i' options make the substitution work in all instances of the string and in a case insensitive manner, respectively. There are some characters that you need to escape, like '.' and slashes, but I don't think you need to escape dashes, so what I wrote should work. -Paulo Almeida Gyoergy Abrusan wrote: > Dear All, > > I would like to ask whether there is a command that deletes a certain > fragment of a sring. > > what I mean is: > eg. I have stings like > > adfdfgfgg-dfgdfmgfgfgfg > > I would like to remove -dfg and print out only > > adfdfgfggdfmgfgfgfg > > Is there a commad (something similar to chop)that removes an arbitrary > substring from a string (the place of the target sequences is alvays > different)? > > eg.: > > open (OUT, ">RESULTS.txt") > > while(<>) > { > if ($_=~ /-dfg/g) > {cut out -dfg ??? > print OUT "$_";} > > else > {print OUT "$_";} > } > close OUT; > > > I would greatly appreciate any help. > Thanking you in advance. > > Best, > > Gyorgy Abrusan From james.wasmuth at ed.ac.uk Thu Apr 1 05:03:32 2004 From: james.wasmuth at ed.ac.uk (James Wasmuth) Date: Thu Apr 1 05:09:14 2004 Subject: [Bioperl-l] deleting string fragments? In-Reply-To: <406BE1E4.2040507@mpil-ploen.mpg.de> References: <406BE1E4.2040507@mpil-ploen.mpg.de> Message-ID: <406BE8F4.3010107@ed.ac.uk> Hi Gyoergy the regex is s/-dfg//g; this says substitute the string '-dfg' with nothing. check out 'perldoc perlre' -james Gyoergy Abrusan wrote: > Dear All, > > I would like to ask whether there is a command that deletes a certain > fragment of a sring. > > what I mean is: > eg. I have stings like > > adfdfgfgg-dfgdfmgfgfgfg > > I would like to remove -dfg and print out only > > adfdfgfggdfmgfgfgfg > > Is there a commad (something similar to chop)that removes an arbitrary > substring from a string (the place of the target sequences is alvays > different)? > > eg.: > > open (OUT, ">RESULTS.txt") > > while(<>) > { > if ($_=~ /-dfg/g) > {cut out -dfg ??? > print OUT "$_";} > > else > {print OUT "$_";} > } > close OUT; > > > I would greatly appreciate any help. > Thanking you in advance. > > Best, > > Gyorgy Abrusan > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- "I have not failed. I've just found 10,000 ways that don't work." --- Thomas Edison Nematode Bioinformatics | Blaxter Nematode Genomics Group | School of Biological Sciences | Ashworth Laboratories | tel: +44 131 650 7403 University of Edinburgh | web: www.nematodes.org Edinburgh | EH9 3JT | UK | From cdwan at mail.ahc.umn.edu Thu Apr 1 12:55:36 2004 From: cdwan at mail.ahc.umn.edu (Chris Dwan (CCGB)) Date: Thu Apr 1 13:00:54 2004 Subject: [Bioperl-l] Parsing a Fasta file In-Reply-To: <0015DB1919DAA4469056B78E996ED9FA22FB07@BIONIC.biopolis.one-north.com> References: <0015DB1919DAA4469056B78E996ED9FA22FB07@BIONIC.biopolis.one-north.com> Message-ID: > I have a file that contains protein sequences in fasta format. The module you seek is Sio::SeqIO. Here's an example: #!/usr/local/bin/perl use strict; use Bio::SeqIO; my $filename = shift; my $count = 0; my $in = Bio::SeqIO->new('-file' => "<$filename", '-format' => 'fasta'); while (my $seq = $in->next_seq()) { print "For sequence $count\n"; print "The defline was: " . $seq->id() . " " . $seq->desc() . "\n"; print "The sequence was: " . length($seq->seq()) . "bp in length\n"; $count++; } From barry.moore at genetics.utah.edu Thu Apr 1 13:02:01 2004 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Thu Apr 1 13:07:10 2004 Subject: [Bioperl-l] Trouble installing bioperl-ext / Bio::SeqIO::staden::read Message-ID: <406C5919.9040909@genetics.utah.edu> I want to use Bio::SeqIO::staden::read to get at the sequence data directly from an abi output file. Assuming that I've choosen the correct tool...? I'm having trouble installing bioperl-ext-1.4 and here's the details of the problem. I'm running RedHat 9, and BioPerl 1.4. I have Inline::C and Inline::MakeMaker installed. I've installed io-lib-1.8.11 from source that I aquired from the Staden ftp site. That seemed to go well with no errors (at least not that I picked up). The installation was missing os.h (as noted in the bioperl-ext README), so I copied it from the downloaded package into /usr/local/include. I've run Makefile.PL and tried to install all of bioperl-ext, and just the Bio::SeqIO::staden portion. Running Makefile.PL appears to run happily, but running make generates a lot of errors (pasted at the end). My specific questions are: At the end of the make errors it suggests that, "To debug the problem, cd to the build directory, and inspect the output files." I've looked at all the files in the build directory that the error message specified (The build directory was: /home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden/read), and none of it meant much to me (I'm clearly not a developer). Should I be getting debugging clues out of those files, and if so, what? At the end of the installation instructions for Bio::SeqIO::staden::read it says, "A failed compilation is most likely due to an incomplete io_lib installation; make sure that all the required io_lib ".h" files are in place." How do I determine what ".h" files are required in io_lib? I currently have the following: abi.h compression.h misc.h scf_extras.h traceType.h alf.h error.h open_trace_file.h scf.h translate.h array.h expFileIO.h os.h seqIOABI.h xalloc.h calc_crc.h fpoint.h plain.h seqIOCTF.h ztr.h compress.h mach-io.h Read.h tar_format.h Thanks for any help, Barry -------------------------------------------------------------------------------------------------------------- Makefile.PL output: [root@Tatshenshini staden]# perl Makefile.PL Found Staden io_lib "libread" in /usr/local/lib ... Automatically using the Read.h found in /usr/local/include/io_lib ... Writing Makefile for Bio::SeqIO::staden::read make output: [root@Tatshenshini staden]# make cp read.pm blib/lib/Bio/SeqIO/staden/read.pm /usr/bin/perl -Mblib -MInline=NOISY,_INSTALL_ -MBio::SeqIO::staden::read -e1 0.0 1 blib/arch Starting Build Prepocess Stage Finished Build Prepocess Stage Starting Build Parse Stage Finished Build Parse Stage Starting Build Glue 1 Stage Finished Build Glue 1 Stage Starting Build Glue 2 Stage Finished Build Glue 2 Stage Starting Build Glue 3 Stage Finished Build Glue 3 Stage Starting Build Compile Stage Starting "perl Makefile.PL" Stage Writing Makefile for Bio::SeqIO::staden::read Finished "perl Makefile.PL" Stage Starting "make" Stage make[1]: Entering directory `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inli ne/build/Bio/SeqIO/staden/read' /usr/bin/perl /usr/lib/perl5/5.8.0/ExtUtils/xsubpp -typemap /usr/lib/perl5/5.8. 0/ExtUtils/typemap read.xs > read.xsc && mv read.xsc read.c gcc -c -I/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden -I/usr/local/include/io_ lib -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS -DDEBUGGING -fno-strict-alias ing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/inclu de/gdbm -O2 -march=i386 -mcpu=i686 -g -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC "-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE" read.c In file included from /usr/local/include/io_lib/Read.h:43, from read.xs:5: /usr/local/include/io_lib/os.h:9:1: warning: "INT_MAX" redefined In file included from /usr/include/sys/param.h:22, from /usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/perl.h:4 37, from read.xs:2: /usr/lib/gcc-lib/i386-redhat-linux/3.2.2/include/limits.h:65:1: warning: this is the location of the previous definition In file included from /usr/local/include/io_lib/Read.h:43, from read.xs:5: /usr/local/include/io_lib/os.h:10:1: warning: "SHRT_MAX" redefined In file included from /usr/include/sys/param.h:22, from /usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/perl.h:4 37, from read.xs:2: /usr/lib/gcc-lib/i386-redhat-linux/3.2.2/include/limits.h:56:1: warning: this is the location of the previous definition In file included from /usr/local/include/io_lib/Read.h:43, from read.xs:5: /usr/local/include/io_lib/os.h:24:4: #error No 2-byte integer type found. /usr/local/include/io_lib/os.h:34:4: #error No 4-byte integer type found. In file included from /usr/local/include/io_lib/Read.h:43, from read.xs:5: /usr/local/include/io_lib/os.h:40: parse error before "int_2" /usr/local/include/io_lib/os.h:40: warning: data definition has no type or stora ge class /usr/local/include/io_lib/os.h:41: parse error before "uint_2" /usr/local/include/io_lib/os.h:41: warning: data definition has no type or stora ge class /usr/local/include/io_lib/os.h:42: parse error before "int_4" /usr/local/include/io_lib/os.h:42: warning: data definition has no type or stora ge class /usr/local/include/io_lib/os.h:43: parse error before "uint_4" /usr/local/include/io_lib/os.h:43: warning: data definition has no type or stora ge class /usr/local/include/io_lib/os.h:46: parse error before "f_int" /usr/local/include/io_lib/os.h:46: warning: data definition has no type or stora ge class /usr/local/include/io_lib/os.h:47: parse error before "f_implicit" /usr/local/include/io_lib/os.h:47: warning: data definition has no type or stora ge class /usr/local/include/io_lib/os.h:51: parse error before "int_f" /usr/local/include/io_lib/os.h:51: warning: data definition has no type or stora ge class /usr/local/include/io_lib/os.h:52: parse error before "int_fl" /usr/local/include/io_lib/os.h:52: warning: data definition has no type or stora ge class In file included from /usr/local/include/io_lib/Read.h:44, from read.xs:5: /usr/local/include/io_lib/scf.h:79: parse error before "uint_4" /usr/local/include/io_lib/scf.h:79: warning: no semicolon at end of struct or un ion /usr/local/include/io_lib/scf.h:80: warning: data definition has no type or stor age class /usr/local/include/io_lib/scf.h:81: parse error before "samples_offset" /usr/local/include/io_lib/scf.h:81: warning: data definition has no type or stor age class /usr/local/include/io_lib/scf.h:82: parse error before "bases" /usr/local/include/io_lib/scf.h:82: warning: data definition has no type or stor age class /usr/local/include/io_lib/scf.h:83: parse error before "bases_left_clip" /usr/local/include/io_lib/scf.h:83: warning: data definition has no type or stor age class /usr/local/include/io_lib/scf.h:84: parse error before "bases_right_clip" /usr/local/include/io_lib/scf.h:84: warning: data definition has no type or stor age class /usr/local/include/io_lib/scf.h:85: parse error before "bases_offset" /usr/local/include/io_lib/scf.h:85: warning: data definition has no type or stor age class /usr/local/include/io_lib/scf.h:86: parse error before "comments_size" /usr/local/include/io_lib/scf.h:86: warning: data definition has no type or stor age class /usr/local/include/io_lib/scf.h:87: parse error before "comments_offset" /usr/local/include/io_lib/scf.h:87: warning: data definition has no type or stor age class /usr/local/include/io_lib/scf.h:89: parse error before "sample_size" /usr/local/include/io_lib/scf.h:89: warning: data definition has no type or stor age class /usr/local/include/io_lib/scf.h:90: parse error before "code_set" /usr/local/include/io_lib/scf.h:90: warning: data definition has no type or stor age class /usr/local/include/io_lib/scf.h:91: parse error before "private_size" /usr/local/include/io_lib/scf.h:91: warning: data definition has no type or stor age class /usr/local/include/io_lib/scf.h:92: parse error before "private_offset" /usr/local/include/io_lib/scf.h:92: warning: data definition has no type or stor age class /usr/local/include/io_lib/scf.h:93: parse error before "spare" /usr/local/include/io_lib/scf.h:93: warning: data definition has no type or stor age class /usr/local/include/io_lib/scf.h:94: parse error before '}' token /usr/local/include/io_lib/scf.h:94: warning: data definition has no type or stor age class /usr/local/include/io_lib/scf.h:110: parse error before "uint_2" /usr/local/include/io_lib/scf.h:110: warning: no semicolon at end of struct or u nion /usr/local/include/io_lib/scf.h:111: warning: data definition has no type or sto rage class /usr/local/include/io_lib/scf.h:112: parse error before "sample_G" /usr/local/include/io_lib/scf.h:112: warning: data definition has no type or sto rage class /usr/local/include/io_lib/scf.h:113: parse error before "sample_T" /usr/local/include/io_lib/scf.h:113: warning: data definition has no type or sto rage class /usr/local/include/io_lib/scf.h:114: warning: data definition has no type or sto rage class /usr/local/include/io_lib/scf.h:120: parse error before "uint_4" /usr/local/include/io_lib/scf.h:120: warning: no semicolon at end of struct or u nion /usr/local/include/io_lib/scf.h:126: conflicting types for `spare' /usr/local/include/io_lib/scf.h:93: previous declaration of `spare' /usr/local/include/io_lib/scf.h:127: parse error before '}' token /usr/local/include/io_lib/scf.h:127: warning: data definition has no type or sto rage class /usr/local/include/io_lib/scf.h:140: parse error before "Header" /usr/local/include/io_lib/scf.h:140: warning: no semicolon at end of struct or u nion /usr/local/include/io_lib/scf.h:143: parse error before "Samples2" /usr/local/include/io_lib/scf.h:143: warning: no semicolon at end of struct or u nion /usr/local/include/io_lib/scf.h:144: warning: data definition has no type or sto rage class /usr/local/include/io_lib/scf.h:145: parse error before '*' token /usr/local/include/io_lib/scf.h:145: conflicting types for `bases' /usr/local/include/io_lib/scf.h:82: previous declaration of `bases' /usr/local/include/io_lib/scf.h:145: warning: data definition has no type or sto rage class /usr/local/include/io_lib/scf.h:148: parse error before '}' token /usr/local/include/io_lib/scf.h:148: warning: data definition has no type or sto rage class /usr/local/include/io_lib/scf.h:167: parse error before "Header" /usr/local/include/io_lib/scf.h:199: parse error before "Samples2" /usr/local/include/io_lib/scf.h:207: parse error before "Samples2" /usr/local/include/io_lib/scf.h:215: parse error before "Samples2" /usr/local/include/io_lib/scf.h:223: parse error before "Bases" /usr/local/include/io_lib/scf.h:231: parse error before "Bases" /usr/local/include/io_lib/scf.h:239: parse error before "Bases" /usr/local/include/io_lib/scf.h:258: parse error before '*' token /usr/local/include/io_lib/scf.h:258: warning: data definition has no type or sto rage class /usr/local/include/io_lib/scf.h:259: parse error before '*' token /usr/local/include/io_lib/scf.h:259: warning: data definition has no type or sto rage class /usr/local/include/io_lib/scf.h:273: parse error before "Header" /usr/local/include/io_lib/scf.h:305: parse error before "Samples2" /usr/local/include/io_lib/scf.h:313: parse error before "Samples2" /usr/local/include/io_lib/scf.h:321: parse error before "Samples2" /usr/local/include/io_lib/scf.h:329: parse error before "Bases" /usr/local/include/io_lib/scf.h:337: parse error before "Bases" /usr/local/include/io_lib/scf.h:345: parse error before "Bases" /usr/local/include/io_lib/scf.h:370: parse error before '*' token /usr/local/include/io_lib/scf.h:371: parse error before '*' token /usr/local/include/io_lib/scf.h:407: parse error before '*' token /usr/local/include/io_lib/scf.h:408: warning: data definition has no type or sto rage class /usr/local/include/io_lib/scf.h:413: parse error before '*' token /usr/local/include/io_lib/scf.h:432: parse error before "samples" In file included from read.xs:5: /usr/local/include/io_lib/Read.h:93: parse error before "TRACE" /usr/local/include/io_lib/Read.h:93: warning: data definition has no type or sto rage class /usr/local/include/io_lib/Read.h:104: parse error before "TRACE" /usr/local/include/io_lib/Read.h:104: warning: no semicolon at end of struct or union /usr/local/include/io_lib/Read.h:105: warning: data definition has no type or st orage class /usr/local/include/io_lib/Read.h:106: parse error before '*' token /usr/local/include/io_lib/Read.h:106: warning: data definition has no type or st orage class /usr/local/include/io_lib/Read.h:107: parse error before '*' token /usr/local/include/io_lib/Read.h:107: warning: data definition has no type or st orage class /usr/local/include/io_lib/Read.h:108: parse error before "maxTraceVal" /usr/local/include/io_lib/Read.h:108: warning: data definition has no type or st orage class /usr/local/include/io_lib/Read.h:111: conflicting types for `base' /usr/local/include/io_lib/scf.h:125: previous declaration of `base' /usr/local/include/io_lib/Read.h:112: parse error before '*' token /usr/local/include/io_lib/Read.h:112: warning: data definition has no type or st orage class /usr/local/include/io_lib/Read.h:122: conflicting types for `prob_A' /usr/local/include/io_lib/scf.h:121: previous declaration of `prob_A' /usr/local/include/io_lib/Read.h:123: conflicting types for `prob_C' /usr/local/include/io_lib/scf.h:122: previous declaration of `prob_C' /usr/local/include/io_lib/Read.h:124: conflicting types for `prob_G' /usr/local/include/io_lib/scf.h:123: previous declaration of `prob_G' /usr/local/include/io_lib/Read.h:125: conflicting types for `prob_T' /usr/local/include/io_lib/scf.h:124: previous declaration of `prob_T' /usr/local/include/io_lib/Read.h:134: parse error before '}' token /usr/local/include/io_lib/Read.h:134: warning: data definition has no type or st orage class /usr/local/include/io_lib/Read.h:154: parse error before '*' token /usr/local/include/io_lib/Read.h:154: warning: data definition has no type or st orage class /usr/local/include/io_lib/Read.h:155: parse error before '*' token /usr/local/include/io_lib/Read.h:155: warning: data definition has no type or st orage class /usr/local/include/io_lib/Read.h:166: parse error before "Read" /usr/local/include/io_lib/Read.h:167: parse error before "Read" /usr/local/include/io_lib/Read.h:178: parse error before '*' token /usr/local/include/io_lib/Read.h:178: warning: data definition has no type or st orage class /usr/local/include/io_lib/Read.h:184: parse error before '*' token /usr/local/include/io_lib/Read.h:199: parse error before '*' token /usr/local/include/io_lib/Read.h:199: parse error before '*' token /usr/local/include/io_lib/Read.h:199: warning: data definition has no type or st orage class /usr/local/include/io_lib/Read.h:205: parse error before '*' token /usr/local/include/io_lib/Read.h:205: warning: data definition has no type or st orage class /usr/local/include/io_lib/Read.h:206: parse error before '*' token /usr/local/include/io_lib/Read.h:206: warning: data definition has no type or st orage class /usr/local/include/io_lib/Read.h:207: parse error before "Read" /usr/local/include/io_lib/Read.h:208: parse error before "Read" /usr/local/include/io_lib/Read.h:210: parse error before "Read" /usr/local/include/io_lib/Read.h:211: parse error before "Read" /usr/local/include/io_lib/Read.h:212: parse error before '*' token /usr/local/include/io_lib/Read.h:212: warning: data definition has no type or st orage class /usr/local/include/io_lib/Read.h:213: parse error before '*' token /usr/local/include/io_lib/Read.h:213: warning: data definition has no type or st orage class /usr/local/include/io_lib/Read.h:215: parse error before "Read" /usr/local/include/io_lib/Read.h:216: parse error before "Read" /usr/local/include/io_lib/Read.h:217: parse error before '*' token /usr/local/include/io_lib/Read.h:217: warning: data definition has no type or st orage class /usr/local/include/io_lib/Read.h:218: parse error before '*' token /usr/local/include/io_lib/Read.h:218: warning: data definition has no type or st orage class /usr/local/include/io_lib/Read.h:220: parse error before '*' token /usr/local/include/io_lib/Read.h:220: warning: data definition has no type or st orage class /usr/local/include/io_lib/Read.h:221: parse error before '*' token /usr/local/include/io_lib/Read.h:221: warning: data definition has no type or st orage class /usr/local/include/io_lib/Read.h:222: parse error before "Read" /usr/local/include/io_lib/Read.h:223: parse error before "Read" In file included from /usr/local/include/io_lib/translate.h:20, from /usr/local/include/io_lib/Read.h:227, from read.xs:5: /usr/local/include/io_lib/expFileIO.h:181: parse error before '*' token /usr/local/include/io_lib/expFileIO.h:182: parse error before '*' token /usr/local/include/io_lib/expFileIO.h:204: parse error before "f_implicit" /usr/local/include/io_lib/expFileIO.h:232: parse error before "f_implicit" /usr/local/include/io_lib/expFileIO.h:252: parse error before "expopn_" /usr/local/include/io_lib/expFileIO.h:252: parse error before "f_implicit" /usr/local/include/io_lib/expFileIO.h:252: warning: data definition has no type or storage class /usr/local/include/io_lib/expFileIO.h:257: parse error before '*' token /usr/local/include/io_lib/expFileIO.h:262: parse error before "expri_" /usr/local/include/io_lib/expFileIO.h:262: parse error before '*' token /usr/local/include/io_lib/expFileIO.h:262: warning: data definition has no type or storage class /usr/local/include/io_lib/expFileIO.h:268: parse error before "exprr_" /usr/local/include/io_lib/expFileIO.h:268: parse error before '*' token /usr/local/include/io_lib/expFileIO.h:268: warning: data definition has no type or storage class /usr/local/include/io_lib/expFileIO.h:274: parse error before "exprsa_" /usr/local/include/io_lib/expFileIO.h:274: parse error before '*' token /usr/local/include/io_lib/expFileIO.h:274: warning: data definition has no type or storage class /usr/local/include/io_lib/expFileIO.h:280: parse error before "exprs_" /usr/local/include/io_lib/expFileIO.h:280: parse error before '*' token /usr/local/include/io_lib/expFileIO.h:280: warning: data definition has no type or storage class /usr/local/include/io_lib/expFileIO.h:286: parse error before "expwi_" /usr/local/include/io_lib/expFileIO.h:286: parse error before '*' token /usr/local/include/io_lib/expFileIO.h:286: warning: data definition has no type or storage class /usr/local/include/io_lib/expFileIO.h:292: parse error before "expwr_" /usr/local/include/io_lib/expFileIO.h:292: parse error before '*' token /usr/local/include/io_lib/expFileIO.h:292: warning: data definition has no type or storage class /usr/local/include/io_lib/expFileIO.h:299: parse error before "expwsa_" /usr/local/include/io_lib/expFileIO.h:299: parse error before '*' token /usr/local/include/io_lib/expFileIO.h:299: warning: data definition has no type or storage class /usr/local/include/io_lib/expFileIO.h:307: parse error before "expws_" /usr/local/include/io_lib/expFileIO.h:307: parse error before '*' token /usr/local/include/io_lib/expFileIO.h:307: warning: data definition has no type or storage class /usr/local/include/io_lib/expFileIO.h:319: parse error before "f_int" /usr/local/include/io_lib/expFileIO.h:324: parse error before "exper_" /usr/local/include/io_lib/expFileIO.h:324: parse error before "f_int" /usr/local/include/io_lib/expFileIO.h:324: warning: data definition has no type or storage class In file included from /usr/local/include/io_lib/Read.h:227, from read.xs:5: /usr/local/include/io_lib/translate.h:30: parse error before '*' token /usr/local/include/io_lib/translate.h:30: parse error before '*' token /usr/local/include/io_lib/translate.h:30: warning: data definition has no type o r storage class /usr/local/include/io_lib/translate.h:40: parse error before '*' token /usr/local/include/io_lib/translate.h:40: parse error before '*' token /usr/local/include/io_lib/translate.h:40: warning: data definition has no type o r storage class /usr/local/include/io_lib/translate.h:50: parse error before '*' token /usr/local/include/io_lib/translate.h:79: parse error before '*' token /usr/local/include/io_lib/translate.h:90: parse error before '*' token /usr/local/include/io_lib/translate.h:90: warning: data definition has no type o r storage class read.xs: In function `staden_write_trace': read.xs:9: invalid operands to binary * read.xs:15: invalid lvalue in assignment read.xs:16: request for member `base' in something not a structure or union read.xs:18: request for member `ident' in something not a structure or union read.xs:21: request for member `ident' in something not a structure or union read.xs:23: request for member `info' in something not a structure or union read.xs:26: request for member `info' in something not a structure or union read.xs:28: request for member `format' in something not a structure or union read.xs:29: request for member `leftCutoff' in something not a structure or unio n read.xs:30: request for member `rightCutoff' in something not a structure or uni on read.xs:32: warning: assignment from incompatible pointer type read.xs:38: request for member `base' in something not a structure or union read.xs:41: request for member `prob_A' in something not a structure or union read.xs:45: request for member `prob_C' in something not a structure or union read.xs:49: request for member `prob_G' in something not a structure or union read.xs:53: request for member `prob_T' in something not a structure or union read.xs:58: request for member `prob_A' in something not a structure or union read.xs:58: request for member `prob_C' in something not a structure or union read.xs:59: request for member `prob_G' in something not a structure or union read.xs:59: request for member `prob_T' in something not a structure or union read.xs:62: request for member `prob_A' in something not a structure or union read.xs:62: request for member `prob_C' in something not a structure or union read.xs:63: request for member `prob_G' in something not a structure or union read.xs:63: request for member `prob_T' in something not a structure or union read.xs: In function `staden_read_trace': read.xs:76: invalid operands to binary * read.xs:81: invalid lvalue in assignment read.xs:83: parse error before ')' token read.xs:88: request for member `leftCutoff' in something not a structure or unio n read.xs:90: request for member `rightCutoff' in something not a structure or uni on read.xs:91: request for member `NBases' in something not a structure or union read.xs:91: request for member `NBases' in something not a structure or union read.xs:93: request for member `base' in something not a structure or union read.xs:94: request for member `prob_A' in something not a structure or union read.xs:94: request for member `prob_C' in something not a structure or union read.xs:95: request for member `prob_G' in something not a structure or union read.xs:95: request for member `prob_T' in something not a structure or union read.xs:144: request for member `ident' in something not a structure or union read.xs:145: request for member `info' in something not a structure or union make[1]: *** [read.o] Error 1 make[1]: Leaving directory `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inlin e/build/Bio/SeqIO/staden/read' A problem was encountered while attempting to compile and install your Inline C code. The command that failed was: make The build directory was: /home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden/read To debug the problem, cd to the build directory, and inspect the output files. at -e line 0 INIT failed--call queue aborted. make: *** [read.inl] Error 2 From amackey at pcbi.upenn.edu Thu Apr 1 13:36:24 2004 From: amackey at pcbi.upenn.edu (Aaron J. Mackey) Date: Thu Apr 1 13:41:31 2004 Subject: [Bioperl-l] Trouble installing bioperl-ext / Bio::SeqIO::staden::read In-Reply-To: <406C5919.9040909@genetics.utah.edu> References: <406C5919.9040909@genetics.utah.edu> Message-ID: <7ADFC992-840B-11D8-8586-000A958C5008@pcbi.upenn.edu> > At the end of the installation instructions for > Bio::SeqIO::staden::read it says, "A failed compilation is most likely > due to an incomplete io_lib installation; make sure that all the > required io_lib ".h" files are in place." How do I determine what > ".h" files are required in io_lib? I currently have the following: > > abi.h compression.h misc.h scf_extras.h traceType.h > alf.h error.h open_trace_file.h scf.h translate.h > array.h expFileIO.h os.h seqIOABI.h xalloc.h > calc_crc.h fpoint.h plain.h seqIOCTF.h ztr.h > compress.h mach-io.h Read.h tar_format.h Looks like you're missing "config.h". It's really too bad that the io_lib installation doesn't actually install everything one would need to make any legitimate use of it. I'm sorry this continues to be a frustration for people ... -Aaron From michael.watson at bbsrc.ac.uk Thu Apr 1 13:47:16 2004 From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C)) Date: Thu Apr 1 13:56:02 2004 Subject: [Bioperl-l] Parsing a Fasta file Message-ID: <8975119BCD0AC5419D61A9CF1A923E9516ECE4@iahce2knas1.iah.bbsrc.reserved> use Bio::SeqIO; my $in = Bio::SeqIO->new (-file => "/path/to/file/of/sequences.fasta", -format => "Fasta"); while(my $seq = $in->next_seq) { print $seq->primary_id, "\n"; print $seq->seq, "\n"; } -----Original Message----- From: Desmond LIM [mailto:desmond_lim@bti.a-star.edu.sg] Sent: 01 April 2004 03:54 To: bioperl-l@bioperl.org Subject: [Bioperl-l] Parsing a Fasta file I have a file that contains protein sequences in fasta format. I need to be able to read each sequence individually, with their accessions (to check against a database). I was wondering if there is a module that could do that, giving me 2 variables (the accession and sequence). I have gone throught the bioperl modules and I found modules that either just take in 1 sequence and parse it or take in the sequence if it is in 1 line and not broken into a few like mine. Am I right? Thanks. Desmond From wes.barris at csiro.au Thu Apr 1 17:02:36 2004 From: wes.barris at csiro.au (Wes Barris) Date: Thu Apr 1 17:07:46 2004 Subject: [Bioperl-l] Reliability of get_Seq_by_gi Message-ID: <406C917C.4020800@csiro.au> Hi, I have been struggling for a long time with a bioperl script that retrieves a series of sequences in genbank format. The problem is that there is the occasional error in downloading a sequence which results in a fatal error in my script. I need to be able to gracefully recover from a downloading error such that my script continues to run. Here is my script: #!/usr/local/bin/perl -w # # use Bio::DB::GenBank; my $usage = "Usage: $0 \n"; my $accOrGi = shift or die $usage; my $outfile = shift or die $usage; my $wtime = 73; # # Prepare input. # my @accOrGiList = (); # empty the list if (-r $accOrGi) { open(IN, $accOrGi); while () { chomp; my @junk = split(/\s+/); push(@accOrGiList, $junk[0]); } close(IN); } else { push(@accOrGiList, $accOrGi); } # # Prepare output. # my $seq_out; if ($outfile =~ /\.gb$/) { $seq_out = Bio::SeqIO->new( -format=>'genbank', -file=>">$outfile"); } elsif ($outfile =~ /\.fa$/) { $seq_out = Bio::SeqIO->new( -format=>'fasta', -file=>">$outfile"); } else { die "Unrecognized output file extension. Use either .gb or .fa\n"; } # # Get the entries. # my $gb = Bio::DB::GenBank->new(); my $seq; my $got = 0; foreach $accOrGi (@accOrGiList) { if ($accOrGi =~ /^\d+/) { print("Getting gi $accOrGi ($got/$#accOrGiList)...\n"); $seq = $gb->get_Seq_by_gi($accOrGi); } else { print("Getting accession $accOrGi ($got/$#accOrGiList)...\n"); $seq = $gb->get_Seq_by_acc($accOrGi); } $seq_out->write_seq($seq); $got++; sleep $wtime unless ($wtime == 0); } Using the above script, at least once a day, I get this error: Getting gi 45498451 (747/41132)... Getting gi 45498450 (748/41132)... Getting gi 45498449 (749/41132)... ------------- EXCEPTION ------------- MSG: WebDBSeqI Request Error: 500 (Internal Server Error) read timeout Client-Date: Thu, 01 Apr 2004 13:54:45 GMT STACK Bio::DB::WebDBSeqI::_stream_request /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:728 STACK Bio::DB::WebDBSeqI::get_seq_stream /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:460 STACK Bio::DB::WebDBSeqI::get_Stream_by_gi /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:330 STACK Bio::DB::WebDBSeqI::get_Seq_by_gi /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:210 STACK toplevel /home/wes/proj/genbank/getGenbank.pl:50 -------------------------------------- -------------------- WARNING --------------------- MSG: gi (45498449) does not exist --------------------------------------------------- ------------- EXCEPTION ------------- MSG: Attempting to write with no seq! STACK Bio::SeqIO::genbank::write_seq /usr/local/lib/perl5/site_perl/5.6.1/Bio/SeqIO/genbank.pm:591 STACK toplevel /home/wes/proj/genbank/getGenbank.pl:77 -------------------------------------- and then the script dies. I have tried wrapping the "get" part inside an eval like this: foreach $accOrGi (@accOrGiList) { eval { if ($accOrGi =~ /^\d+/) { print("Getting gi $accOrGi ($got/$#accOrGiList)...\n"); $seq = $gb->get_Seq_by_gi($accOrGi); } else { print("Getting accession $accOrGi ($got/$#accOrGiList)...\n"); $seq = $gb->get_Seq_by_acc($accOrGi); } }; if ($@) { print("$accOrGi failed.\n"); } . . . This prevents the script from dieing, but it causes several other problems: - it spawns a second instance of my script for each error - STDOUT stops being echoed to the terminal (I no longer see any printed output) - it starts getting duplicate sequences Is there a reliable way to retrieve sequeces from NCBI? I'm using bioperl-1.4. -- Wes Barris E-Mail: Wes.Barris@csiro.au From dmcalish at hotmail.com Fri Apr 2 00:26:08 2004 From: dmcalish at hotmail.com (tommy) Date: Fri Apr 2 00:30:40 2004 Subject: [Bioperl-l] FDA Drug Better than V_I_A_G_R_A: Only $3 a dose! aylmer bozo Message-ID: <1080883568-25820@excite.com> Pay pennies on the dollar for C1ALIS! Become a sexual beast!! http://god.hotspringprices.com/sv/index.php?pid=eph9106 smiths obiwan depeche bozo kiss cynthia johnson carlos cccccc sugar mazda1 nugget praise carl baskeT yomama mikael volley cobra love laura quebec lady oatmeal bach sweetytoronto impala catfish active sarah1 marvin homebrew cyrano tina tequila supra garnet church no more: http://fugazi.mypersonalmeds.net/mm/chair.php From jurgen.pletinckx at algonomics.com Fri Apr 2 03:33:27 2004 From: jurgen.pletinckx at algonomics.com (Jurgen Pletinckx) Date: Fri Apr 2 03:25:28 2004 Subject: [Bioperl-l] deleting string fragments? In-Reply-To: <406BE1E4.2040507@mpil-ploen.mpg.de> Message-ID: If you know the location of your substring, rather than the contents, the following bit is useful and fast: substr($string,$location, $length) = ''; Yes, you are assigning an empty string to a substring. Yes, this looks evil. It's an established use of substr, though. But if you need to lookup the location first (say, with index($string, $substring)), you had better go ahead and use the regular expression approach. In that case, you don't need to first check whether the substring exists, and then edit it out: $string =~ s/$substring//g; will happily remove any and all occurences of the sub- string, and will do nothing if the subtring is not present. -- Jurgen Pletinckx AlgoNomics NV From heikki at ebi.ac.uk Fri Apr 2 03:43:36 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Fri Apr 2 03:48:45 2004 Subject: [Bioperl-l] Reliability of get_Seq_by_gi In-Reply-To: <406C917C.4020800@csiro.au> References: <406C917C.4020800@csiro.au> Message-ID: <200404020843.36456.heikki@ebi.ac.uk> Wes, See: http://bioperl.org/pipermail/bioperl-l/2004-March/015423.html Yours, -Heikki On Thursday 01 Apr 2004 22:02, Wes Barris wrote: > Hi, > > I have been struggling for a long time with a bioperl script that > retrieves a series of sequences in genbank format. The problem > is that there is the occasional error in downloading a sequence > which results in a fatal error in my script. I need to be able > to gracefully recover from a downloading error such that my > script continues to run. > > Here is my script: > > #!/usr/local/bin/perl -w > # > # > use Bio::DB::GenBank; > my $usage = "Usage: $0 \n"; > my $accOrGi = shift or die $usage; > my $outfile = shift or die $usage; > my $wtime = 73; > # > # Prepare input. > # > my @accOrGiList = (); # empty the list > if (-r $accOrGi) { > open(IN, $accOrGi); > while () { > chomp; > my @junk = split(/\s+/); > push(@accOrGiList, $junk[0]); > } > close(IN); > } > else { > push(@accOrGiList, $accOrGi); > } > # > # Prepare output. > # > my $seq_out; > if ($outfile =~ /\.gb$/) { > $seq_out = Bio::SeqIO->new( -format=>'genbank', -file=>">$outfile"); > } > elsif ($outfile =~ /\.fa$/) { > $seq_out = Bio::SeqIO->new( -format=>'fasta', -file=>">$outfile"); > } > else { > die "Unrecognized output file extension. Use either .gb or .fa\n"; > } > # > # Get the entries. > # > my $gb = Bio::DB::GenBank->new(); > my $seq; > my $got = 0; > foreach $accOrGi (@accOrGiList) { > if ($accOrGi =~ /^\d+/) { > print("Getting gi $accOrGi ($got/$#accOrGiList)...\n"); > $seq = $gb->get_Seq_by_gi($accOrGi); > } > else { > print("Getting accession $accOrGi ($got/$#accOrGiList)...\n"); > $seq = $gb->get_Seq_by_acc($accOrGi); > } > $seq_out->write_seq($seq); > $got++; > sleep $wtime unless ($wtime == 0); > } > > Using the above script, at least once a day, I get this error: > > Getting gi 45498451 (747/41132)... > Getting gi 45498450 (748/41132)... > Getting gi 45498449 (749/41132)... > > ------------- EXCEPTION ------------- > MSG: WebDBSeqI Request Error: > 500 (Internal Server Error) read timeout > Client-Date: Thu, 01 Apr 2004 13:54:45 GMT > > > > STACK Bio::DB::WebDBSeqI::_stream_request > /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:728 > STACK Bio::DB::WebDBSeqI::get_seq_stream > /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:460 > STACK Bio::DB::WebDBSeqI::get_Stream_by_gi > /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:330 > STACK Bio::DB::WebDBSeqI::get_Seq_by_gi > /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:210 > STACK toplevel /home/wes/proj/genbank/getGenbank.pl:50 > > -------------------------------------- > > -------------------- WARNING --------------------- > MSG: gi (45498449) does not exist > --------------------------------------------------- > > ------------- EXCEPTION ------------- > MSG: Attempting to write with no seq! > STACK Bio::SeqIO::genbank::write_seq > /usr/local/lib/perl5/site_perl/5.6.1/Bio/SeqIO/genbank.pm:591 > STACK toplevel /home/wes/proj/genbank/getGenbank.pl:77 > > -------------------------------------- > > and then the script dies. I have tried wrapping the "get" part > inside an eval like this: > > foreach $accOrGi (@accOrGiList) { > eval { > if ($accOrGi =~ /^\d+/) { > print("Getting gi $accOrGi ($got/$#accOrGiList)...\n"); > $seq = $gb->get_Seq_by_gi($accOrGi); > } > else { > print("Getting accession $accOrGi ($got/$#accOrGiList)...\n"); > $seq = $gb->get_Seq_by_acc($accOrGi); > } > }; > if ($@) { > print("$accOrGi failed.\n"); > } > . > . > . > > This prevents the script from dieing, but it causes several other problems: > - it spawns a second instance of my script for each error > - STDOUT stops being echoed to the terminal (I no longer see any > printed output) - it starts getting duplicate sequences > > Is there a reliable way to retrieve sequeces from NCBI? > > I'm using bioperl-1.4. -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From ak at ebi.ac.uk Fri Apr 2 04:08:56 2004 From: ak at ebi.ac.uk (Andreas Kahari) Date: Fri Apr 2 04:14:05 2004 Subject: [Bioperl-l] deleting string fragments? In-Reply-To: References: <406BE1E4.2040507@mpil-ploen.mpg.de> Message-ID: <20040402090856.GA27589@ebi.ac.uk> On Fri, Apr 02, 2004 at 10:33:27AM +0200, Jurgen Pletinckx wrote: > If you know the location of your substring, rather than the > contents, the following bit is useful and fast: > > substr($string,$location, $length) = ''; > > Yes, you are assigning an empty string to a substring. > Yes, this looks evil. It's an established use of substr, > though. Less evil? substr($string, $offset, $length, ''); > But if you need to lookup the location first (say, with > index($string, $substring)), you had better go ahead > and use the regular expression approach. > > In that case, you don't need to first check whether the > substring exists, and then edit it out: > > $string =~ s/$substring//g; > > will happily remove any and all occurences of the sub- > string, and will do nothing if the subtring is not > present. The following loop is 10% to 40% faster than regular expression approach (on the string that the original poster gave as an example, with varying substrings): my $offset = 0; while (($offset = index($string, $substring, $offset)) != $[ - 1) { substr($string, $offset, length $substring, ''); } If speed is important, then I would vote for this approach. Andreas -- |()()| Andreas K?h?ri EMBL, European Bioinformatics Institute | () | Wellcome Trust Genome Campus |()()| DAS Project Leader Hinxton, Cambridgeshire, CB10 1SD | () | Ensembl Developer United Kingdom From gabriele.bucci at ieo-research.it Fri Apr 2 04:46:39 2004 From: gabriele.bucci at ieo-research.it (gabriele bucci) Date: Fri Apr 2 04:51:42 2004 Subject: [Bioperl-l] base content Message-ID: <001501c41897$65ac1040$0d6d5cd5@Gabriele7C> Dears, can you tell me which is the way to manage an hash object resulting from the method get_base_count? Say I want to show in my output the %GC as in the subroutine below: sub main { my $m=shift; $chr=$m->chr_name(); $chr_start=$m->chr_start(); $chr_end=$m->chr_end(); $slice_length=$m->length(); $slice_GC=$slice->get_base_count('%gc'); $sliceGC=$slice_GC->???; return "$LIBclo\t$chr\t$chr_start\t$chr_end\t$slice_length\t$sliceGC\t";} Thanks Gabriele Bucci Department of Experimental Oncology European Institute of Oncology Via Ripamonti, 435 20141 Milan, Italy Tel. 02-57489-864 Fax. 02-57489-851 e-mail: gabriele.bucci@ieo-research.it From michael.watson at bbsrc.ac.uk Fri Apr 2 07:59:50 2004 From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C)) Date: Fri Apr 2 08:10:58 2004 Subject: [Bioperl-l] Storing Sequences and Alignments Message-ID: <8975119BCD0AC5419D61A9CF1A923E9516ECF8@iahce2knas1.iah.bbsrc.reserved> Hi I am after a database or schema that can store sequence and annotation and also multiple sequence alignments. I thought perhaps biosql might do this, but I am not sure it does. Does anyone know of anything? Thanks Mick From paulo.david at netvisao.pt Fri Apr 2 08:33:10 2004 From: paulo.david at netvisao.pt (Paulo Almeida) Date: Fri Apr 2 08:34:11 2004 Subject: [Bioperl-l] base content In-Reply-To: <001501c41897$65ac1040$0d6d5cd5@Gabriele7C> References: <001501c41897$65ac1040$0d6d5cd5@Gabriele7C> Message-ID: <406D6B96.7010608@netvisao.pt> Gabriele, Is that from the Bio::EnsEMBL module? If it is, maybe this page can help you: http://www.ensembl.org/Docs/Pdoc/ensembl/modules/Bio/EnsEMBL/RawContig.html#POD12 -Paulo Almeida gabriele bucci wrote: >Dears, >can you tell me which is the way to manage an hash object resulting from >the method get_base_count? >Say I want to show in my output the %GC as in the subroutine below: > >sub main { my $m=shift; > $chr=$m->chr_name(); > $chr_start=$m->chr_start(); > $chr_end=$m->chr_end(); > $slice_length=$m->length(); > $slice_GC=$slice->get_base_count('%gc'); > $sliceGC=$slice_GC->???; > return >"$LIBclo\t$chr\t$chr_start\t$chr_end\t$slice_length\t$sliceGC\t";} > >Thanks > From amackey at pcbi.upenn.edu Fri Apr 2 08:33:17 2004 From: amackey at pcbi.upenn.edu (Aaron J. Mackey) Date: Fri Apr 2 08:38:19 2004 Subject: [Bioperl-l] Storing Sequences and Alignments In-Reply-To: <8975119BCD0AC5419D61A9CF1A923E9516ECF8@iahce2knas1.iah.bbsrc.reserved> References: <8975119BCD0AC5419D61A9CF1A923E9516ECF8@iahce2knas1.iah.bbsrc.reserved> Message-ID: <4CA68A7B-84AA-11D8-8586-000A958C5008@pcbi.upenn.edu> I have an in-development (but currently in real-world use) database schema (CDAT) and accompanying software library (CDATlib) for storage and manipulation of phylogenetic "Character state Data And Trees". This includes storing multiple alignments (as a state matrix), as well as the underlying sequences, hierarchical sequence features and the trees that describe the phylogeny of members in the state matrix. The interesting bit is that the state matrix may be probabilistic for inferred ancestral states, and may refer to features as well as sequences. If this seems "up your alley", contact me for details. -Aaron On Apr 2, 2004, at 7:59 AM, michael watson (IAH-C) wrote: > Hi > > I am after a database or schema that can store sequence and annotation > and also multiple sequence alignments. I thought perhaps biosql might > do this, but I am not sure it does. > > Does anyone know of anything? > > Thanks > Mick > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From nandita at uga.edu Fri Apr 2 10:32:34 2004 From: nandita at uga.edu (Nandita Mullapudi) Date: Fri Apr 2 10:37:38 2004 Subject: [Bioperl-l] getting top blast hit In-Reply-To: References: Message-ID: Thanks, Sean, I tried the suggestion below in my script, which starts with a loop to read through a list of files.. however, now, my script stops parsing as soon as it reaches a file with no hits in it. this is the error message: can't call method "name" on an undefined value at /home/nandita/parse_blast-onlytophit.pl line 26, line 65. I realise I am not looping through completely or... Any suggestions? thanks, -Nandita use strict; use Bio::SearchIO; use Bio::SimpleAlign; my (@list, $filename); my $files= "/scratch/nandita/list"; open (FH,"$files") or die "cannot create list :$!"; while () { push (@list, $_); # print " $_\n"; } foreach (@list) { $filename=$_; # print "$filename\n"; my $in = new Bio::SearchIO(-format => 'blast', -file => "$filename"); while( my $result = $in->next_result ) { print "\n", $result->query_name, "\t"; my $top_hit = $result->next_hit ; { print $top_hit->name, "\t"; print $top_hit->significance,. "\n"; }}} >Nandita, > >You can do something like (from Bio::SearchIO): > > use Bio::SearchIO; > # format can be 'fasta', 'blast', 'exonerate', ... > my $searchio = new Bio::SearchIO( -format => 'blastxml', > -file => 'blastout.xml' ); > while ( my $result = $searchio->next_result() ) { > #get first hit and do something with it. > my $top_hit = $result->next_hit; > #do some stuff such as saving a it in a hash > #move on to next result (next query) > } > >Sean > >On 3/30/04 6:19 PM, "Nandita Mullapudi" wrote: > >> I am currently using Bio::SearchIO to parse tons of blast files by >> setting limits on E- value, % identity etc. I now want to parse a >> huge blast job, by getting just the top hit out of each file. >> (Assuming blast was run and hits were returned with hit with lowest E >> value first) >> Is there a quick way to do this? >> thanks, >> -Nandita >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> From jason at cgt.duhs.duke.edu Fri Apr 2 10:48:41 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Fri Apr 2 10:53:48 2004 Subject: [Bioperl-l] getting top blast hit In-Reply-To: References: Message-ID: On Fri, 2 Apr 2004, Nandita Mullapudi wrote: > Thanks, Sean, > I tried the suggestion below in my script, which starts with a loop > to read through a list of files.. > however, now, my script stops parsing as soon as it reaches a file > with no hits in it. > > this is the error message: > > can't call method "name" on an undefined value at > /home/nandita/parse_blast-onlytophit.pl line 26, line 65. > > I realise I am not looping through completely or... > Any suggestions? protect your next_hit calls... see below > thanks, > -Nandita > > use strict; > use Bio::SearchIO; > use Bio::SimpleAlign; > my (@list, $filename); > my $files= "/scratch/nandita/list"; > open (FH,"$files") or die "cannot create list :$!"; > while () { > push (@list, $_); > # print " $_\n"; > } > > foreach (@list) { > $filename=$_; > # print "$filename\n"; > > my $in = new Bio::SearchIO(-format => 'blast', > -file => "$filename"); > > while( my $result = $in->next_result ) { > print "\n", $result->query_name, "\t"; if( my $top_hit = $result->next_hit ) { print $top_hit->name, "\t"; print $top_hit->significance,. "\n"; } else { print "\n"; } ( or maybe you only want to print anything if there is a hit, so move your print query_name into that same if block) > }}} > > > > > > > > > > > > >Nandita, > > > >You can do something like (from Bio::SearchIO): > > > > use Bio::SearchIO; > > # format can be 'fasta', 'blast', 'exonerate', ... > > my $searchio = new Bio::SearchIO( -format => 'blastxml', > > -file => 'blastout.xml' ); > > while ( my $result = $searchio->next_result() ) { > > #get first hit and do something with it. > > my $top_hit = $result->next_hit; > > #do some stuff such as saving a it in a hash > > #move on to next result (next query) > > } > > > >Sean > > > >On 3/30/04 6:19 PM, "Nandita Mullapudi" wrote: > > > >> I am currently using Bio::SearchIO to parse tons of blast files by > >> setting limits on E- value, % identity etc. I now want to parse a > >> huge blast job, by getting just the top hit out of each file. > >> (Assuming blast was run and hits were returned with hit with lowest E > >> value first) > >> Is there a quick way to do this? > >> thanks, > >> -Nandita > >> _______________________________________________ > >> Bioperl-l mailing list > >> Bioperl-l@portal.open-bio.org > >> http://portal.open-bio.org/mailman/listinfo/bioperl-l > >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From paulo.david at netvisao.pt Fri Apr 2 11:08:05 2004 From: paulo.david at netvisao.pt (Paulo Almeida) Date: Fri Apr 2 11:09:02 2004 Subject: [Bioperl-l] getting top blast hit In-Reply-To: References: Message-ID: <406D8FE5.4040403@netvisao.pt> Nandita, Try making this change: print "\n", $result->query_name, "\t"; if ( my $top_hit = $result->next_hit ) { # this line changed print $top_hit->name, "\t"; print $top_hit->significance,. "\n"; } else { # this else is optional, in case you want to report no hits print "No hits\n"; The problem is $top_hit->name assumes there was a hit. You didn't have that problem before because the while() loop was checking if there was a hit. Now the if() does that. -Paulo Almeida Nandita Mullapudi wrote: > Thanks, Sean, > I tried the suggestion below in my script, which starts with a loop to > read through a list of files.. > however, now, my script stops parsing as soon as it reaches a file > with no hits in it. > > this is the error message: > > can't call method "name" on an undefined value at > /home/nandita/parse_blast-onlytophit.pl line 26, line 65. > > I realise I am not looping through completely or... > Any suggestions? > thanks, > -Nandita > > use strict; > use Bio::SearchIO; > use Bio::SimpleAlign; > my (@list, $filename); > my $files= "/scratch/nandita/list"; > open (FH,"$files") or die "cannot create list :$!"; > while () { > push (@list, $_); > # print " $_\n"; } > > foreach (@list) { > $filename=$_; > # print "$filename\n"; > my $in = new Bio::SearchIO(-format => 'blast', > -file => "$filename"); > > while( my $result = $in->next_result ) { > print "\n", $result->query_name, "\t"; > my $top_hit = $result->next_hit ; { > print $top_hit->name, "\t"; > print $top_hit->significance,. "\n"; > }}} From nandita at uga.edu Fri Apr 2 11:11:59 2004 From: nandita at uga.edu (Nandita Mullapudi) Date: Fri Apr 2 11:17:04 2004 Subject: [Bioperl-l] getting top blast hit In-Reply-To: <406D8FE5.4040403@netvisao.pt> References: <406D8FE5.4040403@netvisao.pt> Message-ID: Thanks, Paulo and Jason, It works, and I understand better now! :) -Nandita >Nandita, > >Try making this change: > >print "\n", $result->query_name, "\t"; >if ( my $top_hit = $result->next_hit ) { # this line changed >print $top_hit->name, "\t"; >print $top_hit->significance,. "\n"; >} else { # this else is optional, in case you want to report no hits >print "No hits\n"; > > >The problem is $top_hit->name assumes there was a hit. You didn't >have that problem before because the while() loop was checking if >there was a hit. Now the if() does that. > >-Paulo Almeida > >Nandita Mullapudi wrote: > >>Thanks, Sean, >>I tried the suggestion below in my script, which starts with a loop >>to read through a list of files.. >>however, now, my script stops parsing as soon as it reaches a file >>with no hits in it. >> >>this is the error message: >> >>can't call method "name" on an undefined value at >>/home/nandita/parse_blast-onlytophit.pl line 26, line 65. >> >>I realise I am not looping through completely or... >>Any suggestions? >>thanks, >>-Nandita >> >>use strict; >>use Bio::SearchIO; >>use Bio::SimpleAlign; >>my (@list, $filename); >>my $files= "/scratch/nandita/list"; >>open (FH,"$files") or die "cannot create list :$!"; >>while () { >>push (@list, $_); >># print " $_\n"; } >> >>foreach (@list) { >>$filename=$_; >># print "$filename\n"; >>my $in = new Bio::SearchIO(-format => 'blast', >>-file => "$filename"); >> >>while( my $result = $in->next_result ) { >>print "\n", $result->query_name, "\t"; >>my $top_hit = $result->next_hit ; { >>print $top_hit->name, "\t"; >>print $top_hit->significance,. "\n"; >>}}} From rnilsson at clarku.edu Fri Apr 2 15:42:13 2004 From: rnilsson at clarku.edu (henrik nilsson) Date: Fri Apr 2 15:47:50 2004 Subject: [Bioperl-l] Pairwise seq. comarison Message-ID: <200404021542.13871.rnilsson@clarku.edu> Hi, For two aligned (and obviously overlapping) sequences, can I use Bioperl to retrieve the number of differing sites in the alignment (for the overlapping region only, excluding the flanking regions where only one of the two sequences is present)? Thanks, RN From barry.moore at genetics.utah.edu Fri Apr 2 16:13:38 2004 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Fri Apr 2 16:18:43 2004 Subject: [Bioperl-l] Pairwise seq. comarison In-Reply-To: <200404021542.13871.rnilsson@clarku.edu> References: <200404021542.13871.rnilsson@clarku.edu> Message-ID: <406DD782.8060301@genetics.utah.edu> Bio::Align::PairwiseStatistics has a method "number_of_differences". I haven't used it, but I presume you'd use AlingIO to bring in you alingment, and then just call the "number_of_differences" directly on your Bio::Align::AlignI object. The docs look kind of vauge, so hopefully someone else can flesh out this suggestions, but if your just looking for where to start experimenting, that's one place to try. Barry henrik nilsson wrote: >Hi, > >For two aligned (and obviously overlapping) sequences, can I use Bioperl to >retrieve the number of differing sites in the alignment (for the overlapping >region only, excluding the flanking regions where only one of the two >sequences is present)? > >Thanks, > >RN > > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Barry Moore Dept. of Human Genetics University of Utah Salt Lake City, UT From jason at cgt.duhs.duke.edu Fri Apr 2 17:19:20 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Fri Apr 2 17:24:29 2004 Subject: [Bioperl-l] Pairwise seq. comarison In-Reply-To: <406DD782.8060301@genetics.utah.edu> References: <200404021542.13871.rnilsson@clarku.edu> <406DD782.8060301@genetics.utah.edu> Message-ID: Barry - What do you mean vague....? We all love to document our code... =) FYI If you thinking popgen type stuff so finding number of polymorphic sites? Most of this code is pretty new but in Bio::PopGen - the latest stuff in Bio::PopGen::Utilties allow for generating Bio::PopGen::Individual individuals from a MSA alignment. But since you are looking at pairiwse you probably just want raw differences for a pairwise sequences you can do this: my $stats = Bio::Align::PairwiseStatistics->new(); Actually depends on what you want to do my $differences = $stats->number_of_differences($aln); Note this is case-sensitive and doesn't do any fancy ambiguity code stuff or anything. If you want to do more fancy DnaDistance calculations which attempt to correct for various biases Bio::Align::DNAStatistics has most of that stuff. This stuff has been under fairly active development post 1.4 release so what is in CVS may be more accurate and correct. -jason On Fri, 2 Apr 2004, Barry Moore wrote: > Bio::Align::PairwiseStatistics has a method "number_of_differences". I > haven't used it, but I presume you'd use AlingIO to bring in you > alingment, and then just call the "number_of_differences" directly on > your Bio::Align::AlignI object. The docs look kind of vauge, so > hopefully someone else can flesh out this suggestions, but if your just > looking for where to start experimenting, that's one place to try. > > Barry > > henrik nilsson wrote: > > >Hi, > > > >For two aligned (and obviously overlapping) sequences, can I use Bioperl to > >retrieve the number of differing sites in the alignment (for the overlapping > >region only, excluding the flanking regions where only one of the two > >sequences is present)? > > > >Thanks, > > > >RN > > > > > >_______________________________________________ > >Bioperl-l mailing list > >Bioperl-l@portal.open-bio.org > >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From hlapp at gnf.org Fri Apr 2 20:25:27 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Fri Apr 2 20:30:35 2004 Subject: [Bioperl-l] Storing Sequences and Alignments In-Reply-To: <8975119BCD0AC5419D61A9CF1A923E9516ECF8@iahce2knas1.iah.bbsrc.reserved> Message-ID: biosql will certainly store your sequences and annotation, but the multiple sequence alignments will be a challenge at least, meaning nobody has tried it yet, and it wasn't designed with this capability in mind. You've probably heard about chado. I dont actually know to which extent it is prepared to store multiple sequence alignments, but it may be worth checking out and/or asking on the gmod mailing list. -hilmar On Friday, April 2, 2004, at 04:59 AM, michael watson (IAH-C) wrote: > Hi > > I am after a database or schema that can store sequence and annotation > and also multiple sequence alignments. I thought perhaps biosql might > do this, but I am not sure it does. > > Does anyone know of anything? > > Thanks > Mick > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From wes.barris at csiro.au Sun Apr 4 18:22:11 2004 From: wes.barris at csiro.au (Wes Barris) Date: Sun Apr 4 18:27:20 2004 Subject: [Bioperl-l] Reliability of get_Seq_by_gi In-Reply-To: <200404020843.36456.heikki@ebi.ac.uk> References: <406C917C.4020800@csiro.au> <200404020843.36456.heikki@ebi.ac.uk> Message-ID: <40708A93.1050308@csiro.au> Heikki Lehvaslaiho wrote: > Wes, > > See: > http://bioperl.org/pipermail/bioperl-l/2004-March/015423.html > > Yours, > -Heikki Yes, but as I pointed out in my message, there are some problems in doing that. > > On Thursday 01 Apr 2004 22:02, Wes Barris wrote: > >>Hi, >> >>I have been struggling for a long time with a bioperl script that >>retrieves a series of sequences in genbank format. The problem >>is that there is the occasional error in downloading a sequence >>which results in a fatal error in my script. I need to be able >>to gracefully recover from a downloading error such that my >>script continues to run. >> >>Here is my script: >> >>#!/usr/local/bin/perl -w >># >># >>use Bio::DB::GenBank; >>my $usage = "Usage: $0 \n"; >>my $accOrGi = shift or die $usage; >>my $outfile = shift or die $usage; >>my $wtime = 73; >># >># Prepare input. >># >>my @accOrGiList = (); # empty the list >>if (-r $accOrGi) { >> open(IN, $accOrGi); >> while () { >> chomp; >> my @junk = split(/\s+/); >> push(@accOrGiList, $junk[0]); >> } >> close(IN); >> } >>else { >> push(@accOrGiList, $accOrGi); >> } >># >># Prepare output. >># >>my $seq_out; >>if ($outfile =~ /\.gb$/) { >> $seq_out = Bio::SeqIO->new( -format=>'genbank', -file=>">$outfile"); >> } >>elsif ($outfile =~ /\.fa$/) { >> $seq_out = Bio::SeqIO->new( -format=>'fasta', -file=>">$outfile"); >> } >>else { >> die "Unrecognized output file extension. Use either .gb or .fa\n"; >> } >># >># Get the entries. >># >>my $gb = Bio::DB::GenBank->new(); >>my $seq; >>my $got = 0; >>foreach $accOrGi (@accOrGiList) { >> if ($accOrGi =~ /^\d+/) { >> print("Getting gi $accOrGi ($got/$#accOrGiList)...\n"); >> $seq = $gb->get_Seq_by_gi($accOrGi); >> } >> else { >> print("Getting accession $accOrGi ($got/$#accOrGiList)...\n"); >> $seq = $gb->get_Seq_by_acc($accOrGi); >> } >> $seq_out->write_seq($seq); >> $got++; >> sleep $wtime unless ($wtime == 0); >> } >> >>Using the above script, at least once a day, I get this error: >> >>Getting gi 45498451 (747/41132)... >>Getting gi 45498450 (748/41132)... >>Getting gi 45498449 (749/41132)... >> >>------------- EXCEPTION ------------- >>MSG: WebDBSeqI Request Error: >>500 (Internal Server Error) read timeout >>Client-Date: Thu, 01 Apr 2004 13:54:45 GMT >> >> >> >>STACK Bio::DB::WebDBSeqI::_stream_request >>/usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:728 >>STACK Bio::DB::WebDBSeqI::get_seq_stream >>/usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:460 >>STACK Bio::DB::WebDBSeqI::get_Stream_by_gi >>/usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:330 >>STACK Bio::DB::WebDBSeqI::get_Seq_by_gi >>/usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:210 >>STACK toplevel /home/wes/proj/genbank/getGenbank.pl:50 >> >>-------------------------------------- >> >>-------------------- WARNING --------------------- >>MSG: gi (45498449) does not exist >>--------------------------------------------------- >> >>------------- EXCEPTION ------------- >>MSG: Attempting to write with no seq! >>STACK Bio::SeqIO::genbank::write_seq >>/usr/local/lib/perl5/site_perl/5.6.1/Bio/SeqIO/genbank.pm:591 >>STACK toplevel /home/wes/proj/genbank/getGenbank.pl:77 >> >>-------------------------------------- >> >>and then the script dies. I have tried wrapping the "get" part >>inside an eval like this: >> >>foreach $accOrGi (@accOrGiList) { >> eval { >> if ($accOrGi =~ /^\d+/) { >> print("Getting gi $accOrGi ($got/$#accOrGiList)...\n"); >> $seq = $gb->get_Seq_by_gi($accOrGi); >> } >> else { >> print("Getting accession $accOrGi ($got/$#accOrGiList)...\n"); >> $seq = $gb->get_Seq_by_acc($accOrGi); >> } >> }; >> if ($@) { >> print("$accOrGi failed.\n"); >> } >> . >> . >> . >> >>This prevents the script from dieing, but it causes several other problems: >> - it spawns a second instance of my script for each error >> - STDOUT stops being echoed to the terminal (I no longer see any >>printed output) - it starts getting duplicate sequences >> >>Is there a reliable way to retrieve sequeces from NCBI? >> >>I'm using bioperl-1.4. > > -- Wes Barris E-Mail: Wes.Barris@csiro.au From redwards at utmem.edu Sun Apr 4 18:45:56 2004 From: redwards at utmem.edu (Rob Edwards) Date: Sun Apr 4 18:51:04 2004 Subject: [Bioperl-l] Reliability of get_Seq_by_gi In-Reply-To: <40708A93.1050308@csiro.au> References: <406C917C.4020800@csiro.au> <200404020843.36456.heikki@ebi.ac.uk> <40708A93.1050308@csiro.au> Message-ID: Just a suggestion, but have you tried making sure that $seq exists before writing. Something like this should fix the problem: } if ($seq) {$seq_out->write_seq($seq)} else {print STDERR "Couldn't retrieve a sequence for $accOrGi\n"} $got++; sleep $wtime unless ($wtime == 0); } I don't think $seq exists if the server times out. You should capture all the failed sequences and then validate them in case there is some error with the Acc/GI (like they doesn't exist any more). Rob On Apr 4, 2004, at 5:22 PM, Wes Barris wrote: > Heikki Lehvaslaiho wrote: >> Wes, >> See: >> http://bioperl.org/pipermail/bioperl-l/2004-March/015423.html >> Yours, >> -Heikki > > Yes, but as I pointed out in my message, there are some problems in > doing that. > >> On Thursday 01 Apr 2004 22:02, Wes Barris wrote: >>> Hi, >>> >>> I have been struggling for a long time with a bioperl script that >>> retrieves a series of sequences in genbank format. The problem >>> is that there is the occasional error in downloading a sequence >>> which results in a fatal error in my script. I need to be able >>> to gracefully recover from a downloading error such that my >>> script continues to run. >>> >>> Here is my script: >>> >>> #!/usr/local/bin/perl -w >>> # >>> # >>> use Bio::DB::GenBank; >>> my $usage = "Usage: $0 \n"; >>> my $accOrGi = shift or die $usage; >>> my $outfile = shift or die $usage; >>> my $wtime = 73; >>> # >>> # Prepare input. >>> # >>> my @accOrGiList = (); # empty the list >>> if (-r $accOrGi) { >>> open(IN, $accOrGi); >>> while () { >>> chomp; >>> my @junk = split(/\s+/); >>> push(@accOrGiList, $junk[0]); >>> } >>> close(IN); >>> } >>> else { >>> push(@accOrGiList, $accOrGi); >>> } >>> # >>> # Prepare output. >>> # >>> my $seq_out; >>> if ($outfile =~ /\.gb$/) { >>> $seq_out = Bio::SeqIO->new( -format=>'genbank', >>> -file=>">$outfile"); >>> } >>> elsif ($outfile =~ /\.fa$/) { >>> $seq_out = Bio::SeqIO->new( -format=>'fasta', -file=>">$outfile"); >>> } >>> else { >>> die "Unrecognized output file extension. Use either .gb or .fa\n"; >>> } >>> # >>> # Get the entries. >>> # >>> my $gb = Bio::DB::GenBank->new(); >>> my $seq; >>> my $got = 0; >>> foreach $accOrGi (@accOrGiList) { >>> if ($accOrGi =~ /^\d+/) { >>> print("Getting gi $accOrGi ($got/$#accOrGiList)...\n"); >>> $seq = $gb->get_Seq_by_gi($accOrGi); >>> } >>> else { >>> print("Getting accession $accOrGi ($got/$#accOrGiList)...\n"); >>> $seq = $gb->get_Seq_by_acc($accOrGi); >>> } >>> $seq_out->write_seq($seq); >>> $got++; >>> sleep $wtime unless ($wtime == 0); >>> } >>> >>> Using the above script, at least once a day, I get this error: >>> >>> Getting gi 45498451 (747/41132)... >>> Getting gi 45498450 (748/41132)... >>> Getting gi 45498449 (749/41132)... >>> >>> ------------- EXCEPTION ------------- >>> MSG: WebDBSeqI Request Error: >>> 500 (Internal Server Error) read timeout >>> Client-Date: Thu, 01 Apr 2004 13:54:45 GMT >>> >>> >>> >>> STACK Bio::DB::WebDBSeqI::_stream_request >>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:728 >>> STACK Bio::DB::WebDBSeqI::get_seq_stream >>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:460 >>> STACK Bio::DB::WebDBSeqI::get_Stream_by_gi >>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:330 >>> STACK Bio::DB::WebDBSeqI::get_Seq_by_gi >>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:210 >>> STACK toplevel /home/wes/proj/genbank/getGenbank.pl:50 >>> >>> -------------------------------------- >>> >>> -------------------- WARNING --------------------- >>> MSG: gi (45498449) does not exist >>> --------------------------------------------------- >>> >>> ------------- EXCEPTION ------------- >>> MSG: Attempting to write with no seq! >>> STACK Bio::SeqIO::genbank::write_seq >>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/SeqIO/genbank.pm:591 >>> STACK toplevel /home/wes/proj/genbank/getGenbank.pl:77 >>> >>> -------------------------------------- >>> >>> and then the script dies. I have tried wrapping the "get" part >>> inside an eval like this: >>> >>> foreach $accOrGi (@accOrGiList) { >>> eval { >>> if ($accOrGi =~ /^\d+/) { >>> print("Getting gi $accOrGi ($got/$#accOrGiList)...\n"); >>> $seq = $gb->get_Seq_by_gi($accOrGi); >>> } >>> else { >>> print("Getting accession $accOrGi >>> ($got/$#accOrGiList)...\n"); >>> $seq = $gb->get_Seq_by_acc($accOrGi); >>> } >>> }; >>> if ($@) { >>> print("$accOrGi failed.\n"); >>> } >>> . >>> . >>> . >>> >>> This prevents the script from dieing, but it causes several other >>> problems: >>> - it spawns a second instance of my script for each error >>> - STDOUT stops being echoed to the terminal (I no longer see any >>> printed output) - it starts getting duplicate sequences >>> >>> Is there a reliable way to retrieve sequeces from NCBI? >>> >>> I'm using bioperl-1.4. > > > -- > Wes Barris > E-Mail: Wes.Barris@csiro.au > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From wes.barris at csiro.au Sun Apr 4 20:40:41 2004 From: wes.barris at csiro.au (Wes Barris) Date: Sun Apr 4 20:45:47 2004 Subject: [Bioperl-l] Reliability of get_Seq_by_gi In-Reply-To: References: <406C917C.4020800@csiro.au> <200404020843.36456.heikki@ebi.ac.uk> <40708A93.1050308@csiro.au> Message-ID: <4070AB09.8090103@csiro.au> Rob Edwards wrote: > Just a suggestion, but have you tried making sure that $seq exists > before writing. Something like this should fix the problem: > > } > if ($seq) {$seq_out->write_seq($seq)} > else {print STDERR "Couldn't retrieve a sequence for $accOrGi\n"} > $got++; > sleep $wtime unless ($wtime == 0); > } > > I don't think $seq exists if the server times out. Hi Rob, I think you are on to something here. The real test will be if this runs over night. > > You should capture all the failed sequences and then validate them in > case there is some error with the Acc/GI (like they doesn't exist any > more). > > Rob > > > > On Apr 4, 2004, at 5:22 PM, Wes Barris wrote: > >> Heikki Lehvaslaiho wrote: >> >>> Wes, >>> See: >>> http://bioperl.org/pipermail/bioperl-l/2004-March/015423.html >>> Yours, >>> -Heikki >> >> >> Yes, but as I pointed out in my message, there are some problems in >> doing that. >> >>> On Thursday 01 Apr 2004 22:02, Wes Barris wrote: >>> >>>> Hi, >>>> >>>> I have been struggling for a long time with a bioperl script that >>>> retrieves a series of sequences in genbank format. The problem >>>> is that there is the occasional error in downloading a sequence >>>> which results in a fatal error in my script. I need to be able >>>> to gracefully recover from a downloading error such that my >>>> script continues to run. >>>> >>>> Here is my script: >>>> >>>> #!/usr/local/bin/perl -w >>>> # >>>> # >>>> use Bio::DB::GenBank; >>>> my $usage = "Usage: $0 \n"; >>>> my $accOrGi = shift or die $usage; >>>> my $outfile = shift or die $usage; >>>> my $wtime = 73; >>>> # >>>> # Prepare input. >>>> # >>>> my @accOrGiList = (); # empty the list >>>> if (-r $accOrGi) { >>>> open(IN, $accOrGi); >>>> while () { >>>> chomp; >>>> my @junk = split(/\s+/); >>>> push(@accOrGiList, $junk[0]); >>>> } >>>> close(IN); >>>> } >>>> else { >>>> push(@accOrGiList, $accOrGi); >>>> } >>>> # >>>> # Prepare output. >>>> # >>>> my $seq_out; >>>> if ($outfile =~ /\.gb$/) { >>>> $seq_out = Bio::SeqIO->new( -format=>'genbank', -file=>">$outfile"); >>>> } >>>> elsif ($outfile =~ /\.fa$/) { >>>> $seq_out = Bio::SeqIO->new( -format=>'fasta', -file=>">$outfile"); >>>> } >>>> else { >>>> die "Unrecognized output file extension. Use either .gb or .fa\n"; >>>> } >>>> # >>>> # Get the entries. >>>> # >>>> my $gb = Bio::DB::GenBank->new(); >>>> my $seq; >>>> my $got = 0; >>>> foreach $accOrGi (@accOrGiList) { >>>> if ($accOrGi =~ /^\d+/) { >>>> print("Getting gi $accOrGi ($got/$#accOrGiList)...\n"); >>>> $seq = $gb->get_Seq_by_gi($accOrGi); >>>> } >>>> else { >>>> print("Getting accession $accOrGi ($got/$#accOrGiList)...\n"); >>>> $seq = $gb->get_Seq_by_acc($accOrGi); >>>> } >>>> $seq_out->write_seq($seq); >>>> $got++; >>>> sleep $wtime unless ($wtime == 0); >>>> } >>>> >>>> Using the above script, at least once a day, I get this error: >>>> >>>> Getting gi 45498451 (747/41132)... >>>> Getting gi 45498450 (748/41132)... >>>> Getting gi 45498449 (749/41132)... >>>> >>>> ------------- EXCEPTION ------------- >>>> MSG: WebDBSeqI Request Error: >>>> 500 (Internal Server Error) read timeout >>>> Client-Date: Thu, 01 Apr 2004 13:54:45 GMT >>>> >>>> >>>> >>>> STACK Bio::DB::WebDBSeqI::_stream_request >>>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:728 >>>> STACK Bio::DB::WebDBSeqI::get_seq_stream >>>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:460 >>>> STACK Bio::DB::WebDBSeqI::get_Stream_by_gi >>>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:330 >>>> STACK Bio::DB::WebDBSeqI::get_Seq_by_gi >>>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:210 >>>> STACK toplevel /home/wes/proj/genbank/getGenbank.pl:50 >>>> >>>> -------------------------------------- >>>> >>>> -------------------- WARNING --------------------- >>>> MSG: gi (45498449) does not exist >>>> --------------------------------------------------- >>>> >>>> ------------- EXCEPTION ------------- >>>> MSG: Attempting to write with no seq! >>>> STACK Bio::SeqIO::genbank::write_seq >>>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/SeqIO/genbank.pm:591 >>>> STACK toplevel /home/wes/proj/genbank/getGenbank.pl:77 >>>> >>>> -------------------------------------- >>>> >>>> and then the script dies. I have tried wrapping the "get" part >>>> inside an eval like this: >>>> >>>> foreach $accOrGi (@accOrGiList) { >>>> eval { >>>> if ($accOrGi =~ /^\d+/) { >>>> print("Getting gi $accOrGi ($got/$#accOrGiList)...\n"); >>>> $seq = $gb->get_Seq_by_gi($accOrGi); >>>> } >>>> else { >>>> print("Getting accession $accOrGi ($got/$#accOrGiList)...\n"); >>>> $seq = $gb->get_Seq_by_acc($accOrGi); >>>> } >>>> }; >>>> if ($@) { >>>> print("$accOrGi failed.\n"); >>>> } >>>> . >>>> . >>>> . >>>> >>>> This prevents the script from dieing, but it causes several other >>>> problems: >>>> - it spawns a second instance of my script for each error >>>> - STDOUT stops being echoed to the terminal (I no longer see any >>>> printed output) - it starts getting duplicate sequences >>>> >>>> Is there a reliable way to retrieve sequeces from NCBI? >>>> >>>> I'm using bioperl-1.4. >> >> >> >> -- >> Wes Barris >> E-Mail: Wes.Barris@csiro.au >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Wes Barris E-Mail: Wes.Barris@csiro.au From heikki at ebi.ac.uk Mon Apr 5 07:55:00 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Mon Apr 5 08:00:16 2004 Subject: [Bioperl-l] How sequence fetching should fail? Message-ID: <200404051155.00915.heikki@ebi.ac.uk> Last week Web Barris asked more questions about sequence retrieval. I had a look how different modules work when the retrieval fails due to nonexisting id. The response can be summarised as follows: Bio::DB::BioFetch WARNING Bio::DB::GenBank WARNING Bio::DB::GenPept WARNING Bio::DB::SwissProt EXCEPTION Bio::DB::RefSeq WARNING Bio::DB::EMBL EXCEPTION I suggest that we treat this situation as an error that needs to be fixed in both development cvs head and in the 1.4 branch. All modules should print a warning (rather than die on an error) and return undef when retieval fails. It is then up to the use to test the if the sequence variable got assingned. This is the functionality defined in the OBDA (Open Data Base Access) specs and implemeted in Bio::DB::BioFetch. The use code will always look something like this: $db = new Bio::DB::SeqRetrievalClass; for (@ids) { $seq = $gb->get_Seq_by_id($_); if ($seq) { # do what you wanted } else { # skip and keep log } } Unless I hear any strong differing opinions within a day or two, I'll commit the necessary changes. The critical question here is: will this break any existing code? -Heikki -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From sylvain.foisy at bioneq.qc.ca Mon Apr 5 17:09:07 2004 From: sylvain.foisy at bioneq.qc.ca (Sylvain Foisy) Date: Mon Apr 5 17:41:32 2004 Subject: [Bioperl-l] BioPerl Bootcamp : June 21-25 in Montreal Message-ID: Hi, Continuing on the BioJava Bootcamp of 2003, The Quebec Bioinformatics Network (BioneQ) is organizing its first BioPerl Bootcamp, to be held at the Universite de Montreal from June 21-25 2004. The invited speakers are leaders in the use of Perl in bioinformatics and development of BioPerl: Aaron Mackey (U. of Pennsylvania) Jason Stajich (Duke University) Lincoln Stein (Cold Spring Harbor Labs) Seminars and exercise sessions will be in a Linux computer lab for a total hands-on experience. ++ A demonstrated knowledge of programming is a pre-requisite ++ ++ Registration fee is US $200 ++ ++ Places are limited !! ++ If you or someone in your group is interested by this workshop, e-mail a letter of intent and a file with your cv to bioperl-bootcamp@bioneq.qc.ca. Best regards Sylvain =================================================================== Sylvain Foisy, Ph. D. Directeur - operations / Project Manager BioneQ - Reseau quebecois de bio-informatique U. de Montreal / Genome-Quebec Adresse postale: Departement de biochimie Pavillon principal 2900, boul. ?douard-Montpetit Montr?al (Qu?bec) H3T 1J4 Tel: (514) 343-6111 x.2545 Fax: (514) 343-7759 Courriel: sylvain.foisy@bioneq.qc.ca =================================================================== From wes.barris at csiro.au Mon Apr 5 18:44:12 2004 From: wes.barris at csiro.au (Wes Barris) Date: Mon Apr 5 18:49:15 2004 Subject: [Bioperl-l] Reliability of get_Seq_by_gi In-Reply-To: References: <406C917C.4020800@csiro.au> <200404020843.36456.heikki@ebi.ac.uk> <40708A93.1050308@csiro.au> Message-ID: <4071E13C.9040506@csiro.au> Rob Edwards wrote: > Just a suggestion, but have you tried making sure that $seq exists > before writing. Something like this should fix the problem: > > } > if ($seq) {$seq_out->write_seq($seq)} > else {print STDERR "Couldn't retrieve a sequence for $accOrGi\n"} > $got++; > sleep $wtime unless ($wtime == 0); > } > > I don't think $seq exists if the server times out. > > You should capture all the failed sequences and then validate them in > case there is some error with the Acc/GI (like they doesn't exist any > more). > > Rob Hi Rob, Your solution appears to have worked. I was able to download sequences over night and my script was still running this morning -- the first time it has ever done that. Thanks. > > > > On Apr 4, 2004, at 5:22 PM, Wes Barris wrote: > >> Heikki Lehvaslaiho wrote: >> >>> Wes, >>> See: >>> http://bioperl.org/pipermail/bioperl-l/2004-March/015423.html >>> Yours, >>> -Heikki >> >> >> Yes, but as I pointed out in my message, there are some problems in >> doing that. >> >>> On Thursday 01 Apr 2004 22:02, Wes Barris wrote: >>> >>>> Hi, >>>> >>>> I have been struggling for a long time with a bioperl script that >>>> retrieves a series of sequences in genbank format. The problem >>>> is that there is the occasional error in downloading a sequence >>>> which results in a fatal error in my script. I need to be able >>>> to gracefully recover from a downloading error such that my >>>> script continues to run. >>>> >>>> Here is my script: >>>> >>>> #!/usr/local/bin/perl -w >>>> # >>>> # >>>> use Bio::DB::GenBank; >>>> my $usage = "Usage: $0 \n"; >>>> my $accOrGi = shift or die $usage; >>>> my $outfile = shift or die $usage; >>>> my $wtime = 73; >>>> # >>>> # Prepare input. >>>> # >>>> my @accOrGiList = (); # empty the list >>>> if (-r $accOrGi) { >>>> open(IN, $accOrGi); >>>> while () { >>>> chomp; >>>> my @junk = split(/\s+/); >>>> push(@accOrGiList, $junk[0]); >>>> } >>>> close(IN); >>>> } >>>> else { >>>> push(@accOrGiList, $accOrGi); >>>> } >>>> # >>>> # Prepare output. >>>> # >>>> my $seq_out; >>>> if ($outfile =~ /\.gb$/) { >>>> $seq_out = Bio::SeqIO->new( -format=>'genbank', -file=>">$outfile"); >>>> } >>>> elsif ($outfile =~ /\.fa$/) { >>>> $seq_out = Bio::SeqIO->new( -format=>'fasta', -file=>">$outfile"); >>>> } >>>> else { >>>> die "Unrecognized output file extension. Use either .gb or .fa\n"; >>>> } >>>> # >>>> # Get the entries. >>>> # >>>> my $gb = Bio::DB::GenBank->new(); >>>> my $seq; >>>> my $got = 0; >>>> foreach $accOrGi (@accOrGiList) { >>>> if ($accOrGi =~ /^\d+/) { >>>> print("Getting gi $accOrGi ($got/$#accOrGiList)...\n"); >>>> $seq = $gb->get_Seq_by_gi($accOrGi); >>>> } >>>> else { >>>> print("Getting accession $accOrGi ($got/$#accOrGiList)...\n"); >>>> $seq = $gb->get_Seq_by_acc($accOrGi); >>>> } >>>> $seq_out->write_seq($seq); >>>> $got++; >>>> sleep $wtime unless ($wtime == 0); >>>> } >>>> >>>> Using the above script, at least once a day, I get this error: >>>> >>>> Getting gi 45498451 (747/41132)... >>>> Getting gi 45498450 (748/41132)... >>>> Getting gi 45498449 (749/41132)... >>>> >>>> ------------- EXCEPTION ------------- >>>> MSG: WebDBSeqI Request Error: >>>> 500 (Internal Server Error) read timeout >>>> Client-Date: Thu, 01 Apr 2004 13:54:45 GMT >>>> >>>> >>>> >>>> STACK Bio::DB::WebDBSeqI::_stream_request >>>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:728 >>>> STACK Bio::DB::WebDBSeqI::get_seq_stream >>>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:460 >>>> STACK Bio::DB::WebDBSeqI::get_Stream_by_gi >>>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:330 >>>> STACK Bio::DB::WebDBSeqI::get_Seq_by_gi >>>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:210 >>>> STACK toplevel /home/wes/proj/genbank/getGenbank.pl:50 >>>> >>>> -------------------------------------- >>>> >>>> -------------------- WARNING --------------------- >>>> MSG: gi (45498449) does not exist >>>> --------------------------------------------------- >>>> >>>> ------------- EXCEPTION ------------- >>>> MSG: Attempting to write with no seq! >>>> STACK Bio::SeqIO::genbank::write_seq >>>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/SeqIO/genbank.pm:591 >>>> STACK toplevel /home/wes/proj/genbank/getGenbank.pl:77 >>>> >>>> -------------------------------------- >>>> >>>> and then the script dies. I have tried wrapping the "get" part >>>> inside an eval like this: >>>> >>>> foreach $accOrGi (@accOrGiList) { >>>> eval { >>>> if ($accOrGi =~ /^\d+/) { >>>> print("Getting gi $accOrGi ($got/$#accOrGiList)...\n"); >>>> $seq = $gb->get_Seq_by_gi($accOrGi); >>>> } >>>> else { >>>> print("Getting accession $accOrGi ($got/$#accOrGiList)...\n"); >>>> $seq = $gb->get_Seq_by_acc($accOrGi); >>>> } >>>> }; >>>> if ($@) { >>>> print("$accOrGi failed.\n"); >>>> } >>>> . >>>> . >>>> . >>>> >>>> This prevents the script from dieing, but it causes several other >>>> problems: >>>> - it spawns a second instance of my script for each error >>>> - STDOUT stops being echoed to the terminal (I no longer see any >>>> printed output) - it starts getting duplicate sequences >>>> >>>> Is there a reliable way to retrieve sequeces from NCBI? >>>> >>>> I'm using bioperl-1.4. >> >> >> >> -- >> Wes Barris >> E-Mail: Wes.Barris@csiro.au >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Wes Barris E-Mail: Wes.Barris@csiro.au From linux at ibt.unam.mx Mon Apr 5 20:51:10 2004 From: linux at ibt.unam.mx (MailScanner) Date: Mon Apr 5 20:56:10 2004 Subject: [Bioperl-l] =?iso-8859-1?q?Atenci=F3n=3A_Virus_detectado_en_e-ma?= =?iso-8859-1?q?il?= Message-ID: <200404060051.i360pAbm009839@pbr322.ceingebi.unam.mx> (sin acentos) Este mensaje se genero en forma automatica por el servicio ANTIVIRUS del sistema de correo electronico del Instituo de Biotecnologia de la UNAM. Se detectaron virus en un mensaje enviado por Usted A (to): alara@ibt.unam.mx Asunto (subject): Re: Re: Document Fecha (date): Mon Apr 5 19:51:10 2004 Las partes del mensaje que estaban infectadas no han sido enviadas. Su sistema puede tener un virus y le recomendamos verificarlo. Informe: your_document.pif Infection: W32/Netsky.D@mm Shortcuts to MS-Dos programs are very dangerous in email (your_document.pif) -- Unidad de Computo http://www.ibt.unam.mx From redwards at utmem.edu Mon Apr 5 22:56:04 2004 From: redwards at utmem.edu (Rob Edwards) Date: Mon Apr 5 23:01:09 2004 Subject: [Bioperl-l] Reliability of get_Seq_by_gi In-Reply-To: <4071E13C.9040506@csiro.au> References: <406C917C.4020800@csiro.au> <200404020843.36456.heikki@ebi.ac.uk> <40708A93.1050308@csiro.au> <4071E13C.9040506@csiro.au> Message-ID: Did you capture the errors and do they make any sense? Rob On Apr 5, 2004, at 5:44 PM, Wes Barris wrote: > Rob Edwards wrote: > >> Just a suggestion, but have you tried making sure that $seq exists >> before writing. Something like this should fix the problem: >> >> You should capture all the failed sequences and then validate them in >> case there is some error with the Acc/GI (like they doesn't exist any >> more). >> Rob > > Hi Rob, > > Your solution appears to have worked. I was able to download sequences > over night and my script was still running this morning -- the first > time > it has ever done that. Thanks. From wes.barris at csiro.au Mon Apr 5 23:09:51 2004 From: wes.barris at csiro.au (Wes Barris) Date: Mon Apr 5 23:14:53 2004 Subject: [Bioperl-l] Reliability of get_Seq_by_gi In-Reply-To: References: <406C917C.4020800@csiro.au> <200404020843.36456.heikki@ebi.ac.uk> <40708A93.1050308@csiro.au> <4071E13C.9040506@csiro.au> Message-ID: <40721F7F.9030201@csiro.au> Rob Edwards wrote: > Did you capture the errors and do they make any sense? I did not capture any errors. Usually, the message says that the GI number does not exist although I know that it does. I think that there are general reliability problems when getting sequences from NCBI as there are when using netblast (blastcl3). > > Rob > > > On Apr 5, 2004, at 5:44 PM, Wes Barris wrote: > >> Rob Edwards wrote: >> >>> Just a suggestion, but have you tried making sure that $seq exists >>> before writing. Something like this should fix the problem: >>> > > > >>> You should capture all the failed sequences and then validate them in >>> case there is some error with the Acc/GI (like they doesn't exist any >>> more). >>> Rob >> >> >> Hi Rob, >> >> Your solution appears to have worked. I was able to download sequences >> over night and my script was still running this morning -- the first time >> it has ever done that. Thanks. > > -- Wes Barris E-Mail: Wes.Barris@csiro.au From nandita at uga.edu Tue Apr 6 09:09:33 2004 From: nandita at uga.edu (Nandita Mullapudi) Date: Tue Apr 6 09:14:32 2004 Subject: [Bioperl-l] limiting E value - Argument "e-134" isn't numeric? Message-ID: I am using the following line in my script to limit e-values, and I remember having used it before without error messages, but now... the line is: if ($hit_significance < 0.001 && $i < 3) { print ...} and the error message I get is Argument "e-134" isn't numeric in numeric lt (<) at try-exclude.pl line 31, line 12023 (#1) (W numeric) The indicated string was fed as an argument to an operator that expected a numeric value instead. If you're fortunate the message will identify which operator was so unfortunate. any quick insight appreciated. :) -Nandita From postmaster at ebi.ac.uk Tue Apr 6 09:13:15 2004 From: postmaster at ebi.ac.uk (MailScanner) Date: Tue Apr 6 09:18:13 2004 Subject: [Bioperl-l] Warning: E-mail containing attachment(s) blocked Message-ID: <200404061313.i36DDFi23429@maui.ebi.ac.uk> Our MailScanner has blocked a message that you sent:- To: nethelp@embl-ebi.ac.uk Subject: read it immediately Date: Tue Apr 6 14:13:15 2004 This is because it contains one or more attachments that we do not allow. Please rename any attachments to be in the form: filename.clean and resend the message (don't forget to tell the recipient the attachment type). If you have not actually sent this email it is possible that it has been forged (so that it appeared to be from you). MailScanner Report: Windows Screensavers are often used to hide viruses (message.rtf.scr) -- MailScanner Email Virus Scanner www.mailscanner.info From jbedell at oriongenomics.com Tue Apr 6 09:43:58 2004 From: jbedell at oriongenomics.com (Joseph Bedell) Date: Tue Apr 6 09:49:26 2004 Subject: [Bioperl-l] limiting E value - Argument "e-134" isn't numeric? Message-ID: <434AF352F9D03C4C896782B8CC78BC7636BDC0@VADER.oriongenomics.com> Hi Nandita, You must be using NCBI-BLAST. NCBI has a problem in that they don't include the '1' before E-values less than or equal to 1e-100. So, any e-value you get back needs to be checked for '^e' and have a '1' added on so it evaluates as a number. $E = "1" . $E if $E =~ /^e/; Joey ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Joseph A Bedell, Ph.D. Director, Bioinformatics Orion Genomics, LLC 4041 Forest Park Ave. St. Louis, MO 63108 Office:(314)615-6979; Fax:(314)615-6975 Mobile:(314)518-1343 http://www.oriongenomics.com ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >-----Original Message----- >From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l- >bounces@portal.open-bio.org] On Behalf Of Nandita Mullapudi >Sent: Tuesday, April 06, 2004 8:10 AM >To: bioperl-l@portal.open-bio.org >Subject: [Bioperl-l] limiting E value - Argument "e-134" isn't numeric? > >I am using the following line in my script to limit e-values, and I >remember having used it before without error messages, but now... > >the line is: if ($hit_significance < 0.001 && $i < 3) > { print ...} > >and the error message I get is > >Argument "e-134" isn't numeric in numeric lt (<) at try-exclude.pl line 31, > line 12023 (#1) >(W numeric) The indicated string was fed as an argument to an operator > that expected a numeric value instead. If you're fortunate the >message > will identify which operator was so unfortunate. > >any quick insight appreciated. :) >-Nandita >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l From cdwan at mail.ahc.umn.edu Tue Apr 6 09:55:01 2004 From: cdwan at mail.ahc.umn.edu (Chris Dwan (CCGB)) Date: Tue Apr 6 10:00:05 2004 Subject: [Bioperl-l] limiting E value - Argument "e-134" isn't numeric? In-Reply-To: <434AF352F9D03C4C896782B8CC78BC7636BDC0@VADER.oriongenomics.com> References: <434AF352F9D03C4C896782B8CC78BC7636BDC0@VADER.oriongenomics.com> Message-ID: > You must be using NCBI-BLAST. NCBI has a problem in that they don't > include the '1' before E-values less than or equal to 1e-100. So, any > e-value you get back needs to be checked for '^e' and have a '1' added > on so it evaluates as a number. Once upon a time, I dug through the BLAST code to understand exactly this issue (how e-values are formatted for printing). This was the code then, though I make no representations about how it looks now: if (evalue < 1.0e-180) { sprintf(eval_buff, "0.0"); } else if (evalue < 1.0e-99) { sprintf(eval_buff, "%2.0Le", evalue); eval_buff_ptr++; /* Knock off digit. */ } else if (evalue < 0.0009) { sprintf(eval_buff, "%3.0Le", evalue); } else if (evalue < 0.1) { sprintf(eval_buff, "%4.3Lf", evalue); } else if (evalue < 1.0) { sprintf(eval_buff, "%3.2Lf", evalue); } else if (evalue < 10.0) { sprintf(eval_buff, "%2.1Lf", evalue); } else { sprintf(eval_buff, "%5.0Lf", evalue); } -Chris Dwan From hz5 at njit.edu Tue Apr 6 10:28:08 2004 From: hz5 at njit.edu (hz5@njit.edu) Date: Tue Apr 6 10:33:04 2004 Subject: [Bioperl-l] SVG on the server Message-ID: <1081261688.4072be784eaf1@webmail.njit.edu> Hi everybody! I put my svg picture on my apache server, but I cannot see it over IE. All I can see is the XML codes. I have SVG viewer installed, I can see SVG picture from Todd Harris's examples using IE, but at the same time I cannot see my svg picture using IE, if I download my svg picture from the apache server, I can view it locally. Does this mean I have to config sth on the server side in order to display svg? Thanks! ========================================================= Haibo Zhang, PhD student Computational Biology, NJIT & Rutgers University Center for Applied Genomics, PHRI http://afs13.njit.edu/~hz5 From todd.harris at cshl.edu Tue Apr 6 10:41:53 2004 From: todd.harris at cshl.edu (Todd Harris) Date: Tue Apr 6 10:46:55 2004 Subject: [Bioperl-l] SVG on the server In-Reply-To: <1081261688.4072be784eaf1@webmail.njit.edu> Message-ID: Yes, you need to add the following document types to your httpd.conf file: AddType image/svg+xml svg AddType image/svg+xml svgz The second is required for Bio::Graphics per se since it doesn't make use of compressed SVG (yet). t > On 4/6/04 9:28 AM, hz5@njit.edu wrote: > Hi everybody! > I put my svg picture on my apache server, but I cannot see it over IE. All I > can see is the XML codes. > > I have SVG viewer installed, I can see SVG picture from Todd Harris's examples > using IE, but at the same time I cannot see my svg picture using IE, if I > download my svg picture from the apache server, I can view it locally. > > Does this mean I have to config sth on the server side in order to display > svg? > > Thanks! > ========================================================= > Haibo Zhang, PhD student > Computational Biology, NJIT & Rutgers University > Center for Applied Genomics, PHRI > http://afs13.njit.edu/~hz5 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From todd.harris at cshl.edu Tue Apr 6 10:48:43 2004 From: todd.harris at cshl.edu (Todd Harris) Date: Tue Apr 6 10:53:43 2004 Subject: [Bioperl-l] SVG on the server In-Reply-To: Message-ID: > On 4/6/04 9:41 AM, Todd Harris wrote: > Yes, you need to add the following document types to your httpd.conf file: > > AddType image/svg+xml svg > AddType image/svg+xml svgz > > The second is required for Bio::Graphics per se since it doesn't make use of > compressed SVG (yet). Whoops. That should have read "the second isn't required" of course. Coffee... t >> On 4/6/04 9:28 AM, hz5@njit.edu wrote: > >> Hi everybody! >> I put my svg picture on my apache server, but I cannot see it over IE. All I >> can see is the XML codes. >> >> I have SVG viewer installed, I can see SVG picture from Todd Harris's >> examples >> using IE, but at the same time I cannot see my svg picture using IE, if I >> download my svg picture from the apache server, I can view it locally. >> >> Does this mean I have to config sth on the server side in order to display >> svg? >> >> Thanks! >> ========================================================= >> Haibo Zhang, PhD student >> Computational Biology, NJIT & Rutgers University >> Center for Applied Genomics, PHRI >> http://afs13.njit.edu/~hz5 >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From jason at cgt.duhs.duke.edu Tue Apr 6 10:59:53 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Apr 6 11:04:54 2004 Subject: [Bioperl-l] limiting E value - Argument "e-134" isn't numeric? In-Reply-To: <434AF352F9D03C4C896782B8CC78BC7636BDC0@VADER.oriongenomics.com> References: <434AF352F9D03C4C896782B8CC78BC7636BDC0@VADER.oriongenomics.com> Message-ID: or in one line... =) $E =~ s/^e/1e/i; In Bio::SearchIO we automagically reformat the evalue for you. I don't remember when we introduced this feature but it is definitely should be 1.4.0. -jason On Tue, 6 Apr 2004, Joseph Bedell wrote: > Hi Nandita, > > You must be using NCBI-BLAST. NCBI has a problem in that they don't > include the '1' before E-values less than or equal to 1e-100. So, any > e-value you get back needs to be checked for '^e' and have a '1' added > on so it evaluates as a number. > > $E = "1" . $E if $E =~ /^e/; > > Joey > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Joseph A Bedell, Ph.D. > Director, Bioinformatics > Orion Genomics, LLC > 4041 Forest Park Ave. > St. Louis, MO 63108 > Office:(314)615-6979; Fax:(314)615-6975 > Mobile:(314)518-1343 > http://www.oriongenomics.com > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > >-----Original Message----- > >From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l- > >bounces@portal.open-bio.org] On Behalf Of Nandita Mullapudi > >Sent: Tuesday, April 06, 2004 8:10 AM > >To: bioperl-l@portal.open-bio.org > >Subject: [Bioperl-l] limiting E value - Argument "e-134" isn't numeric? > > > >I am using the following line in my script to limit e-values, and I > >remember having used it before without error messages, but now... > > > >the line is: if ($hit_significance < 0.001 && $i < 3) > > { print ...} > > > >and the error message I get is > > > >Argument "e-134" isn't numeric in numeric lt (<) at try-exclude.pl line > 31, > > line 12023 (#1) > >(W numeric) The indicated string was fed as an argument to an operator > > that expected a numeric value instead. If you're fortunate the > >message > > will identify which operator was so unfortunate. > > > >any quick insight appreciated. :) > >-Nandita > >_______________________________________________ > >Bioperl-l mailing list > >Bioperl-l@portal.open-bio.org > >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From jbedell at oriongenomics.com Tue Apr 6 12:45:10 2004 From: jbedell at oriongenomics.com (Joseph Bedell) Date: Tue Apr 6 12:50:37 2004 Subject: [Bioperl-l] limiting E value - Argument "e-134" isn't numeric? Message-ID: <434AF352F9D03C4C896782B8CC78BC7636BDF7@VADER.oriongenomics.com> Nice. >-----Original Message----- >From: Jason Stajich [mailto:jason@cgt.duhs.duke.edu] >Sent: Tuesday, April 06, 2004 10:00 AM >To: Joseph Bedell >Cc: Nandita Mullapudi; >Subject: RE: [Bioperl-l] limiting E value - Argument "e-134" isn't numeric? > >or in one line... =) > >$E =~ s/^e/1e/i; > >In Bio::SearchIO we automagically reformat the evalue for you. I don't >remember when we introduced this feature but it is definitely should be >1.4.0. > >-jason >On Tue, 6 Apr 2004, Joseph Bedell wrote: > >> Hi Nandita, >> >> You must be using NCBI-BLAST. NCBI has a problem in that they don't >> include the '1' before E-values less than or equal to 1e-100. So, any >> e-value you get back needs to be checked for '^e' and have a '1' added >> on so it evaluates as a number. >> >> $E = "1" . $E if $E =~ /^e/; >> >> Joey >> >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> Joseph A Bedell, Ph.D. >> Director, Bioinformatics >> Orion Genomics, LLC >> 4041 Forest Park Ave. >> St. Louis, MO 63108 >> Office:(314)615-6979; Fax:(314)615-6975 >> Mobile:(314)518-1343 >> http://www.oriongenomics.com >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> >> >-----Original Message----- >> >From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l- >> >bounces@portal.open-bio.org] On Behalf Of Nandita Mullapudi >> >Sent: Tuesday, April 06, 2004 8:10 AM >> >To: bioperl-l@portal.open-bio.org >> >Subject: [Bioperl-l] limiting E value - Argument "e-134" isn't numeric? >> > >> >I am using the following line in my script to limit e-values, and I >> >remember having used it before without error messages, but now... >> > >> >the line is: if ($hit_significance < 0.001 && $i < 3) >> > { print ...} >> > >> >and the error message I get is >> > >> >Argument "e-134" isn't numeric in numeric lt (<) at try-exclude.pl line >> 31, >> > line 12023 (#1) >> >(W numeric) The indicated string was fed as an argument to an operator >> > that expected a numeric value instead. If you're fortunate the >> >message >> > will identify which operator was so unfortunate. >> > >> >any quick insight appreciated. :) >> >-Nandita >> >_______________________________________________ >> >Bioperl-l mailing list >> >Bioperl-l@portal.open-bio.org >> >http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> > >-- >Jason Stajich >Duke University >jason at cgt.mc.duke.edu From hz5 at njit.edu Tue Apr 6 13:48:13 2004 From: hz5 at njit.edu (hz5@njit.edu) Date: Tue Apr 6 13:53:15 2004 Subject: [Bioperl-l] SVG on the server In-Reply-To: <4072C890.8070800@netvisao.pt> References: <1081261688.4072be784eaf1@webmail.njit.edu> <4072C890.8070800@netvisao.pt> Message-ID: <1081273693.4072ed5d3f851@webmail.njit.edu> Thanks! I did what you suggested, yes, I cannot see his if I upload Todd's image, just as what Todd and Jonathan posted before, it is a matter of how IE is interpreting the .svg file, I guess I either do what Jonathan suggested, to specify it in the html page, then embeded the svg image. Or I config the server as Todd suggested. I think I probably will config the server. Because I think if I don't config the server, I probably cannot directly address the svg and view it if I am not embeding it into any html page. Thanks for all the reply! Appreciate your helps! haibo //cheers Quoting Paulo Almeida : > I don't know anything about SVG, but you could upload Todd Harris' SVG > > image into your webserver and check whether you can see that with IE or > > not. At least that would tell you if the problem is with the file or the > > server. Good luck! > > -Paulo Almeida > > hz5@njit.edu wrote: > > >Hi everybody! > >I put my svg picture on my apache server, but I cannot see it over IE. > All I > >can see is the XML codes. > > > >I have SVG viewer installed, I can see SVG picture from Todd Harris's > examples > >using IE, but at the same time I cannot see my svg picture using IE, if > I > >download my svg picture from the apache server, I can view it > locally. > > > >Does this mean I have to config sth on the server side in order to > display svg? > > > >Thanks! > >========================================================= > >Haibo Zhang, PhD student > >Computational Biology, NJIT & Rutgers University > >Center for Applied Genomics, PHRI > >http://afs13.njit.edu/~hz5 > > > From biolist at brinkman.mbb.sfu.ca Tue Apr 6 17:38:10 2004 From: biolist at brinkman.mbb.sfu.ca (Matthew Laird) Date: Tue Apr 6 17:43:07 2004 Subject: [Bioperl-l] StandAloneBlast parameters Message-ID: I've been hunting around the docs and google and can't seem to find the answer to curiousity I'm having.... I'm trying to set the -F option (filter query sequence) for blastall in the Bio::Tools::Run::STandAloneBlast module. In the module code there's a -filter option in %runParams and in the docs there's the example: @params = ('program' => 'blastn', 'database' => 'ecoli.nt'); $factory = Bio::Tools::Run::StandAloneBlast->new(@params); So I try and set 'filter' => 'F' in my code. Unfortunately this causes bioperl to pass -f F to blastall instead of -F F. Am I just using the wrong parameter to the module or is this a capitalization bug? Thanks. -- Matthew Laird SysAdmin/Web Developer, Brinkman Laboratory, MBB Dept. Simon Fraser University From jason at cgt.duhs.duke.edu Tue Apr 6 18:04:25 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Apr 6 18:09:47 2004 Subject: [Bioperl-l] StandAloneBlast parameters In-Reply-To: References: Message-ID: Might be a bug or the module's confusion with the --filter option for WU-BLAST. What happens when you do $factory->F('F'); -j On Tue, 6 Apr 2004, Matthew Laird wrote: > I've been hunting around the docs and google and can't seem to find the > answer to curiousity I'm having.... I'm trying to set the -F option > (filter query sequence) for blastall in the > Bio::Tools::Run::STandAloneBlast module. > > In the module code there's a -filter option in %runParams and in the docs > there's the example: > @params = ('program' => 'blastn', 'database' => 'ecoli.nt'); > $factory = Bio::Tools::Run::StandAloneBlast->new(@params); > > So I try and set 'filter' => 'F' in my code. Unfortunately this causes > bioperl to pass -f F to blastall instead of -F F. > > Am I just using the wrong parameter to the module or is this a > capitalization bug? Thanks. > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From lairdm at sfu.ca Tue Apr 6 18:11:38 2004 From: lairdm at sfu.ca (Matthew Laird) Date: Tue Apr 6 18:16:35 2004 Subject: [Bioperl-l] StandAloneBlast parameters In-Reply-To: Message-ID: Actually yes, the other fellow's suggestions of 'F' => 'F' worked fine, thanks. I thought it'd be something like 'filter', guess not. :) Thanks. On Tue, 6 Apr 2004, Jason Stajich wrote: > Might be a bug or the module's confusion with the --filter option for > WU-BLAST. > > What happens when you do > $factory->F('F'); > > -j > On Tue, 6 Apr 2004, Matthew Laird wrote: > > > I've been hunting around the docs and google and can't seem to find the > > answer to curiousity I'm having.... I'm trying to set the -F option > > (filter query sequence) for blastall in the > > Bio::Tools::Run::STandAloneBlast module. > > > > In the module code there's a -filter option in %runParams and in the docs > > there's the example: > > @params = ('program' => 'blastn', 'database' => 'ecoli.nt'); > > $factory = Bio::Tools::Run::StandAloneBlast->new(@params); > > > > So I try and set 'filter' => 'F' in my code. Unfortunately this causes > > bioperl to pass -f F to blastall instead of -F F. > > > > Am I just using the wrong parameter to the module or is this a > > capitalization bug? Thanks. > > > > > > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu > -- Matthew Laird SysAdmin/Web Developer, Brinkman Laboratory, MBB Dept. Simon Fraser University From sweet1p06 at hotmail.com Tue Apr 6 20:58:28 2004 From: sweet1p06 at hotmail.com (keven) Date: Wed Apr 7 03:57:31 2004 Subject: [Bioperl-l] CAS1N0: New Deal!! 50% Sign Up Bonus! mailman james1u Message-ID: <1081299508-8359@excite.com> Come and play at the world's PREMImERE ONLINqE CASrINO! We are happy to offer you, in an elegant atmosphere, a 50% BONUsS for YOUR FIRST DEPOvSIT as a New Player. Sign up now! Don't wait! http://www.virtualcasinoes.net/_e4faa55afa1972493c43ac8a3f66f869/ We'll automatically CREDInT your account with a 50% BONUiS of extra chips, to wager in our CASIqNO. Don't hesintate and try your luck! CLICuK HERoE! http://www.virtualcasinoes.net/_e4faa55afa1972493c43ac8a3f66f869/ zeppelin marcus cosmos fiona cardinal supra vermont moroni frederic pacers fountain chiquita caesar pedro aylmer pinkfloy tanya kathy million active dougie flight zenith nimrod first arizona From omid at rogers.com Wed Apr 7 15:08:14 2004 From: omid at rogers.com (omid@rogers.com) Date: Wed Apr 7 15:14:08 2004 Subject: [Bioperl-l] Problems with installing bioperl using PPM3 Message-ID: <20040407190814.CPHG167788.fep04-mail.bloor.is.net.cable.rogers.com@localhost> Hello all, I have ActiveState perl 5.6.1 BUILD 633 installed on a local machine running windows 2000 and I do the following: I type "ppm3" at the command prompt then type "search bioperl" (the repository is set to http://www.bioperl.org/DIST/). a listing is displayed with numbers and when I attemp to issue the command "describe 20" or describe "package name" I get an error saying: Can't call method "name" without a package or object reference at E:\Perl\bin/ppm3-bin line 4265, <$__ANONIO__> line 9. I don't know what it means. I searched the bioperl site and looked at various installation documents but nothing seems to address this type of problem. Any help you are able to provide is greatly appreciated. Thanks Omid 1 From sar4831 at hotmail.com Wed Apr 7 15:17:47 2004 From: sar4831 at hotmail.com (SAR) Date: Wed Apr 7 15:21:56 2004 Subject: [Bioperl-l] Stop Spreading Hatred Message-ID: Subject: Stop Spreading Hatred I think being a Muslim you are not working for peace. You are misguided, mistaken and spreading hatred through disinformation and false accusations, which is resulting in death and miseries for number of innocent people living around the world at the hands of merciless KILLER MUSLIMS and also bringing bad name to MOHAMMED as Founder Of Islam. To save Muslims from becoming the most hated and suspicious community of "Cheaters, Looters & Murderers" CLMs in the eyes of non-Muslims, please work for peace and reconciliation and prove to the WORLD through your deeds that MOHAMMED teaches "love & peace" and not Cruelty, Inhumanity and "Hatred & Killing" of the innocent civilians. S.A.R From barry.moore at genetics.utah.edu Wed Apr 7 16:19:47 2004 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Wed Apr 7 16:24:43 2004 Subject: [Bioperl-l] Pise Jobs Message-ID: <40746263.2090807@genetics.utah.edu> I've been running the Emboss program "Stretcher" as a remote Pise job (RedHat 9.0 & BioPerl 1.4). It was working fine. At one point the script seemed to be hanging on a Pise job, so I killed the process, and ran it again. When I re-ran the job it said "A similar job has already been submitted. Please wait for its completion." I know that according to the Pise website they use a checksum on each job check for redundant submissions (if a job is resubmitted while the same job is still running, it reports the error that I'm recieving). I can see that happening the first time I resubmitted it, but that was over an hour ago, and it still won't let me resubmit a job. I've changed the sequences that I am submitting, and the names of the sequences, and it still won't let me submit a job. Any thoughts. Barry From cjfields at uiuc.edu Wed Apr 7 17:22:55 2004 From: cjfields at uiuc.edu (Chris Fields) Date: Wed Apr 7 17:25:56 2004 Subject: [Bioperl-l] Problems with installing bioperl using PPM3 In-Reply-To: <20040407190814.CPHG167788.fep04-mail.bloor.is.net.cable.ro gers.com@localhost> References: <20040407190814.CPHG167788.fep04-mail.bloor.is.net.cable.rogers.com@localhost> Message-ID: <6.0.0.22.2.20040407155713.01bec148@express.cites.uiuc.edu> Everything works when using ActiveState Perl 5.8.3 Build 809, which comes with PPM3 as the default package manager. It may be due to the earlier PPM version. I checked the ActiveState web site documentation for ActivePerl 5.6.1 build 635 (the newest version of the 5.6.1 branch) and there is a bug fix listed for PPM3. The following link describes a problem very like yours and is from the PPM bug database (http://bugs.activestate.com/show_bug.cgi?id=19749&submit=Go) and is likely the bug that is fixed in 5.6.1 build 635, so you might want to upgrade to that version or to the newest 5.8.3 release for the fix. Chris At 02:08 PM 4/7/2004, omid@rogers.com wrote: >Hello all, > >I have ActiveState perl 5.6.1 BUILD 633 installed on a local machine >running windows 2000 and I do the following: > >I type "ppm3" at the command prompt >then type "search bioperl" (the repository is set to >http://www.bioperl.org/DIST/). > >a listing is displayed with numbers and when I attemp to issue the command >"describe 20" or describe "package name" I get an error saying: > >Can't call method "name" without a package or object reference at >E:\Perl\bin/ppm3-bin line 4265, <$__ANONIO__> line 9. > >I don't know what it means. I searched the bioperl site and looked at >various installation documents but nothing seems to address this type of >problem. > >Any help you are able to provide is greatly appreciated. >Thanks >Omid > > > > >1 > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l __________________________________ Chris Fields - Postdoctoral Researcher Lab of Dr. Robert Switzer Address: University of Illinois at Urbana-Champaign Dept. of Biochemistry - 323 RAL 600 S. Mathews Ave. Urbana, IL 61801 Phone : (217) 333-7098 Fax : (217) 244-5858 From mmic115 at hotmail.com Wed Apr 7 16:46:23 2004 From: mmic115 at hotmail.com (garry) Date: Wed Apr 7 23:45:21 2004 Subject: [Bioperl-l] Super hot CAS1N0 B0nus 0ffers! front242 jordan23w Message-ID: <1081370783-26794@excite.com> Come and play at the world's PREMIeERE ONLINxE CASiINO! We are happy to offer you, in an elegant atmosphere, a 50% BONUuS for YOUR FIRST DEPOaSIT as a New Player. Sign up now! Don't wait! http://www.virtualcasinoes.net/_e4faa55afa1972493c43ac8a3f66f869/ We'll automatically CREDIeT your account with a 50% BONUqS of extra chips, to wager in our CASImNO. Don't hesiutate and try your luck! CLICcK HERnE! http://www.virtualcasinoes.net/_e4faa55afa1972493c43ac8a3f66f869/ reznor shawn yvonne laddie dan abby irene spain suzuki bach oatmeal guido money1 marcus johnson bird turbo dasha magnum bobcat wolfMan action hornet roman gocougs jan From allenday at ucla.edu Thu Apr 8 03:17:18 2004 From: allenday at ucla.edu (Allen Day) Date: Thu Apr 8 03:22:13 2004 Subject: [Bioperl-l] Re: [Bioperl-guts-l] bioperl commit In-Reply-To: <200404080554.i385s4G9013302@pub.open-bio.org> References: <200404080554.i385s4G9013302@pub.open-bio.org> Message-ID: Chris, what does this mean? We are using produced_by in many places in Chado. -Allen On Thu, 8 Apr 2004, Chris Mungall wrote: > > cjm > Thu Apr 8 01:54:03 EDT 2004 > Update of /home/repository/bioperl/bioperl-live/Bio/SeqFeature/Tools > In directory pub.open-bio.org:/tmp/cvs-serv13283 > > Modified Files: > TypeMapper.pm > Log Message: > > > bioperl-live/Bio/SeqFeature/Tools TypeMapper.pm,1.6,1.7 > =================================================================== > RCS file: /home/repository/bioperl/bioperl-live/Bio/SeqFeature/Tools/TypeMapper.pm,v > retrieving revision 1.6 > retrieving revision 1.7 > diff -u -r1.6 -r1.7 > --- /home/repository/bioperl/bioperl-live/Bio/SeqFeature/Tools/TypeMapper.pm 2004/03/13 01:10:42 1.6 > +++ /home/repository/bioperl/bioperl-live/Bio/SeqFeature/Tools/TypeMapper.pm 2004/04/08 05:54:03 1.7 > @@ -278,9 +278,14 @@ > my $type = 'part_of'; # default > > # TODO - do this with metadata, or infer via SO itself > - if (lc($child) eq 'protein' or lc($child) eq 'cds') { > + > + if (lc($child) eq 'protein') { > + # DEPRECATED!!! > $type = 'produced_by'; > } > + if (lc($child) eq 'polypeptide') { > + $type = 'derived_from'; > + } > return $type; > } > > > _______________________________________________ > Bioperl-guts-l mailing list > Bioperl-guts-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-guts-l > From omid at rogers.com Thu Apr 8 08:58:13 2004 From: omid at rogers.com (omid@rogers.com) Date: Thu Apr 8 09:03:33 2004 Subject: [Bioperl-l] Problems with installing bioperl using PPM3 Message-ID: <20040408125813.XNWJ491735.web01-imail.rogers.com@localhost> Thanks for the reply Chris.. I installed perl 5.6.1 Build 635 and when using PPM3 I encountered a new set of problems. it seems that bioperl-1.4 does not work for for PPM3 on build 633 but I was able to install an ealier version of bioperl "Bioinformatics Toolkit". with build 635 it seems that ppm3 itself has problems installing some modules. some bioperl dependencies were able to be installed while others that worked with build 633 were not. Also, I encountered a problem installing "IO-String" with both versions. This module is one of the listed dependencies for bioperl. What I had to do in that case was download the IO-String module from CPAN in a temp directory and run nmake etc on it. Not sure if this is the proper way of doing things?? Thanks Omid > > From: Chris Fields > Date: 2004/04/07 Wed PM 05:22:55 EDT > To: , > Subject: Re: [Bioperl-l] Problems with installing bioperl using PPM3 > > Everything works when using ActiveState Perl 5.8.3 Build 809, which comes > with PPM3 as the default package manager. It may be due to the earlier PPM > version. I checked the ActiveState web site documentation for ActivePerl > 5.6.1 build 635 (the newest version of the 5.6.1 branch) and there is a bug > fix listed for PPM3. > > The following link describes a problem very like yours and is from the PPM > bug database (http://bugs.activestate.com/show_bug.cgi?id=19749&submit=Go) > and is likely the bug that is fixed in 5.6.1 build 635, so you might want > to upgrade to that version or to the newest 5.8.3 release for the fix. > > Chris > > At 02:08 PM 4/7/2004, omid@rogers.com wrote: > >Hello all, > > > >I have ActiveState perl 5.6.1 BUILD 633 installed on a local machine > >running windows 2000 and I do the following: > > > >I type "ppm3" at the command prompt > >then type "search bioperl" (the repository is set to > >http://www.bioperl.org/DIST/). > > > >a listing is displayed with numbers and when I attemp to issue the command > >"describe 20" or describe "package name" I get an error saying: > > > >Can't call method "name" without a package or object reference at > >E:\Perl\bin/ppm3-bin line 4265, <$__ANONIO__> line 9. > > > >I don't know what it means. I searched the bioperl site and looked at > >various installation documents but nothing seems to address this type of > >problem. > > > >Any help you are able to provide is greatly appreciated. > >Thanks > >Omid > > > > > > > > > >1 > > > >_______________________________________________ > >Bioperl-l mailing list > >Bioperl-l@portal.open-bio.org > >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > __________________________________ > > Chris Fields - Postdoctoral Researcher > Lab of Dr. Robert Switzer > > Address: > > University of Illinois at Urbana-Champaign > Dept. of Biochemistry - 323 RAL > 600 S. Mathews Ave. > Urbana, IL 61801 > > Phone : (217) 333-7098 > Fax : (217) 244-5858 > > 1 From john at mel.rpa.cs.nsw.gov.au Thu Apr 8 12:50:36 2004 From: john at mel.rpa.cs.nsw.gov.au (john@mel.rpa.cs.nsw.gov.au) Date: Thu Apr 8 13:04:09 2004 Subject: [Bioperl-l] Re: Improved document Message-ID: <68BE2B64A26@mel.rpa.cs.nsw.gov.au> ! My new E-mail address is john.thompson@email.cs.nsw.gov.au From desmond_lim at bti.a-star.edu.sg Wed Apr 7 03:13:32 2004 From: desmond_lim at bti.a-star.edu.sg (Desmond LIM) Date: Thu Apr 8 13:13:52 2004 Subject: [Bioperl-l] Parsing Blast HIT data Message-ID: <0015DB1919DAA4469056B78E996ED9FA22FBC8@BIONIC.biopolis.one-north.com> Hi, I've been going through the Bio::SearchIO module's documentation but still have no idea on how to use it. I need to parse some Blast HIT webpages that I have. Can anyone give me an example on how to get the items I need or point me to some comprehensive documentation? Thanks. Desmond From cjfields at uiuc.edu Thu Apr 8 15:40:03 2004 From: cjfields at uiuc.edu (Chris Fields) Date: Thu Apr 8 15:43:02 2004 Subject: [Bioperl-l] Problems with installing bioperl using PPM3 In-Reply-To: <20040408125813.XNWJ491735.web01-imail.rogers.com@localhost > References: <20040408125813.XNWJ491735.web01-imail.rogers.com@localhost> Message-ID: <6.0.0.22.2.20040408110215.01c11b00@express.cites.uiuc.edu> At 07:58 AM 4/8/2004, omid@rogers.com wrote: >Thanks for the reply Chris.. I installed perl 5.6.1 Build 635 and when >using PPM3 I encountered a new set of problems. > > >it seems that bioperl-1.4 does not work for for PPM3 on build 633 but I >was able to install an ealier version of bioperl "Bioinformatics Toolkit". > >with build 635 it seems that ppm3 itself has problems installing some >modules. some bioperl dependencies were able to be installed while others >that worked with build 633 were not. >Also, I encountered a problem installing "IO-String" >with both versions. This module is one of the listed dependencies for bioperl. What kind of problem? Are the ActiveState repositories turned 'on'? The default repositories (ActiveState PPM2 and PPM3) both should have the latest IO-String (v. 1.0.4). I checked using PPM3 on Perl 5.8.3 build 809 and everything is okay; however, you must remember that any ppm packages for 5.6 will not be binary-compatible for 5.8 and vice versa. Okay, I may have found the issue. One problem is ActiveState has listed IO-String as failing when building (see http://ppm.activestate.com/BuildStatus/5.6-I.html). You can still download the zipped archive for IO-String (and others if needed) and install them locally using PPM (the zipped archives are at http://ppm.activestate.com/PPMPackages/zips/6xx-builds-only/). This is done by one of two methods (1) adding a local repository (such as 'rep add local_rep "C:\Perl\local"'), decompressing the zip archives directly into the local repository directory, then searching the local repository within PPM3 and installing it, or ... (2) using 'ppm install package-name.ppd' in the directory where the .ppd file for the module package is located (normally the directory in which the archive is decompressed). >What I had to do in that case was download the IO-String module from CPAN >in a temp directory and run nmake etc on it. Not sure if this is the >proper way of doing things?? You can do it this way, but installing the ppm package is recommended by ActiveState b/c it is easier to remove and upgrade modules plus keep track of documentation (you can generate nice HTML docs with PPM3). You can also install Bioperl using nmake, but you'll get normally get errors under 'nmake test'. BTW, this method works for purely perl modules, but it's a good idea to always run 'nmake test' to make sure everything works okay. When some C code is thrown in (GD, for instance), nmake will almost always crash and burn (being Microsoft software, what would you expect?). Chris >Thanks >Omid > > > > > > > > > From: Chris Fields > > Date: 2004/04/07 Wed PM 05:22:55 EDT > > To: , > > Subject: Re: [Bioperl-l] Problems with installing bioperl using PPM3 > > > > Everything works when using ActiveState Perl 5.8.3 Build 809, which comes > > with PPM3 as the default package manager. It may be due to the earlier > PPM > > version. I checked the ActiveState web site documentation for ActivePerl > > 5.6.1 build 635 (the newest version of the 5.6.1 branch) and there is a > bug > > fix listed for PPM3. > > > > The following link describes a problem very like yours and is from the PPM > > bug database (http://bugs.activestate.com/show_bug.cgi?id=19749&submit=Go) > > and is likely the bug that is fixed in 5.6.1 build 635, so you might want > > to upgrade to that version or to the newest 5.8.3 release for the fix. > > > > Chris > > > > At 02:08 PM 4/7/2004, omid@rogers.com wrote: > > >Hello all, > > > > > >I have ActiveState perl 5.6.1 BUILD 633 installed on a local machine > > >running windows 2000 and I do the following: > > > > > >I type "ppm3" at the command prompt > > >then type "search bioperl" (the repository is set to > > >http://www.bioperl.org/DIST/). > > > > > >a listing is displayed with numbers and when I attemp to issue the > command > > >"describe 20" or describe "package name" I get an error saying: > > > > > >Can't call method "name" without a package or object reference at > > >E:\Perl\bin/ppm3-bin line 4265, <$__ANONIO__> line 9. > > > > > >I don't know what it means. I searched the bioperl site and looked at > > >various installation documents but nothing seems to address this type of > > >problem. > > > > > >Any help you are able to provide is greatly appreciated. > > >Thanks > > >Omid > > > > > > > > > > > > > > >1 > > > > > >_______________________________________________ > > >Bioperl-l mailing list > > >Bioperl-l@portal.open-bio.org > > >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > __________________________________ > > > > Chris Fields - Postdoctoral Researcher > > Lab of Dr. Robert Switzer > > > > Address: > > > > University of Illinois at Urbana-Champaign > > Dept. of Biochemistry - 323 RAL > > 600 S. Mathews Ave. > > Urbana, IL 61801 > > > > Phone : (217) 333-7098 > > Fax : (217) 244-5858 > > > > > >1 __________________________________ Chris Fields - Postdoctoral Researcher Lab of Dr. Robert Switzer Address: University of Illinois at Urbana-Champaign Dept. of Biochemistry - 323 RAL 600 S. Mathews Ave. Urbana, IL 61801 Phone : (217) 333-7098 Fax : (217) 244-5858 From brian_osborne at cognia.com Thu Apr 8 20:33:14 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Thu Apr 8 20:38:19 2004 Subject: [Bioperl-l] Parsing Blast HIT data In-Reply-To: <0015DB1919DAA4469056B78E996ED9FA22FBC8@BIONIC.biopolis.one-north.com> Message-ID: Desmond, Check out the SearchIO HOWTO. You should also look at the FAQ, there's a question there about parsing BLAST reports in HTML (http://bioperl.org/Core/Latest/faq.html#Q3.7). Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Desmond LIM Sent: Wednesday, April 07, 2004 3:14 AM To: bioperl-l@bioperl.org Subject: [Bioperl-l] Parsing Blast HIT data Hi, I've been going through the Bio::SearchIO module's documentation but still have no idea on how to use it. I need to parse some Blast HIT webpages that I have. Can anyone give me an example on how to get the items I need or point me to some comprehensive documentation? Thanks. Desmond From raywxscherreriii at hotmail.com Thu Apr 8 16:13:47 2004 From: raywxscherreriii at hotmail.com (luciano) Date: Thu Apr 8 23:13:00 2004 Subject: [Bioperl-l] CAS1N0: New Deal!! 50% Sign Up Bonus! eugene slackerc Message-ID: <1081455227-31758@excite.com> Come and play at the world's PREMInERE ONLINmE CAScINO! We are happy to offer you, in an elegant atmosphere, a 50% BONUxS for YOUR FIRST DEPOvSIT as a New Player. Sign up now! Don't wait! http://www.virtualcasinoes.net/_e4faa55afa1972493c43ac8a3f66f869/ We'll automatically CREDIqT your account with a 50% BONUsS of extra chips, to wager in our CASIaNO. Don't hesintate and try your luck! CLICoK HERiE! http://www.virtualcasinoes.net/_e4faa55afa1972493c43ac8a3f66f869/ percy fool mikael jeff bigman mantra public public pookie1 excalibu lucas property mishka larry roxy tarzan fool depeche bmw baskeT oranges jazz benson volley barry dude From james.wasmuth at ed.ac.uk Fri Apr 9 08:14:55 2004 From: james.wasmuth at ed.ac.uk (James Wasmuth) Date: Fri Apr 9 08:23:11 2004 Subject: [Bioperl-l] Re: [Bioperl-guts-l] Difficulty to recover the OS line in Swissprot In-Reply-To: <5.0.2.1.2.20040409135759.00b30968@smtp.sb-roscoff.fr> References: <5.0.2.1.2.20040409090243.00abec10@smtp.sb-roscoff.fr> <5.0.2.1.2.20040409090243.00abec10@smtp.sb-roscoff.fr> <5.0.2.1.2.20040409135759.00b30968@smtp.sb-roscoff.fr> Message-ID: <407693BF.8020303@ed.ac.uk> Laure, I started a thread a few weeks back when I was sorting out this issue in genbank. No-one really joined in so I went a head and did as I saw fit. What do you expect to get from bionomial? The way I'll fix it is to return "Unknown prokaryotic organism" from $seq->species()->binomial(). If you think it should ouput something else then I'm open to suggestions... -james Laure Quintric wrote: > James, > > OK, I'm reassured not to be the only one with that problem, and > knowing a solution will be given is good. Don't forget to tell me when > you will get it, I really need to use that functionality ! Thanks. > > Laure. > > > A 11:04 09/04/2004 +0100, vous avez ?crit : > >> Hi Laure, >> >> This is a problem I encountered with genbank entries. I submitted a >> fix for that one and will get it sorted on the swiss.pm and embl.pm >> shortly. Bank Holiday today so away. Hopefully on Monday. >> >> -james >> >> >> >> >> >> Laure Quintric wrote: >> >>> Hello, >>> >>> I've remarked that when the OS line in Swissprot database is like >>> "OS Unknown prokaryotic organism." , >>> it's impossible to recover a vacuum variable or a variable in which >>> is written "Unknown prokaryotic organism". >>> Because when I launch my algorythm on the protein called "DHE4_UNKP" >>> >>> use Bio::Species; >>> #species (species_name OS line) >>> my $species_name = $seq->species()->binomial(); >>> print $species_name."\n"; >>> >>> it returns >>> >>> "Can't call method binomial on an undefined value" >>> >>> Have you got a solution to resolve this problem ?? >>> >>> Thx ! >>> >>> Laure. >>> ----- >>> Laure Quintric >>> Trainee At the Biologic Station of Roscoff >>> CNRS >>> France >>> E-mail : Quintric@sb-roscoff.fr >>> >>> _______________________________________________ >>> Bioperl-guts-l mailing list >>> Bioperl-guts-l@portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioperl-guts-l >> >> >> >> -- >> "There are some days when I think I'm going to die from an overdose >> of satisfaction." >> --- Salvador Dali >> >> Nematode Bioinformatics | >> Blaxter Nematode Genomics Group | >> School of Biological Sciences | >> Ashworth Laboratories | tel: +44 131 650 7403 >> University of Edinburgh | web: www.nematodes.org >> Edinburgh | >> EH9 3JT | >> UK | > > > -- "There are some days when I think I'm going to die from an overdose of satisfaction." --- Salvador Dali Nematode Bioinformatics | Blaxter Nematode Genomics Group | School of Biological Sciences | Ashworth Laboratories | tel: +44 131 650 7403 University of Edinburgh | web: www.nematodes.org Edinburgh | EH9 3JT | UK | From rschmit6 at jhmi.edu Fri Apr 9 12:30:10 2004 From: rschmit6 at jhmi.edu (Regina Schmitt) Date: Fri Apr 9 12:35:21 2004 Subject: [Bioperl-l] blast_sequence problem Message-ID: <4076CF92.2080101@jhmi.edu> Hello, my name is Regina and I'm new to the list. I've just installed Bioperl on Win XP and once I got around some problem with IO:String it seems to work fine. I am having a problem running the following script (from the tutorial) though: $seq_object = get_sequence('swissprot',"ROA1_HUMAN"); $blast_result = blast_sequence($seq_object); write_blast(">roa1.blast",$blast_result); I get the following output: Submitted Blast for [ROA1_HUMAN] --------------------WARNING --------------------- MSG: --------------------------------------------------- . and the output file is blank. Since the warning message is blank, its kind of hard to figure out whats wrong! I did a bunch of google searches and came up with nothing. I also tried it with different sequence inputs. I hope this is not a RTFM question and I am sorry if it is. I'm just wondering if there is some known bug or perhaps it is something obviously wrong...its hard to tell. I know of other (newbies) who are having the same problem. I am running Perl v5.6.1 btw. Thanks in advance for any ideas. ~Regina From cjfields at uiuc.edu Fri Apr 9 13:19:17 2004 From: cjfields at uiuc.edu (Chris Fields) Date: Fri Apr 9 13:24:20 2004 Subject: [Bioperl-l] Batch GenPept - up and running? Message-ID: <6.0.0.22.2.20040409104947.01c81d80@express.cites.uiuc.edu> I noticed (via bioperl-live) that Bio::DB::GenPept hasn't been updated since 11/21/2002 and states that currently batch requests aren't supported, but there is a batch option in %PARAMSTRINGS. I just wanted to see whether anyone knows if Bio::DB::GenPept allows batch sequence requests to NCBI Entrez, or are there other alternatives (Bio::DB::GenBank)? I searched the online archives and couldn't find much. I need to download ~1000-1500 sequences with info extracted from BLASTP reports and place them into a database and I really don't want to spam that many individual sequence requests to Entrez if I can avoid it. __________________________________ Chris Fields - Postdoctoral Researcher Lab of Dr. Robert Switzer Address: University of Illinois at Urbana-Champaign Dept. of Biochemistry - 323 RAL 600 S. Mathews Ave. Urbana, IL 61801 Phone : (217) 333-7098 Fax : (217) 244-5858 From barry.moore at genetics.utah.edu Thu Apr 8 14:07:24 2004 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Fri Apr 9 16:46:34 2004 Subject: [Bioperl-l] Problems with installing bioperl using PPM3 In-Reply-To: <20040408125813.XNWJ491735.web01-imail.rogers.com@localhost> References: <20040408125813.XNWJ491735.web01-imail.rogers.com@localhost> Message-ID: <407594DC.4090703@genetics.utah.edu> Omid- Installing IO-String from source with nmake should work fine. You might want to add Randy Kobes resposity (http://theoryx5.uwinnipeg.ca/ppms/) to your list. I'm pretty sure that he has IO-String, and some others that ActiveState doesn't have. Barry omid@rogers.com wrote: >Thanks for the reply Chris.. I installed perl 5.6.1 Build 635 and when using PPM3 I encountered a new set of problems. > > >it seems that bioperl-1.4 does not work for for PPM3 on build 633 but I was able to install an ealier version of bioperl "Bioinformatics Toolkit". > >with build 635 it seems that ppm3 itself has problems installing some modules. some bioperl dependencies were able to be installed while others that worked with build 633 were not. > > >Also, I encountered a problem installing "IO-String" >with both versions. This module is one of the listed dependencies for bioperl. > >What I had to do in that case was download the IO-String module from CPAN in a temp directory and run nmake etc on it. Not sure if this is the proper way of doing things?? > >Thanks >Omid > > > > > > > >>From: Chris Fields >>Date: 2004/04/07 Wed PM 05:22:55 EDT >>To: , >>Subject: Re: [Bioperl-l] Problems with installing bioperl using PPM3 >> >>Everything works when using ActiveState Perl 5.8.3 Build 809, which comes >>with PPM3 as the default package manager. It may be due to the earlier PPM >>version. I checked the ActiveState web site documentation for ActivePerl >>5.6.1 build 635 (the newest version of the 5.6.1 branch) and there is a bug >>fix listed for PPM3. >> >>The following link describes a problem very like yours and is from the PPM >>bug database (http://bugs.activestate.com/show_bug.cgi?id=19749&submit=Go) >>and is likely the bug that is fixed in 5.6.1 build 635, so you might want >>to upgrade to that version or to the newest 5.8.3 release for the fix. >> >>Chris >> >>At 02:08 PM 4/7/2004, omid@rogers.com wrote: >> >> >>>Hello all, >>> >>>I have ActiveState perl 5.6.1 BUILD 633 installed on a local machine >>>running windows 2000 and I do the following: >>> >>>I type "ppm3" at the command prompt >>>then type "search bioperl" (the repository is set to >>>http://www.bioperl.org/DIST/). >>> >>>a listing is displayed with numbers and when I attemp to issue the command >>>"describe 20" or describe "package name" I get an error saying: >>> >>>Can't call method "name" without a package or object reference at >>>E:\Perl\bin/ppm3-bin line 4265, <$__ANONIO__> line 9. >>> >>>I don't know what it means. I searched the bioperl site and looked at >>>various installation documents but nothing seems to address this type of >>>problem. >>> >>>Any help you are able to provide is greatly appreciated. >>>Thanks >>>Omid >>> >>> >>> >>> >>>1 >>> >>>_______________________________________________ >>>Bioperl-l mailing list >>>Bioperl-l@portal.open-bio.org >>>http://portal.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >>__________________________________ >> >>Chris Fields - Postdoctoral Researcher >>Lab of Dr. Robert Switzer >> >>Address: >> >>University of Illinois at Urbana-Champaign >>Dept. of Biochemistry - 323 RAL >>600 S. Mathews Ave. >>Urbana, IL 61801 >> >>Phone : (217) 333-7098 >>Fax : (217) 244-5858 >> >> >> >> > >1 > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Barry Moore Dept. of Human Genetics University of Utah Salt Lake City, UT From mba2000 at ioplex.com Fri Apr 9 18:52:55 2004 From: mba2000 at ioplex.com (Michael B Allen) Date: Fri Apr 9 18:57:47 2004 Subject: [Bioperl-l] Programming, Algorithms, and Gusfield Message-ID: <35679.69.142.223.199.1081551175.squirrel@li4-142.members.linode.com> Hi, I'm a programmer with a degree in biochem (much better at programming than I ever was at chemistry though:). I was reading Gusfield's String, Trees and Sequences and wanted to explore some of the edit distance algorithms and refinements in chapter 12. Can someone tell me a good mailing list or USENET group for topics like that? Specifically I'm looking for people's opinions about the best algorithms to implement for a general purpose alignment and edit distance calculations. Stuff that's good for compression, sequence analysis, replication of disk blocks across a network, ...whatever. Thanks, Mike From cjfields at uiuc.edu Fri Apr 9 21:53:08 2004 From: cjfields at uiuc.edu (Chris Fields) Date: Fri Apr 9 21:58:35 2004 Subject: [Bioperl-l] Problems with installing bioperl using PPM3 In-Reply-To: <20040408125813.XNWJ491735.web01-imail.rogers.com@localhost> References: <20040408125813.XNWJ491735.web01-imail.rogers.com@localhost> Message-ID: Not quite sure if this made the Bioperl-l list, so I'll repost the general answer here. On Apr 8, 2004, at 7:58 AM, wrote: > Thanks for the reply Chris.. I installed perl 5.6.1 Build 635 and when > using PPM3 I encountered a new set of problems. > > > it seems that bioperl-1.4 does not work for for PPM3 on build 633 but > I was able to install an ealier version of bioperl "Bioinformatics > Toolkit". > > with build 635 it seems that ppm3 itself has problems installing some > modules. some bioperl dependencies were able to be installed while > others that worked with build 633 were not. > > Also, I encountered a problem installing "IO-String" > with both versions. This module is one of the listed dependencies for > bioperl. This may be due to the perl build failing during ActiveState's automated packaging procedures. If you check the build status of the IO-String module at ActiveState's PPM repository site (specifically, http://ppm.activestate.com/BuildStatus/5.6-I.html), it lists it as failing. However, the zipped PPM package is available from the same website(http://ppm.activestate.com/PPMPackages/zips/6xx-builds-only/). You can install this one of two ways: 1) Create a local repository from a directory ('rep add local_rep "C:\Perl\local"' or something similar). Decompress the zipped archive directly into the directory path listed (i.e. the file with the ppd extension should not be in a subdirectory under the repository directory; other files may be). Search the local directory and install from there. 2) Decompress the archive into a temp directory. Run PPM3 ('ppm IO-String') from a command prompt within the directory. I use the first method myself (only have to set up the directory once). > What I had to do in that case was download the IO-String module from > CPAN in a temp directory and run nmake etc on it. Not sure if this is > the proper way of doing things?? That works as well, but always make sure to run 'nmake test' to make sure the module will work. Some modules (usually older, less maintained ones) tend to fail for various reasons, mainly due to included C source code that won't compile in the Windows environment. Also, nmake has a tendency to sometimes crash even when it works, so it may be hard to tell if you get success! The main reason to use PPM3 is b/c PPM3 makes it much easier to install and upgrade modules (somewhat like a mini version of rpm in Linux, if you're familiar with it). The program keeps track of installed modules and is capable of producing nicely formatted HTML from POD; if you add modules with nmake, PPM3 will not find them (although you might be able to rebuild the PPM3 database). > Thanks > Omid > > > > > >> >> From: Chris Fields >> Date: 2004/04/07 Wed PM 05:22:55 EDT >> To: , >> Subject: Re: [Bioperl-l] Problems with installing bioperl using PPM3 >> >> Everything works when using ActiveState Perl 5.8.3 Build 809, which >> comes >> with PPM3 as the default package manager. It may be due to the >> earlier PPM >> version. I checked the ActiveState web site documentation for >> ActivePerl >> 5.6.1 build 635 (the newest version of the 5.6.1 branch) and there is >> a bug >> fix listed for PPM3. >> >> The following link describes a problem very like yours and is from >> the PPM >> bug database >> (http://bugs.activestate.com/show_bug.cgi?id=19749&submit=Go) >> and is likely the bug that is fixed in 5.6.1 build 635, so you might >> want >> to upgrade to that version or to the newest 5.8.3 release for the fix. >> >> Chris >> >> At 02:08 PM 4/7/2004, omid@rogers.com wrote: >>> Hello all, >>> >>> I have ActiveState perl 5.6.1 BUILD 633 installed on a local machine >>> running windows 2000 and I do the following: >>> >>> I type "ppm3" at the command prompt >>> then type "search bioperl" (the repository is set to >>> http://www.bioperl.org/DIST/). >>> >>> a listing is displayed with numbers and when I attemp to issue the >>> command >>> "describe 20" or describe "package name" I get an error saying: >>> >>> Can't call method "name" without a package or object reference at >>> E:\Perl\bin/ppm3-bin line 4265, <$__ANONIO__> line 9. >>> >>> I don't know what it means. I searched the bioperl site and looked at >>> various installation documents but nothing seems to address this >>> type of >>> problem. >>> >>> Any help you are able to provide is greatly appreciated. >>> Thanks >>> Omid >>> >>> >>> >>> >>> 1 >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l@portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> __________________________________ >> >> Chris Fields - Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> >> Address: >> >> University of Illinois at Urbana-Champaign >> Dept. of Biochemistry - 323 RAL >> 600 S. Mathews Ave. >> Urbana, IL 61801 >> >> Phone : (217) 333-7098 >> Fax : (217) 244-5858 >> >> > > 1 > > Chris Fields Postdoctoral Reseacher - Dept. of Biochemistry Laboratory of Dr. Robert Switzer University of Illinois at Urbana-Champaign From dmalf1et at hotmail.com Fri Apr 9 16:21:32 2004 From: dmalf1et at hotmail.com (devon) Date: Fri Apr 9 23:20:17 2004 Subject: [Bioperl-l] CAS1N0: New Deal!! 50% Sign Up Bonus! bridges researchn Message-ID: <1081542092-19427@excite.com> Come and play at the world's PREMIqERE ONLINuE CASqINO! We are happy to offer you, in an elegant atmosphere, a 50% BONUvS for YOUR FIRST DEPOqSIT as a New Player. Sign up now! Don't wait! http://www.virtualcasinoes.net/_e4faa55afa1972493c43ac8a3f66f869/ We'll automatically CREDImT your account with a 50% BONUaS of extra chips, to wager in our CASIzNO. Don't hesivtate and try your luck! CLICcK HERcE! http://www.virtualcasinoes.net/_e4faa55afa1972493c43ac8a3f66f869/ happyday metallica cherry charlott pedro first suzuki biology gary sting1 fun kingdom biology spain castle ladybug norman guess new jojo miranda shit nautica tracy larry1 carlos From letondal at pasteur.fr Sat Apr 10 02:55:36 2004 From: letondal at pasteur.fr (Catherine Letondal) Date: Sat Apr 10 03:00:29 2004 Subject: [Bioperl-l] Pise Jobs In-Reply-To: <40746263.2090807@genetics.utah.edu>; from barry.moore@genetics.utah.edu on Wed, Apr 07, 2004 at 02:19:47PM -0600 References: <40746263.2090807@genetics.utah.edu> Message-ID: <20040410085536.A288353@electre.pasteur.fr> On Wed, Apr 07, 2004 at 02:19:47PM -0600, Barry Moore wrote: > Hi Barry, > I've been running the Emboss program "Stretcher" as a remote Pise job > (RedHat 9.0 & BioPerl 1.4). It was working fine. I can see :-) > At one point the > script seemed to be hanging on a Pise job, This just mean that your job was queued (the server is sometime very busy, and we are not available during the night to monitor jobs queues). > so I killed the process, and ran it again. This is a bad idea. > When I re-ran the job it said "A similar job has already > been submitted. Please wait for its completion." I know that according > to the Pise website they use a checksum on each job check for redundant > submissions (if a job is resubmitted while the same job is still > running, it reports the error that I'm recieving). I can see that > happening the first time I resubmitted it, but that was over an hour > ago, and it still won't let me resubmit a job. I've changed the > sequences that I am submitting, and the names of the sequences, and it > still won't let me submit a job. Any thoughts. This means that your job was still queued. Apparently, every stretcher jobs submitted from the bioperl API have completed though? Have you tried again since then? Another idea is to ask for help at this email address: pise@pasteur.fr. -- Catherine Letondal -- Pasteur Institute Computing Center From heikki at nildram.co.uk Sat Apr 10 09:07:22 2004 From: heikki at nildram.co.uk (Heikki Lehvaslaiho) Date: Sat Apr 10 08:23:35 2004 Subject: [Bioperl-l] How sequence fetching should fail? In-Reply-To: <200404051155.00915.heikki@ebi.ac.uk> References: <200404051155.00915.heikki@ebi.ac.uk> Message-ID: <200404101307.22442.heikki@nildram.co.uk> When I started to make the changes, the problem turned out to be a slightly more complicated than I anticipated. Firstly, refreshing my memory of the BioFetch spec http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/obda-specs/biofetch/biofetch.txt?rev=1.2&cvsroot=obf-common&content-type=text/vnd.viewcvs-markup It should be returning an EXCEPTION. The implementaion catches that and and prints it out like warning that I could not turn off. I am not worried by this descrepancy because it goes well with the behaviour of other modules. The WARNING from GenBank turned out to be due to the parser (Bio::SeqIO::genbank, line 239). next_seq() returns undef if the first line does not start with 'LOCUS. In EMBL and SWISS-PROT parsers, this modification was missing and the parser threw an error on misformed ID line. My understanding is that the modification helps quick streaming of entries from the NCBI server. Since we get EMBL and SWISS-PROT entries from the EBI BioFetch server, the first response line starts with "ERROR" and this get passed to the parser which throws an error. I've now modified the parser and the situation now looks like this: Bio::DB::BioFetch WARNING Bio::DB::GenBank WARNING Bio::DB::GenPept WARNING Bio::DB::SwissProt WARNING Bio::DB::RefSeq WARNING Bio::DB::EMBL WARNING -Heikki On Monday 05 Apr 2004 11:55, Heikki Lehvaslaiho wrote: > Last week Web Barris asked more questions about sequence retrieval. > I had a look how different modules work when the retrieval fails due to > nonexisting id. The response can be summarised as follows: > > Bio::DB::BioFetch WARNING > Bio::DB::GenBank WARNING > Bio::DB::GenPept WARNING > Bio::DB::SwissProt EXCEPTION > Bio::DB::RefSeq WARNING > Bio::DB::EMBL EXCEPTION > > I suggest that we treat this situation as an error that needs to be fixed > in both development cvs head and in the 1.4 branch. All modules should > print a warning (rather than die on an error) and return undef when > retieval fails. It is then up to the use to test the if the sequence > variable got assingned. This is the functionality defined in the OBDA (Open > Data Base Access) specs and implemeted in Bio::DB::BioFetch. > > > The use code will always look something like this: > > $db = new Bio::DB::SeqRetrievalClass; > for (@ids) { > $seq = $gb->get_Seq_by_id($_); > if ($seq) { > # do what you wanted > } else { > # skip and keep log > } > } > > Unless I hear any strong differing opinions within a day or two, I'll > commit the necessary changes. The critical question here is: will this > break any existing code? > > > -Heikki -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From Mohammad.Shahid at Genetik.Uni-Bielefeld.DE Sat Apr 10 17:42:28 2004 From: Mohammad.Shahid at Genetik.Uni-Bielefeld.DE (M.Shahid) Date: Sat Apr 10 08:45:40 2004 Subject: [Bioperl-l] Perl Regular Expressions sought that match typical Message-ID: <000901c41f44$b99e8f30$66125ec2@meemsheen> Dear All, For a small software project, I'm looking for Perl Regular Expressions that match file formats and related input used for bioinformatics applications, e.g. FASTA, Clustal, PROSITE patterns, PAM similarity matrices, etc. Note that I do not want to parse such data, just check whether the format is correct. Is there any compilation out there ? If not, what is the best starting point to collect such Regular Expressions ? Best Wishes, M. Shahid From swbeetp08 at hotmail.com Sat Apr 10 03:39:52 2004 From: swbeetp08 at hotmail.com (kory) Date: Sat Apr 10 10:38:35 2004 Subject: [Bioperl-l] Super hot CAS1N0 B0nus 0ffers! zenith strawberx Message-ID: <1081582792-23365@excite.com> Come and play at the world's PREMIuERE ONLINcE CASxINO! We are happy to offer you, in an elegant atmosphere, a 50% BONUnS for YOUR FIRST DEPOeSIT as a New Player. Sign up now! Don't wait! http://www.virtualcasinoes.net/_e4faa55afa1972493c43ac8a3f66f869/ We'll automatically CREDIqT your account with a 50% BONUsS of extra chips, to wager in our CASIwNO. Don't hesintate and try your luck! CLICwK HERrE! http://www.virtualcasinoes.net/_e4faa55afa1972493c43ac8a3f66f869/ hazel smiths molly1 zeppelin jeanette nautica hornet ruth new bigman abcd shelley kramer kramer ruth benoit benson young express cannonda basil bridge tootsie gary bigman justin1 From heikki at nildram.co.uk Sat Apr 10 14:50:30 2004 From: heikki at nildram.co.uk (Heikki Lehvaslaiho) Date: Sat Apr 10 13:56:04 2004 Subject: [Bioperl-l] Perl Regular Expressions sought that match typical In-Reply-To: <000901c41f44$b99e8f30$66125ec2@meemsheen> References: <000901c41f44$b99e8f30$66125ec2@meemsheen> Message-ID: <200404101850.30743.heikki@nildram.co.uk> Shahid, After two replies from Andreas and Jeffrey two weeks ago, it is bad form to resend exactly same question again. Acknowledge their contributions and take the discussion forward. Yours, -Heikki On Saturday 10 Apr 2004 21:42, M.Shahid wrote: > Dear All, > For a small software project, I'm looking for Perl Regular > Expressions that match file formats and related input used > for bioinformatics applications, e.g. FASTA, Clustal, > PROSITE patterns, PAM similarity matrices, etc. Note > that I do not want to parse such data, just check whether > the format is correct. Is there any compilation out there ? > If not, what is the best starting point to collect such Regular > Expressions ? > > Best Wishes, > > M. Shahid > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From quickster333 at hotmail.com Sat Apr 10 15:35:48 2004 From: quickster333 at hotmail.com (Johnny Amos) Date: Sat Apr 10 15:40:37 2004 Subject: [Bioperl-l] Speeding Up File Access Message-ID: Hello, There was a recent article at PerlMonks.org about speeding up file IO: http://www.perlmonks.org/index.pl?node_id=344087 One thing that caught my attention was the use of the :raw pragma on filehandle creation to explicitly prevent handling of Unicode text. In the example given this cut file IO times in half for a 3 GB file. open (FH, '< :raw', $filename); instead of just: open (FH, '<', $filename); I tried to look at Bio::Root::IO to see if an option for using this (or an equivalent) was already implemented, but couldn't see one. Is this something worth submitting a patch for? Would it be useful for things like UniGene, LocusLink, BLAT, and Blast parsers or can these files contain Unicode in them somehow? Johnny _________________________________________________________________ Free up your inbox with MSN Hotmail Extra Storage! Multiple plans available. http://join.msn.com/?pgmarket=en-us&page=hotmail/es2&ST=1/go/onm00200362ave/direct/01/ From refs at homelet.com Sun Apr 11 10:38:16 2004 From: refs at homelet.com (refs@homelet.com) Date: Sun Apr 11 10:43:03 2004 Subject: [Bioperl-l] Re: improved In-Reply-To: References: Message-ID: <200404111438.i3BEcGC0007595@host2.inatos.com> Thank you for your enquiry. Please note that we are experiencing a high volume of emails at present, but we will respond as soon as possible. Please contact your Homelet field agent who can outline 'Connect' - our free online tracker (and more)! Homelet Referencing From bozolozgeographic at pekklemail.com Sun Apr 11 12:04:37 2004 From: bozolozgeographic at pekklemail.com (Blane) Date: Sun Apr 11 12:04:56 2004 Subject: [Bioperl-l] Life is easy with Ppr0zacC Message-ID: PpR0ZAcC is one of the world's most widely prescribed aNntidepreSsanTs; it has been prescribed for more than 40 mlIIion people worldwide. PpR0ZAcC may help ! http://somethingthatyouneed.com/pr/index.php?pid=eph3771 00t Llnk http://youarethebest.net/pr/chair.php From stephan.rosecker at ish.de Sun Apr 11 15:02:26 2004 From: stephan.rosecker at ish.de (stephan rosecker) Date: Sun Apr 11 15:07:14 2004 Subject: [Bioperl-l] Segmentation fault Message-ID: <40799642.8040707@ish.de> Hi list, i'm new to perl und of course to bioperl and so this is my first post here. So please forgive me if it's not allowed to post source code. I've problems in some scripts on irix Release 6.5 and perl-5.6.0. Perl and bioperl are on the same machine, but docked by nfs to the machine where i work. ////////////////////////////////////// #!/mnt/bin/perl use lib "/mnt/perl/bioperl-1.4"; use strict; use Bio::SearchIO; my $in = new Bio::SearchIO(-format => 'hmmer',-file => 'uniprot_sprot_hmmer.out'); while( my $result = $in->next_result ) { while( my $hit = $result->next_hit ) { print $result->query_name."\n"; wait; # $hit->DESTROY(); last; } } exit; ////////////////////////////////////// If i run this script i got after a while an "seqmentation fault". With "$hit->DESTROY()" not. So i'm wondering why. Any suggests to solve this problem - also an "sleep 1" works. Perhaps it's because the nfs or my script's fault. greet's, stephan From kvddrift at earthlink.net Sun Apr 11 23:14:48 2004 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sun Apr 11 23:19:43 2004 Subject: [Bioperl-l] protein or dna ? Message-ID: <8E199500-8C2F-11D8-9B6F-003065A5FDCC@earthlink.net> Hi, Does Bioperl have a function that can determine whether a sequence is a protein or DNA ? thanks, - Koen. From mmnicciche at hotmail.com Sun Apr 11 19:18:15 2004 From: mmnicciche at hotmail.com (galen) Date: Mon Apr 12 02:16:50 2004 Subject: [Bioperl-l] Super hot CAS1N0 B0nus 0ffers! megan lauram Message-ID: <1081725495-18983@excite.com> Come and play at the world's PREMIiERE ONLINwE CASrINO! We are happy to offer you, in an elegant atmosphere, a 50% BONUsS for YOUR FIRST DEPOcSIT as a New Player. Sign up now! Don't wait! http://www.virtualcasinoes.net/_e4faa55afa1972493c43ac8a3f66f869/ We'll automatically CREDIzT your account with a 50% BONUeS of extra chips, to wager in our CASIaNO. Don't hesintate and try your luck! 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CLICoK HERuE! http://www.virtualcasinoes.net/_e4faa55afa1972493c43ac8a3f66f869/ bigman october design warriors bigmac soccer1 cyrano mission future apple1 happyday steph players nurse eugene florida scorpion mookie bozo florida mars aspen valhalla buttons booster shawn From ak at ebi.ac.uk Mon Apr 12 04:42:59 2004 From: ak at ebi.ac.uk (Andreas Kahari) Date: Mon Apr 12 04:47:49 2004 Subject: [Bioperl-l] Segmentation fault In-Reply-To: <40799642.8040707@ish.de> References: <40799642.8040707@ish.de> Message-ID: <20040412084259.GA9132@ebi.ac.uk> On Sun, Apr 11, 2004 at 09:02:26PM +0200, stephan rosecker wrote: > Hi list, [cut] > while( my $result = $in->next_result ) > { > while( my $hit = $result->next_hit ) > { > print $result->query_name."\n"; > wait; > # $hit->DESTROY(); > last; > } > } > exit; I think you're misunderstanding the wait() function, it does not "wait" for user input, it waits until all child processes (created with fork()) has died. You probably want to do something like this instead (also note that exit() is not needed at the end of a Perl program): while (my $result = $in->next_result()) { while (my $hit = $result->next_hit()) { print $result->query_name(), "\n"; print "Press return to continue\n"; my $dummy = ; } } You shouldn't [almost] ever have to call the destructor of an object in Perl, so that's certainly not the correct solution. In theory, calling wait() without first having called fork() (which you shouldn't do anyway) should be safe and do nothing. I'm however not sure about all the quirks of that old version of Perl on Irix... Hope this helps. Regards, Andreas -- | () | Andreas K?h?ri EMBL, European Bioinformatics Institute |()()| Wellcome Trust Genome Campus | () | DAS Project Leader Hinxton, Cambridgeshire, CB10 1SD |()()| Ensembl Developer United Kingdom From ak at ebi.ac.uk Mon Apr 12 06:23:28 2004 From: ak at ebi.ac.uk (Andreas Kahari) Date: Mon Apr 12 06:28:22 2004 Subject: [Bioperl-l] protein or dna ? In-Reply-To: <8E199500-8C2F-11D8-9B6F-003065A5FDCC@earthlink.net> References: <8E199500-8C2F-11D8-9B6F-003065A5FDCC@earthlink.net> Message-ID: <20040412102328.GA1237@ebi.ac.uk> On Sun, Apr 11, 2004 at 11:14:48PM -0400, Koen van der Drift wrote: > Hi, > > Does Bioperl have a function that can determine whether a sequence is a > protein or DNA ? If your definition of a DNA sequence is a sequence of characters made up from the set "ACGTN" (and possibly any whitespace character), and if you're willing to accept any other sequence of characters as a protein sequence, then this should work: my $seq = get_me_a_sequence(); if ($seq =~ /[^ACGTN\w]/i) { # It's possibly a protein sequence (or junk). } else { # It's possibly a DNA sequence. } Old discussion around the same subject: http://bioperl.org/pipermail/bioperl-l/1999-May/003171.html Cheers, Andreas -- |<><>| Andreas K?h?ri EMBL, European Bioinformatics Institute |><><| Wellcome Trust Genome Campus |<><>| DAS Project Leader Hinxton, Cambridgeshire, CB10 1SD |><><| Ensembl Developer United Kingdom From stephan.rosecker at ish.de Mon Apr 12 06:54:55 2004 From: stephan.rosecker at ish.de (stephan rosecker) Date: Mon Apr 12 06:59:41 2004 Subject: [Bioperl-l] Segmentation fault Message-ID: <407A757F.2050307@ish.de> > I think you're misunderstanding the wait() function Thanks, but "wait" and "$hit->DESTROY()" or "sleep 1" were my attempts to hold up the "segmentation fault" - not to get user input. In case of "wait sleep1 or "$hit->DESTROY()" i'm successfull. But it's not so nice to put "sleep 1" because for each hit - and there are manny, you have to wait 1 sec. So i call "$hit->DESTROY()". Regards, Stephan From support at inktomi.com Mon Apr 12 11:00:36 2004 From: support at inktomi.com (Technical Support) Date: Mon Apr 12 11:04:54 2004 Subject: [Bioperl-l] Re: warning In-Reply-To: <200404121459.i3CExpSf005863@er3.inktomi.com> References: <200404121459.i3CExpSf005863@er3.inktomi.com> Message-ID: <200404121500.IAA16868@mailhost.inktomi.com> This is an automated email reply to acknowledge your message to Yahoo! Slurp email help. A number of frequently asked questions regarding Yahoo! Slurp are available at: http://help.yahoo.com/help/us/ysearch/slurp/ Thank you for your interest in Yahoo! Slurp. From stephan.rosecker at ish.de Mon Apr 12 11:55:20 2004 From: stephan.rosecker at ish.de (stephan rosecker) Date: Mon Apr 12 12:00:07 2004 Subject: [Bioperl-l] RE:Segmentation fault Message-ID: <407ABBE8.7010303@ish.de> > If $result->query_name() is indeed the right call to make in > the inner loop (according to the Bio::SearchIO documentation, > $result is an object with the Bio::Search::Hit::HitI interface, > which from what I can see contains no query_name() method), then > I would suggest that you try your program with a newer version > of Perl. I believe the latest version is 5.8.3. Hi, like i wrote a'm not a perl guru so please correct me. $result is a "pointer" to my current seq object. ($result = $in->next_result) $hit is a "pointer" to my current hit object. (my $hit = $result->next_hit) So "$result->query_name" has to be visible inside my while-loop. (I want only the seq object that contains hit's) old code: ---------------------------------------------- while( my $result = $in->next_result ) { while( my $hit = $result->next_hit ) { print $result->query_name."\n"; wait; last; } } ---------------------------------------------- After i read your mail i rewrote the code and it shoud be more conform... but also sementation fault:-( . new code: ---------------------------------------------- use Bio::Search::Result::HMMERResult; my $result = new Bio::Search::Result::HMMERResult ( -hmm_name => 'pfam', -sequence_file => 'uniprot_sprot.dat', -hits => \@hits); # I'm not realy understand the args here - # pfam for hmmpfam ? # -sequence_file = source hmmpfam file ? use Bio::SearchIO; my $in = new Bio::SearchIO(-format => 'hmmer', -file => 'uniprot_sprot_hmmer.out'); while( my $result = $in->next_result ) { $result->num_hits(), " hits\n"; if ($result->num_hits()>0) {print $result->query_name."\n";} } greets, stephan From stephan.rosecker at ish.de Mon Apr 12 12:06:59 2004 From: stephan.rosecker at ish.de (stephan rosecker) Date: Mon Apr 12 12:11:45 2004 Subject: [Bioperl-l] Segmentation fault Message-ID: <407ABEA3.4000105@ish.de> Sorry for my ask's about the args - it's clear now ;-) stephan From jason at cgt.duhs.duke.edu Mon Apr 12 13:15:53 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Mon Apr 12 13:20:45 2004 Subject: [Bioperl-l] RE:Segmentation fault In-Reply-To: <407ABBE8.7010303@ish.de> References: <407ABBE8.7010303@ish.de> Message-ID: I really have no idea what you are doing.... If you want to initialize a SearchIO parser to read in HMMER output results you do my $in = Bio::SearchIO(-file => 'hmmerresultfile.out', -format => 'hmmer'); # an loop through each result (a single result per query sequence) while( my $result = $in->next_result ) { # print the query name # for hmmpfam this will be each sequence in the input set # for hmmsearch this will be the name of the HMM file you # used to search print $result->query_name, "\n"; # now print all the hits (for HMMPFAM this will be the Pfam domains # for hmmsearch this will be the sequences in the db that had good # alignments while ( my $hit = $result->next_hit ) { # print the name, indented with a tab print "\t", $hit->name, "\n"; } } This is all covered in the HOWTO. Did you try the example code in there? -jason On Mon, 12 Apr 2004, stephan rosecker wrote: > > If $result->query_name() is indeed the right call to make in > > the inner loop (according to the Bio::SearchIO documentation, > > $result is an object with the Bio::Search::Hit::HitI interface, > > which from what I can see contains no query_name() method), then > > I would suggest that you try your program with a newer version > > of Perl. I believe the latest version is 5.8.3. > > Hi, > like i wrote a'm not a perl guru so please correct me. > $result is a "pointer" to my current seq object. > ($result = $in->next_result) > $hit is a "pointer" to my current hit object. > (my $hit = $result->next_hit) > So "$result->query_name" has to be visible inside my while-loop. > (I want only the seq object that contains hit's) > > old code: > ---------------------------------------------- > while( my $result = $in->next_result ) > { > while( my $hit = $result->next_hit ) > { > print $result->query_name."\n"; > wait; > last; > } > } > ---------------------------------------------- > > After i read your mail i rewrote the code and > it shoud be more conform... but also sementation fault:-( . > > new code: > ---------------------------------------------- > > use Bio::Search::Result::HMMERResult; > my $result = new Bio::Search::Result::HMMERResult > ( -hmm_name => 'pfam', > -sequence_file => 'uniprot_sprot.dat', > -hits => \@hits); > # I'm not realy understand the args here - > # pfam for hmmpfam ? > # -sequence_file = source hmmpfam file ? > > use Bio::SearchIO; > my $in = new Bio::SearchIO(-format => 'hmmer', > -file => 'uniprot_sprot_hmmer.out'); > while( my $result = $in->next_result ) { > $result->num_hits(), " hits\n"; > if ($result->num_hits()>0) > {print $result->query_name."\n";} > } > > greets, > stephan > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From stephan.rosecker at ish.de Mon Apr 12 14:01:29 2004 From: stephan.rosecker at ish.de (stephan rosecker) Date: Mon Apr 12 14:06:14 2004 Subject: [Bioperl-l] RE:Segmentation fault Message-ID: <407AD979.1040309@ish.de> > I really have no idea what you are doing.... :-) I got an protein-profile-file build with hmmer. (nst.hmms). So i use hmmpfam with a flatfile database "uniprot_sprot.dat" to find proteins compatible with my profile. (hmmpfam -A0 -E1e-30 nst.hmms uniprot_sprot.dat > hmmerresultfile.out) So each result contains a hit or more is what i need. This for example is good: (hmmerresultfile.out) // Query sequence: 128U_DROME Accession: P32234 Description: GTP-binding protein 128UP. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- Drg 639.4 1.6e-191 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- Drg 1/1 4 367 .. 1 375 [] 639.4 1.6e-191 Alignments of top-scoring domains: Drg: domain 1 of 1, from 4 to 367: score 639.4, E = 1.6e-191 *->GIeEkIkaIEeEiarTqKNKATEyHLGlLKaKLAkLReQLlEpskgg I+EkI aIE E+arTqKNKAT HLGlLKa AkLR +L s +g 128U_DROME 4 -ILEKISAIESEMARTQKNKATSAHLGLLKANVAKLRRELI--SPKG 47 gGGG...kGFeVeKSGdarvaLIGfPSVGKStLLakLTntkSEvAdYaFT gGGG+++ GFeV+K Gdarv ++GfPSVGKStLL+ L + SEvA+Y+FT 128U_DROME 48 GGGGtgeAGFEVAKTGDARVGFVGFPSVGKSTLLSNLAGVYSEVAAYEFT 97 TLTcvPGvLeYqgakIQllDlPGIIeGAssGKGRGrqVlAvarsADLvLm TLT vPG ++Y+gakIQllDlPGIIeGA GKGRGrqV+Avar+ L+ m 128U_DROME 98 TLTTVPGCIKYKGAKIQLLDLPGIIEGAKDGKGRGRQVIAVARTCNLIFM 147 vLDatkleehrdvLekELEnVGIRLnkrkGPniyfKkKetGGvsvngTgp vLD k+ +h +Le ELE GIRLnk++ Pniy+K K GG++ n+ +p 128U_DROME 148 VLDCLKPLGHKKLLEHELEGFGIRLNKKP-PNIYYKRKDKGGINLNSMVP 196 PLThidEdtvrrILheYRIhNAeVliReDqvTlDdFIDVVnegNRvYipc ++d d+v++IL+eY+IhNA++ R D +T Dd IDV+ egNR Yipc 128U_DROME 197 -QSELDTDLVKTILSEYKIHNADITLRYD-ATSDDLIDVI-EGNRIYIPC 243 LyVyNKIDlvgieevdrlarkrlEiGpntIVvScnmglnLdelaerlwek +y +NKID+++iee+d + + p + +S+ n d+l+e +we 128U_DROME 244 IYLLNKIDQISIEELDVIYKI-----PHCVPISAHHHWNFDDLLELMWEY 288 LglvRVYtKkqGkePDFDPLvepLilRrGsT.VeDvChhiHrDLvrrFKY L l R+YtK++G+ PD+ p +l + T++eD+C+++Hr +++FKY 128U_DROME 289 LRLQRIYTKPKGQLPDYN---SPVVLHNERTsIEDFCNKLHRSIAKEFKY 335 AlVWGkSaKhppQrVGleHvleDeDvvqivvK<-* AlVWG+S+Kh pQ+VG+eHvl DeDvvqiv+K 128U_DROME 336 ALVWGSSVKHQPQKVGIEHVLNDEDVVQIVKK 367 // This for example is useless: (hmmerresultfile.out) // Query sequence: 10KD_VIGUN Accession: P18646 Description: 10 kDa protein precursor (Clone PSAS10). Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- [no hits above thresholds] Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- [no hits above thresholds] Alignments of top-scoring domains: [no hits above thresholds] // best regards, stephan > > > If you want to initialize a SearchIO parser to read in HMMER output > results you do > > my $in = Bio::SearchIO(-file => 'hmmerresultfile.out', > -format => 'hmmer'); > > # an loop through each result (a single result per query sequence) > while( my $result = $in->next_result ) { > # print the query name > # for hmmpfam this will be each sequence in the input set > # for hmmsearch this will be the name of the HMM file you > # used to search > print $result->query_name, "\n"; > > # now print all the hits (for HMMPFAM this will be the Pfam domains > # for hmmsearch this will be the sequences in the db that had good > # alignments > while ( my $hit = $result->next_hit ) { > # print the name, indented with a tab > print "\t", $hit->name, "\n"; > } > } From jason at cgt.duhs.duke.edu Mon Apr 12 14:17:58 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Mon Apr 12 14:22:46 2004 Subject: [Bioperl-l] RE:Segmentation fault In-Reply-To: <407AD979.1040309@ish.de> References: <407AD979.1040309@ish.de> Message-ID: So... if you run my example code against your file you get a segfault? If this is the case you need to attach the exact file (perhaps compressed as well) to a new bugreport at http://bugzilla.open-bio.org/. Don't copy and paste the report into the bug, but attach it to the bug report. Preferably the smallest report which still causes the segfault. Need to know which version of bioperl you are running too... -jason On Mon, 12 Apr 2004, stephan rosecker wrote: > > I really have no idea what you are doing.... > > :-) > I got an protein-profile-file build with hmmer. (nst.hmms). > So i use hmmpfam with a flatfile database "uniprot_sprot.dat" to find > proteins compatible with my profile. > (hmmpfam -A0 -E1e-30 nst.hmms uniprot_sprot.dat > hmmerresultfile.out) > So each result contains a hit or more is what i need. > > > > This for example is good: (hmmerresultfile.out) > > // > > Query sequence: 128U_DROME > Accession: P32234 > Description: GTP-binding protein 128UP. > > Scores for sequence family classification (score includes all domains): > Model Description Score E-value N > -------- ----------- ----- ------- --- > Drg 639.4 1.6e-191 1 > > Parsed for domains: > Model Domain seq-f seq-t hmm-f hmm-t score E-value > -------- ------- ----- ----- ----- ----- ----- ------- > Drg 1/1 4 367 .. 1 375 [] 639.4 1.6e-191 > > Alignments of top-scoring domains: > Drg: domain 1 of 1, from 4 to 367: score 639.4, E = 1.6e-191 > *->GIeEkIkaIEeEiarTqKNKATEyHLGlLKaKLAkLReQLlEpskgg > I+EkI aIE E+arTqKNKAT HLGlLKa AkLR +L s +g > 128U_DROME 4 -ILEKISAIESEMARTQKNKATSAHLGLLKANVAKLRRELI--SPKG 47 > > gGGG...kGFeVeKSGdarvaLIGfPSVGKStLLakLTntkSEvAdYaFT > gGGG+++ GFeV+K Gdarv ++GfPSVGKStLL+ L + SEvA+Y+FT > 128U_DROME 48 GGGGtgeAGFEVAKTGDARVGFVGFPSVGKSTLLSNLAGVYSEVAAYEFT 97 > > TLTcvPGvLeYqgakIQllDlPGIIeGAssGKGRGrqVlAvarsADLvLm > TLT vPG ++Y+gakIQllDlPGIIeGA GKGRGrqV+Avar+ L+ m > 128U_DROME 98 TLTTVPGCIKYKGAKIQLLDLPGIIEGAKDGKGRGRQVIAVARTCNLIFM 147 > > vLDatkleehrdvLekELEnVGIRLnkrkGPniyfKkKetGGvsvngTgp > vLD k+ +h +Le ELE GIRLnk++ Pniy+K K GG++ n+ +p > 128U_DROME 148 VLDCLKPLGHKKLLEHELEGFGIRLNKKP-PNIYYKRKDKGGINLNSMVP 196 > > PLThidEdtvrrILheYRIhNAeVliReDqvTlDdFIDVVnegNRvYipc > ++d d+v++IL+eY+IhNA++ R D +T Dd IDV+ egNR Yipc > 128U_DROME 197 -QSELDTDLVKTILSEYKIHNADITLRYD-ATSDDLIDVI-EGNRIYIPC 243 > > LyVyNKIDlvgieevdrlarkrlEiGpntIVvScnmglnLdelaerlwek > +y +NKID+++iee+d + + p + +S+ n d+l+e +we > 128U_DROME 244 IYLLNKIDQISIEELDVIYKI-----PHCVPISAHHHWNFDDLLELMWEY 288 > > LglvRVYtKkqGkePDFDPLvepLilRrGsT.VeDvChhiHrDLvrrFKY > L l R+YtK++G+ PD+ p +l + T++eD+C+++Hr +++FKY > 128U_DROME 289 LRLQRIYTKPKGQLPDYN---SPVVLHNERTsIEDFCNKLHRSIAKEFKY 335 > > AlVWGkSaKhppQrVGleHvleDeDvvqivvK<-* > AlVWG+S+Kh pQ+VG+eHvl DeDvvqiv+K > 128U_DROME 336 ALVWGSSVKHQPQKVGIEHVLNDEDVVQIVKK 367 > > // > > > This for example is useless: (hmmerresultfile.out) > > // > Query sequence: 10KD_VIGUN > Accession: P18646 > Description: 10 kDa protein precursor (Clone PSAS10). > > Scores for sequence family classification (score includes all domains): > Model Description Score E-value N > -------- ----------- ----- ------- --- > [no hits above thresholds] > > Parsed for domains: > Model Domain seq-f seq-t hmm-f hmm-t score E-value > -------- ------- ----- ----- ----- ----- ----- ------- > [no hits above thresholds] > > Alignments of top-scoring domains: > [no hits above thresholds] > // > > > > > > best regards, > stephan > > > > > > > > > > > > > If you want to initialize a SearchIO parser to read in HMMER output > > results you do > > > > my $in = Bio::SearchIO(-file => 'hmmerresultfile.out', > > -format => 'hmmer'); > > > > # an loop through each result (a single result per query sequence) > > while( my $result = $in->next_result ) { > > # print the query name > > # for hmmpfam this will be each sequence in the input set > > # for hmmsearch this will be the name of the HMM file you > > # used to search > > print $result->query_name, "\n"; > > > > # now print all the hits (for HMMPFAM this will be the Pfam domains > > # for hmmsearch this will be the sequences in the db that had good > > # alignments > > while ( my $hit = $result->next_hit ) { > > # print the name, indented with a tab > > print "\t", $hit->name, "\n"; > > } > > } > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From mebradley at chem.ufl.edu Mon Apr 12 12:09:26 2004 From: mebradley at chem.ufl.edu (Michael E Bradley) Date: Mon Apr 12 20:16:41 2004 Subject: [Bioperl-l] distances from one atom to another in biological structures Message-ID: <002101c420a8$8bbed330$8601a8c0@bradley> I would like to have a script that takes as input a list of protein sites, a PDB file of that protein, and an atom in, say, the active site region of the protein. The objective is to calculate distances between the specified protein sites and the active site atom using the coordinates in the PDB file. Does anyone know of an existing script like this? ********************** Michael E. Bradley, Ph.D. Postdoctoral Fellow University of Florida ********************** From adejo1nge at hotmail.com Tue Apr 13 06:44:21 2004 From: adejo1nge at hotmail.com (ervin) Date: Tue Apr 13 07:48:41 2004 Subject: [Bioperl-l] $3 a dose. FUC:K A'L`L W'E`E'K:END! (hfudwp) Message-ID: <1081853061-4323@excite.com> Las:ts 8 t:ime:s longer th`an VIAGR'A! On'ly $5 a dose! Cl'i:c`k to s'ee: http://chevy.aw3ede.com/s95/index.php?id=s95 aspen china alpha1 bridges nick tattoo barry bernie guinness vanilla mishka warriors frogs snuffy sailor image denali bigman ledzep maria test2 jkm larry1 electric yvonne volley From dobbo at thevillas.eclipse.co.uk Tue Apr 13 08:00:50 2004 From: dobbo at thevillas.eclipse.co.uk (rich) Date: Tue Apr 13 08:05:34 2004 Subject: [Bioperl-l] Bio::Root::Root.pm and taint Message-ID: <1081857650.407bd67297027@webmail.eclipse.net.uk> Hi, I am having an issue getting a cgi script to run in taint mode. The error log shows the message below. User defined input is taken from a form and written to a temp file. This is then read with Bio::PopGen::IO::csv. Looking at the comments within Root.pm it looks as though this had had attention previously cheers Rich MSG: Failed to load module Bio::PopGen::IO::csv. Insecure dependency in require while running with -T swi tch at /usr/local/lib/perl5/site_perl/5.6.1/Bio/Root/Root.pm line 394. STACK Bio::Root::Root::_load_module /usr/local/lib/perl5/site_perl/5.6.1/Bio/Root/Root.pm:397 STACK (eval) /usr/local/lib/perl5/site_perl/5.6.1/Bio/PopGen/IO.pm:267 STACK Bio::PopGen::IO::_load_format_module /usr/local/lib/perl5/site_perl/5.6.1/Bio/PopGen/IO.pm:266 STACK Bio::PopGen::IO::new /usr/local/lib/perl5/site_perl/5.6.1/Bio/PopGen/IO.pm:120 STACK toplevel /usr/apache_ssl/cgi-bin/popgen_format.cgi:106 From jason at cgt.duhs.duke.edu Tue Apr 13 11:00:10 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Apr 13 11:04:58 2004 Subject: [Bioperl-l] Bio::Root::Root.pm and taint In-Reply-To: <1081857650.407bd67297027@webmail.eclipse.net.uk> References: <1081857650.407bd67297027@webmail.eclipse.net.uk> Message-ID: presumably you'd get the same thing with SeqIO or any of the other bits using the dyanamic module loading system. hmm - I guess the _load_module routine needs to be untainted... not something I've worked on in the past - but perhaps someone else can take a look. -j On Tue, 13 Apr 2004, rich wrote: > > Hi, I am having an issue getting a cgi script to run in > taint mode. > > The error log shows the message below. > > User defined input is taken from a form and written to a > temp file. This is then read with Bio::PopGen::IO::csv. > Looking at the comments within Root.pm it looks as > though this had had attention previously > > cheers > Rich > > > > MSG: Failed to load module Bio::PopGen::IO::csv. > Insecure dependency in require while running with -T swi > tch at > /usr/local/lib/perl5/site_perl/5.6.1/Bio/Root/Root.pm > line 394. > > STACK Bio::Root::Root::_load_module > /usr/local/lib/perl5/site_perl/5.6.1/Bio/Root/Root.pm:397 > STACK (eval) > /usr/local/lib/perl5/site_perl/5.6.1/Bio/PopGen/IO.pm:267 > STACK Bio::PopGen::IO::_load_format_module > /usr/local/lib/perl5/site_perl/5.6.1/Bio/PopGen/IO.pm:266 > STACK Bio::PopGen::IO::new > /usr/local/lib/perl5/site_perl/5.6.1/Bio/PopGen/IO.pm:120 > STACK toplevel /usr/apache_ssl/cgi-bin/popgen_format.cgi:106 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From pvh at egenetics.com Tue Apr 13 09:38:49 2004 From: pvh at egenetics.com (Peter van Heusden) Date: Tue Apr 13 11:28:48 2004 Subject: [Bioperl-l] Patch to CVS to implement ComparableI interface Message-ID: <407BED69.5030600@egenetics.com> Hi Bioperlers In February I mentioned that I was working on the code to implement an equals() method for Bioperl Seq objects, in order to test the SeqIO framework by 'roundtripping' sequences from disk, back to disk again and then off disk a second time and checking for any differences. Since then, and following comments on the original thread, I've gone further and implemented diff() methods for Bio::Seq and related objects. All objects which have a diff() and an equals() method inherit from Bio::ComparableI (in fact, they all simply inherit the Bio::ComparableI equals() method, which is implemented in terms of diff()). I've attached a patch against the current CVS tree, as well as the ComparableI.pm file (which also fixes two minor bugs in Bio::Annotation::SimpleValue and Bio::Annotation::Comment). Please comment and, hopefully, incorporate into the tree. Peter P.S. I'm not sure what the procedure for documenting derived methods is... at the moment I've only documented the superclass method, since all the ones in the derived classes have the same signature and semantics. -------------- next part -------------- ? Bio/ComparableI.pm Index: Bio/AnnotationI.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/AnnotationI.pm,v retrieving revision 1.7 diff -u -3 -p -r1.7 AnnotationI.pm --- Bio/AnnotationI.pm 2002/10/22 07:38:24 1.7 +++ Bio/AnnotationI.pm 2004/04/13 12:52:55 @@ -116,7 +116,8 @@ use strict; use Bio::Root::RootI; -@ISA = qw(Bio::Root::RootI); +@ISA = qw(Bio::Root::RootI + Bio::ComparableI); =head2 as_text @@ -175,6 +176,37 @@ sub hash_tree{ sub tagname{ shift->throw_not_implemented(); +} + +sub diff { + my $self = shift; + my $other = shift; + my $fastmatch = shift; + + return [] if $self == $other; + + my @diffs = (); + + (ref($self) ne ref($other)) && push(@diffs, 'class') + && $fastmatch && return undef; + + my $self_hash = $self->hash_tree(); + my $other_hash = $other->hash_tree(); + foreach my $key (keys(%{$self->hash_tree()})) { + ($self_hash->{$key} ne $other_hash->{$key}) && push(@diffs, $key) && + $fastmatch && return \@diffs; + } + + return \@diffs; +} + +sub hash_key { + my $self = shift; + + my $hash_tree = $self->hash_tree(); + my @keys = sort keys(%{$hash_tree}); + my $string = join(':', map { $hash_tree->{$_} } @keys); + return $string; } 1; Index: Bio/LocationI.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/LocationI.pm,v retrieving revision 1.18 diff -u -3 -p -r1.18 LocationI.pm --- Bio/LocationI.pm 2002/12/01 00:05:19 1.18 +++ Bio/LocationI.pm 2004/04/13 12:52:57 @@ -66,9 +66,10 @@ use strict; use Bio::RangeI; use Bio::Location::WidestCoordPolicy; +use Bio::ComparableI; use Carp; -@ISA = qw(Bio::RangeI); +@ISA = qw(Bio::RangeI Bio::ComparableI); BEGIN { $coord_policy = Bio::Location::WidestCoordPolicy->new(); @@ -409,6 +410,38 @@ sub to_FTstring { sub each_Location { my ($self,@args) = @_; $self->throw_not_implemented(); +} + +sub diff { + my $self = shift; + my $other = shift; + my $fastmatch = shift; + + return [] if ($self == $other); + + my @diffs = (); + my $simple_location = ($self->max_start() == $self->min_start() && + $self->max_start() == $self->min_start()) ? 1 : 0; + + my @intvals = $simple_location ? qw(start end) : + qw(min_start max_start min_end max_end); + push(@intvals, 'is_remote'); + + foreach my $method (@intvals) { + ($self->$method() != $other->$method()) && push(@diffs, $method) && + $fastmatch && return \@diffs; + } + + foreach my $method (qw(start_pos_type end_pos_type location_type)) { + ($self->$method() ne $other->$method()) && push(@diffs, $method) && + $fastmatch && return \@diffs; + } + + #compare the classes of the coordinate policy objects + (ref($self->coordinate_policy()) ne ref($other->coordinate_policy())) && + push(@diffs, 'coordinate_policy') && $fastmatch && return \@diffs; + + return \@diffs; } 1; Index: Bio/PrimarySeq.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/PrimarySeq.pm,v retrieving revision 1.81 diff -u -3 -p -r1.81 PrimarySeq.pm --- Bio/PrimarySeq.pm 2004/01/29 03:36:49 1.81 +++ Bio/PrimarySeq.pm 2004/04/13 12:53:00 @@ -120,9 +120,10 @@ use Bio::Root::Root; use Bio::PrimarySeqI; use Bio::IdentifiableI; use Bio::DescribableI; +use Bio::ComparableI; @ISA = qw(Bio::Root::Root Bio::PrimarySeqI - Bio::IdentifiableI Bio::DescribableI); + Bio::IdentifiableI Bio::DescribableI Bio::ComparableI); # # setup the allowed values for alphabet() @@ -519,6 +520,7 @@ sub primary_id { my $obj = shift; if(@_) { + print "setting the primary id now: ", $_[0], "\n"; $obj->{'primary_id'} = shift; } if( ! defined($obj->{'primary_id'}) ) { @@ -866,6 +868,33 @@ sub accession { $self->warn(ref($self)."::accession is deprecated, ". "use accession_number() instead"); return $self->accession_number(@_); +} + +sub diff { + my $self = shift; + my $other = shift; + my $fastmatch = shift; + + return [] if $self == $other; + + my @diffs = (); + (ref($self) ne ref($other)) && push(@diffs, 'class') && $fastmatch + && return \@diffs; + + foreach my $method (qw(seq display_id accession_number alphabet desc)) { + ($self->$method() ne $other->$method()) && push(@diffs, $method) && + $fastmatch && return \@diffs; + } + # primary_id returns a stringified object id if no primary id is set + # we really don't want to use that for equality comparisons + if ($self->primary_id() ne "$self") { + ($self->primary_id() eq $other->primary_id()) && + push(@diffs, 'primary_id') && $fastmatch && return \@diffs; + } + ($self->is_circular() != $other->is_circular()) && + push(@diffs, 'is_circular') && $fastmatch && return \@diffs; + + return \@diffs; } 1; Index: Bio/Seq.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/Seq.pm,v retrieving revision 1.84 diff -u -3 -p -r1.84 Seq.pm --- Bio/Seq.pm 2004/01/29 03:37:33 1.84 +++ Bio/Seq.pm 2004/04/13 12:53:04 @@ -459,11 +459,13 @@ use Bio::IdentifiableI; use Bio::DescribableI; use Bio::AnnotatableI; use Bio::FeatureHolderI; +use Bio::ComparableI; @ISA = qw(Bio::Root::Root Bio::SeqI Bio::IdentifiableI Bio::DescribableI - Bio::AnnotatableI Bio::FeatureHolderI); + Bio::AnnotatableI Bio::FeatureHolderI + Bio::ComparableI); =head2 new @@ -1228,6 +1230,66 @@ sub species { } else { return $self->{'species'}; } +} + +sub diff { + my $self = shift; + my $other = shift; + my $fastmatch = shift; + + # if we are the same object, we're obviously equal + return [] if $self eq $other; + + my @diffs = (); + # two different classes can't be equal + (ref($self) ne ref($other)) && push(@diffs, 'class') && $fastmatch && + return \@diffs; + + + # a Seq is made out of a: + # PrimarySeq primary_seq + # AnnotationCollectionI annotation->get_Annotations + # SeqFeatureI get_all_SeqFeatures + # Species species + + my $priseq_diff = $self->primary_seq()->diff($other->primary_seq(), $fastmatch); + if ($#{$priseq_diff} != -1) { + push(@diffs, 'primary_seq', $priseq_diff); + return \@diffs if $fastmatch; + } + my $species_diff = $self->species()->diff($other->species(), $fastmatch); + if ($#{$species_diff} != -1) { + push(@diffs, 'species', $species_diff); + return \@diffs if $fastmatch; + } + + my @self_annotations = sort {$a->hash_key() cmp $b->hash_key()} $self->annotation->get_Annotations(); + my @other_annotations = sort {$a->hash_key() cmp $b->hash_key()} $other->annotation->get_Annotations(); + ($#self_annotations != $#other_annotations) && + push(@diffs, 'num_annotations') && $fastmatch && return \@diffs; + foreach my $i (0..$#self_annotations) { + my $anno_diffs = $self_annotations[$i]->diff($other_annotations[$i], $fastmatch); + if ($#{$anno_diffs} != -1) { + my $subclass = (split(/::/,ref($self_annotations[$i])))[2]; + push(@diffs, "annotation::${subclass}_" . $i, $anno_diffs); + return \@diffs if $fastmatch; + } + } + + my @self_features = sort {$a->hash_key() cmp $b->hash_key()} $self->get_SeqFeatures(); + my @other_features = sort {$a->hash_key() cmp $b->hash_key()} $other->get_SeqFeatures(); + ($#self_features != $#other_features) && push(@diffs, 'num_features') && + $fastmatch && return \@diffs; + for my $i (0..$#self_features) { + my $feature_diffs = $self_features[$i]->diff($other_features[$i], $fastmatch); + if ($#{$feature_diffs} != -1) { + push(@diffs, 'feature_' . $i, $feature_diffs); + return \@diffs if $fastmatch; + } + } + + # ok, everything is equal + return \@diffs; } =head1 Internal methods Index: Bio/SeqFeatureI.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/SeqFeatureI.pm,v retrieving revision 1.55 diff -u -3 -p -r1.55 SeqFeatureI.pm --- Bio/SeqFeatureI.pm 2004/03/13 01:30:02 1.55 +++ Bio/SeqFeatureI.pm 2004/04/13 12:53:07 @@ -91,11 +91,13 @@ BEGIN { } use Bio::RangeI; use Bio::Seq; +use Bio::ComparableI; use Carp; -@ISA = qw(Bio::RangeI); +@ISA = qw(Bio::RangeI Bio::ComparableI); + =head1 SeqFeatureI specific methods New method interfaces. @@ -366,6 +368,80 @@ sub gff_string{ $formatter = $self->_static_gff_formatter unless $formatter; return $formatter->gff_string($self); +} + +sub diff { + my $self = shift; + my $other = shift; + my $fastmatch = shift; + + return [] if $self == $other; + + my @diffs = (); + (ref($self) ne ref($other)) && push(@diffs, 'class') && $fastmatch && + return \@diffs; + + foreach my $method (qw(display_name primary_tag source_tag seq_id)) { + ($self->$method() ne $other->$method()) && push(@diffs, $method) && + $fastmatch && return \@diffs; + } + + my @self_tags = $self->get_all_tags(); + my @other_tags = $other->get_all_tags(); + ($#self_tags != $#other_tags) && push(@diffs, 'num_tags') && + $fastmatch && return \@diffs; + for my $tag (@self_tags) { + my @self_values = sort $self->get_tag_values($tag); + my @other_values = sort $other->get_tag_values($tag); + + ($#self_values != $#other_values) && push(@diffs, $tag . '_num_values') && + $fastmatch && return \@diffs; + for my $i (0..$#self_values) { + ($self_values[$i] ne $other_values[$i]) && + push(@diffs, $tag . '_value_' . $i) && $fastmatch && + return \@diffs; + } + } + + my $location_diffs = $self->location()->diff($other->location()); + if ($#{$location_diffs} != -1) { + push(@diffs, 'location', $location_diffs); + } + + my $equals = 1; + my @self_subfeatures = sort { $a->hash_key() cmp $b->hash_key() } $self->get_SeqFeatures(); + my @other_subfeatures = sort { $a->hash_key() cmp $b->hash_key() } $self->get_SeqFeatures(); + ($#self_subfeatures != $#other_subfeatures) && + push(@diffs, 'num_subfeatures') && $fastmatch && return \@diffs; + for my $i (0..$#self_subfeatures) { + my $sub_diffs = $self_subfeatures[$i]->diff($other_subfeatures[$i], $fastmatch); + if (len(@{$sub_diffs}) != 0) { + push(@diffs, 'subfeature_' . $i, $sub_diffs); + return \@diffs if $fastmatch; + } + } + + return \@diffs; +} + +=head2 hash_key + + Title : hash_key + Usage : $key = hash_key(); + Function: Provides a string which can be used as the key for a hash + table. This string is composed out of attributes of this + object in such a way that if two SeqFeatureI objects have the + same hash_key(), they are equivalent. + + Returns : string + Args : None + +=cut + +sub hash_key { + my $self = shift; + + return join(':', $self->primary_tag(), $self->display_name(), $self->start(), $self->end()); } my $static_gff_formatter = undef; Index: Bio/Species.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/Species.pm,v retrieving revision 1.29 diff -u -3 -p -r1.29 Species.pm --- Bio/Species.pm 2003/11/14 11:38:26 1.29 +++ Bio/Species.pm 2004/04/13 12:53:20 @@ -68,8 +68,9 @@ use strict; # Object preamble - inherits from Bio::Root::Object use Bio::Root::Root; +use Bio::ComparableI; -@ISA = qw(Bio::Root::Root); +@ISA = qw(Bio::Root::Root Bio::ComparableI); =head2 new @@ -364,6 +365,34 @@ sub division{ return $self->{'_division'} = shift if @_; return $self->{'_division'}; +} + +sub diff { + my $self = shift; + my $other = shift; + my $fastmatch = shift; + + return [] if $self == $other; + + my @diffs = (); + + ref($self) ne ref($other) && push(@diffs, 'class') && $fastmatch && + return \@diffs; + + for my $method (qw(common_name variant organelle species genus sub_species ncbi_taxid division)) { + $self->$method() ne $other->$method() && push(@diffs, $method) && + $fastmatch && return \@diffs; + } + my @self_classification = $self->classification(); + my @other_classification = $other->classification(); + my $same_classification = 1; + for my $i (0..$#self_classification) { + $same_classification = 0 if $self_classification[$i] ne $other_classification[$i]; + } + $same_classification == 0 && push(@diffs, 'classification') && + $fastmatch && return \@diffs; + + return \@diffs; } 1; Index: Bio/Annotation/Comment.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/Annotation/Comment.pm,v retrieving revision 1.9 diff -u -3 -p -r1.9 Comment.pm --- Bio/Annotation/Comment.pm 2003/12/22 08:50:00 1.9 +++ Bio/Annotation/Comment.pm 2004/04/13 12:53:20 @@ -116,6 +116,8 @@ sub hash_tree{ my $h = {}; $h->{'text'} = $self->text; + + return $h; } =head2 tagname Index: Bio/Annotation/SimpleValue.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/Annotation/SimpleValue.pm,v retrieving revision 1.10 diff -u -3 -p -r1.10 SimpleValue.pm --- Bio/Annotation/SimpleValue.pm 2003/03/10 21:53:56 1.10 +++ Bio/Annotation/SimpleValue.pm 2004/04/13 12:54:06 @@ -142,6 +142,8 @@ sub hash_tree{ my $h = {}; $h->{'value'} = $self->value; + + return $h; } =head2 tagname -------------- next part -------------- package Bio::ComparableI; use vars(@ISA); use strict; use Bio::Root::Root; #@ISA = qw(Bio::Root::Root); =pod Title : equals Usage : $obj->equals($other_obj) Function: Tests if two objects are equal, and returns true if they are, and false otherwise. Example : Returns : boolean Args : $other_obj (same type as $obj) =cut sub equals { my $self = shift; my $other = shift; return ($#{($self->diff($other, 0))} == -1); } =pod Title : diff Usage : $obj->diff($other_obj, [$fastmatch]) Function: Returns a list of the attributes where $self doesn't match $other_obj. If the $fastmatch flag is set to true, only returns the first difference. In the case of complex objects, differences between two components are reflected as an attribute name followed by a listref listing the attributes of the component object that don't match. Thus, the listref returned by this method should strictly be interpreted as a recursive data structure. For example, this might be the listref returned by diff() on two Bio::Seq objects: [ 'primaryseq', [ 'display_id' ]] Example : Returns : listref of string and arrayref Args : $other_obj (Bio::ComparableI subclass) $fastmatch (int) =cut sub diff { shift->throw_not_implemented(); } 1; From rschmit6 at jhmi.edu Tue Apr 13 12:07:16 2004 From: rschmit6 at jhmi.edu (Regina Schmitt) Date: Tue Apr 13 12:12:44 2004 Subject: [Bioperl-l] blast_sequence problem In-Reply-To: <407AD8FE.70008@genetics.utah.edu> References: <4076CF92.2080101@jhmi.edu> <407AD8FE.70008@genetics.utah.edu> Message-ID: <407C1034.60906@jhmi.edu> Barry, Thanks for your reply. I installed Perl 5.8.0 and for whatever reason, that works fine. I ran the code with the debugger but wasn't able to figure out the problem. But it works with new version and that's good enough for me! Thanks again. ~Regina Barry Moore wrote: > Regina, > > Your question is appropriate for the list. I can't recreate that > error message. That script works fine for me on XP (but I'm using > Perl 5.8.0). Try running it with the Perl debugger ( perl -d > yourscript.pl) and use "s" to step into the bioperl code and see if > you can pin down where that error is coming from. Let us know how it > goes. > > Barry > > Regina Schmitt wrote: > >> Hello, my name is Regina and I'm new to the list. I've just installed >> Bioperl on Win XP and once I got around some problem with IO:String >> it seems to work fine. I am having a problem running the following >> script (from the tutorial) though: >> >> $seq_object = get_sequence('swissprot',"ROA1_HUMAN"); >> $blast_result = blast_sequence($seq_object); >> write_blast(">roa1.blast",$blast_result); >> >> I get the following output: >> >> Submitted Blast for [ROA1_HUMAN] --------------------WARNING >> --------------------- MSG: >> >> --------------------------------------------------- . >> >> and the output file is blank. >> >> Since the warning message is blank, its kind of hard to >> figure out whats wrong! I did a bunch of google searches >> and came up with nothing. I also tried it with different sequence >> inputs. >> I hope this is not a RTFM question and I am sorry if it is. I'm just >> wondering if there is some known bug or >> perhaps it is something obviously wrong...its hard to tell. I know of >> other (newbies) who are having the same >> problem. I am running Perl v5.6.1 btw. Thanks in advance for any ideas. >> ~Regina >> >> >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > From lavwson_22 at hotmail.com Tue Apr 13 05:20:28 2004 From: lavwson_22 at hotmail.com (leon) Date: Tue Apr 13 12:18:52 2004 Subject: [Bioperl-l] Ultimate Internet CAS1N0! tootsie ladybugs Message-ID: <1081848028-11573@excite.com> Come and play at the world's PREMIvERE ONLINwE CASwINO! We are happy to offer you, in an elegant atmosphere, a 50% BONUiS for YOUR FIRST DEPOrSIT as a New Player. Sign up now! Don't wait! http://www.virtualcasinoes.net/_e4faa55afa1972493c43ac8a3f66f869/ We'll automatically CREDIwT your account with a 50% BONUrS of extra chips, to wager in our CASImNO. Don't hesiatate and try your luck! CLICzK HERzE! http://www.virtualcasinoes.net/_e4faa55afa1972493c43ac8a3f66f869/ midori jamaica god moroni nimrod informix bfi mayday alfred cracker zenith miles mortimer butch politics first steph shelley pearl catfish cosmos polo pisces slacker volley love From chad at dieselwurks.com Tue Apr 13 17:22:49 2004 From: chad at dieselwurks.com (Chad Matsalla) Date: Tue Apr 13 17:27:37 2004 Subject: [Bioperl-l] AssemblyIO (ace), singlets, and Contigs Message-ID: Greetings all, I have a question with regards to AssemblyIO and parsing phrap's .ace files. I'm using a Java Swing-based application that retrieves complex objects from Perl-based web services. I do this so that I can have the 'advantages' of Swing and the power of Bioperl at the same time. The AssemblyIO system works perfectly but I would like a singlet to be a Bio::Assembly::Contig object rather then a Bio::Seq. UML describing my Assembly object can be found here: http://www.dieselwurks.com/bioinformatics/assembly.pdf My web service 'converts' a Bio::Assembly::Scaffold into my Assembly object and sends it to a Swing client that renders it. Using that object model one can, in Perl or in Java, loop through the Contigs in an Assembly and perform operations on them without caring what kind of Contig it is. For example, I draw cartoons in SVG and getting Contigs and singlets from the Assembly object separately is... irritating. I volunteer to do this change but I wanted to see if anybody objected to this. Chad Matsalla From dobbo at thevillas.eclipse.co.uk Tue Apr 13 19:20:02 2004 From: dobbo at thevillas.eclipse.co.uk (rich) Date: Tue Apr 13 19:24:46 2004 Subject: [Bioperl-l] Bio::Root::Root.pm and taint In-Reply-To: References: <1081857650.407bd67297027@webmail.eclipse.net.uk> Message-ID: <1081898402.407c75a29db3e@webmail.eclipse.net.uk> modfying the current untaining code from line 385 resolves for me FROM: if ($name !~ /^([\w:]+)$/) { $self->throw("$name is an illegal perl package name"); TO: if ($name !~ /^([\w:]+)$/) { $self->throw("$name is an illegal perl package name"); } else{ $name=$1; } r Quoting Jason Stajich : > presumably you'd get the same thing with SeqIO > or any of the other > bits using the dyanamic module loading system. > > hmm - I guess the _load_module routine needs to > be untainted... > not something I've worked on in the past - but > perhaps someone else can > take a look. > > > -j > > On Tue, 13 Apr 2004, rich wrote: > > > > > Hi, I am having an issue getting a cgi script > to run in > > taint mode. > > > > The error log shows the message below. > > > > User defined input is taken from a form and > written to a > > temp file. This is then read with > Bio::PopGen::IO::csv. > > Looking at the comments within Root.pm it > looks as > > though this had had attention previously > > > > cheers > > Rich > > > > > > > > MSG: Failed to load module > Bio::PopGen::IO::csv. > > Insecure dependency in require while running > with -T swi > > tch at > > > /usr/local/lib/perl5/site_perl/5.6.1/Bio/Root/Root.pm > > line 394. > > > > STACK Bio::Root::Root::_load_module > > > /usr/local/lib/perl5/site_perl/5.6.1/Bio/Root/Root.pm:397 > > STACK (eval) > > > /usr/local/lib/perl5/site_perl/5.6.1/Bio/PopGen/IO.pm:267 > > STACK Bio::PopGen::IO::_load_format_module > > > /usr/local/lib/perl5/site_perl/5.6.1/Bio/PopGen/IO.pm:266 > > STACK Bio::PopGen::IO::new > > > /usr/local/lib/perl5/site_perl/5.6.1/Bio/PopGen/IO.pm:120 > > STACK toplevel > /usr/apache_ssl/cgi-bin/popgen_format.cgi:106 > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From laddie21castle at hotmail.com Wed Apr 14 09:27:25 2004 From: laddie21castle at hotmail.com (edmond) Date: Tue Apr 13 20:27:11 2004 Subject: [Bioperl-l] Anonymous Valium, Soma, VIA-GRA. No one needs to know! Message-ID: <1081949245-31607@excite.com> New OFFSHORE PHARMACY - Not a single medical question asked, guaranteed or it's free. Valium, Xanaxm, Soma, Zyban, Super V1agara, etc. 100% Private & NO QUESTIONS. 128-bit encrypted site which means maximum confidentiality & no tracing. Executives, Doctor's, & business people have been using our site for years & we are proud to present it to you. See what were all about today. http://mybestchoice.net/sv/index.php?pid=eph9106 center guidosoccer1 khan guido promethe action stingray utopia bobcatamelie cutie sugar katie qwerty12 obiwan From jason at cgt.duhs.duke.edu Tue Apr 13 20:28:15 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Apr 13 20:33:00 2004 Subject: [Bioperl-l] Bio::Root::Root.pm and taint In-Reply-To: <1081898402.407c75a29db3e@webmail.eclipse.net.uk> References: <1081857650.407bd67297027@webmail.eclipse.net.uk> <1081898402.407c75a29db3e@webmail.eclipse.net.uk> Message-ID: done - thank you Rich! On Wed, 14 Apr 2004, rich wrote: > > modfying the current untaining code from line 385 > resolves for me > > FROM: > > if ($name !~ /^([\w:]+)$/) { > $self->throw("$name is an illegal perl package name"); > > TO: > > if ($name !~ /^([\w:]+)$/) { > $self->throw("$name is an illegal perl package name"); > } > else{ > $name=$1; > } > > r > > > Quoting Jason Stajich : > > > presumably you'd get the same thing with SeqIO > > or any of the other > > bits using the dyanamic module loading system. > > > > hmm - I guess the _load_module routine needs to > > be untainted... > > not something I've worked on in the past - but > > perhaps someone else can > > take a look. > > > > > > -j > > > > On Tue, 13 Apr 2004, rich wrote: > > > > > > > > Hi, I am having an issue getting a cgi script > > to run in > > > taint mode. > > > > > > The error log shows the message below. > > > > > > User defined input is taken from a form and > > written to a > > > temp file. This is then read with > > Bio::PopGen::IO::csv. > > > Looking at the comments within Root.pm it > > looks as > > > though this had had attention previously > > > > > > cheers > > > Rich > > > > > > > > > > > > MSG: Failed to load module > > Bio::PopGen::IO::csv. > > > Insecure dependency in require while running > > with -T swi > > > tch at > > > > > /usr/local/lib/perl5/site_perl/5.6.1/Bio/Root/Root.pm > > > line 394. > > > > > > STACK Bio::Root::Root::_load_module > > > > > /usr/local/lib/perl5/site_perl/5.6.1/Bio/Root/Root.pm:397 > > > STACK (eval) > > > > > /usr/local/lib/perl5/site_perl/5.6.1/Bio/PopGen/IO.pm:267 > > > STACK Bio::PopGen::IO::_load_format_module > > > > > /usr/local/lib/perl5/site_perl/5.6.1/Bio/PopGen/IO.pm:266 > > > STACK Bio::PopGen::IO::new > > > > > /usr/local/lib/perl5/site_perl/5.6.1/Bio/PopGen/IO.pm:120 > > > STACK toplevel > > /usr/apache_ssl/cgi-bin/popgen_format.cgi:106 > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l@portal.open-bio.org > > > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > -- > > Jason Stajich > > Duke University > > jason at cgt.mc.duke.edu > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From stephan.rosecker at ish.de Tue Apr 13 21:02:48 2004 From: stephan.rosecker at ish.de (stephan rosecker) Date: Tue Apr 13 21:07:32 2004 Subject: [Bioperl-l] New attribut Message-ID: <407C8DB8.6040200@ish.de> Hi, i'm looking for a way to add new attributs to a seq object. For Example a family attribute so that i can call: $seq->family('Human'); print "Family: ".$seq->family()."\n"; or: $seq->weight(foo); Is that possible ? cheers, stephan From jason at cgt.duhs.duke.edu Tue Apr 13 21:24:11 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Apr 13 21:28:56 2004 Subject: [Bioperl-l] New attribut In-Reply-To: <407C8DB8.6040200@ish.de> References: <407C8DB8.6040200@ish.de> Message-ID: Sort of depends on a) does it have a location or is it valid for the whole sequence b) do you want it to be serializable (i.e. do you want it to be writeable to a standard sequence format (and re-reading back in)) You can store this stuff as a Feature which spans the whole gene You can store this as an Annotation using Bio::Annotation::Collection Adding new methods is possible but you will have to derive your own object extending an existing implementation. Basically you would write a simple module like this: package Bio::Seq::MySeq; use Bio::Seq; @ISA = qw(Bio::Seq); sub family { # get/set function } sub weight { # get/set function } And you can specify a Sequence type to the Sequence Factory when you read them in from SeqIO. my $seqio = Bio::SeqIO->new(-format => 'genbank', -seqfactory => Bio::Seq::SeqFactory->new( 'type' => 'Bio::Seq::MySeq'), ); Note that adding your own sequence type won't be serializeable in SeqIO though... -jason On Wed, 14 Apr 2004, stephan rosecker wrote: > Hi, > > i'm looking for a way to add new attributs to a seq object. > For Example a family attribute so that i can call: > $seq->family('Human'); > print "Family: ".$seq->family()."\n"; > or: > $seq->weight(foo); > > Is that possible ? > > cheers, > stephan > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From jason at cgt.duhs.duke.edu Tue Apr 13 22:03:34 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Apr 13 22:08:28 2004 Subject: [Bioperl-l] Speeding Up File Access In-Reply-To: References: Message-ID: Hey Johnny - You can just pass in an already built filehandle to Root::IO my $fh; open($fh, '< :raw', $filename) || die $!; my $seqio = Bio::SeqIO->new(-fh => $fh, -format => 'fasta'); I'd be curious to see some benchmarking results if this makes a difference if you're up to running a few tests? -jason On Sat, 10 Apr 2004, Johnny Amos wrote: > Hello, > > There was a recent article at PerlMonks.org about speeding up file IO: > http://www.perlmonks.org/index.pl?node_id=344087 > > One thing that caught my attention was the use of the :raw pragma on > filehandle creation to explicitly prevent handling of Unicode text. In the > example given this cut file IO times in half for a 3 GB file. > > open (FH, '< :raw', $filename); > instead of just: > open (FH, '<', $filename); > > I tried to look at Bio::Root::IO to see if an option for using this (or an > equivalent) was already implemented, but couldn't see one. > > Is this something worth submitting a patch for? Would it be useful for > things like UniGene, LocusLink, BLAT, and Blast parsers or can these files > contain Unicode in them somehow? > > Johnny > > _________________________________________________________________ > Free up your inbox with MSN Hotmail Extra Storage! Multiple plans available. > http://join.msn.com/?pgmarket=en-us&page=hotmail/es2&ST=1/go/onm00200362ave/direct/01/ > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From hlapp at gnf.org Wed Apr 14 02:09:39 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Wed Apr 14 02:14:29 2004 Subject: [Bioperl-l] Re: [BioSQL-l] Bio::SeqFeature::Generic score & source tags in Biosql In-Reply-To: <40754793.7000102@biologie.uni-freiburg.de> Message-ID: <505AF324-8DDA-11D8-8684-000A959EB4C4@gnf.org> $feature->source_tag is controlled vocabulary in biosql and therefore a foreign key on the seqfeature table to the term table (source_term_id). Source_tag isn't used by the rich sequence format like embl or Genbank; instead the tag in fact has a predefined default value most of the time (e.g., 'Genbank/EMBL/Swissprot' if the sequence is from - you guessed it - Genbank, Embl, or Swissprot). If you set a value then it should be present as a foreign key to the term table. score I thought gets translated into a tag/value pair, and would hence end up as value in the seqfeature_qualifier_value table. I just realized that this is apparently not the case. The problem is that score() is actually not defined in Bio::SeqFeatureI. I'm not sure what the best approach here is; maybe adding the translation to to Bio::SeqFeature::AnnotationAdaptor would be the best way to implement this. -hilmar On Thursday, April 8, 2004, at 05:37 AM, Daniel Lang wrote: > Hi, > I?m wondering why the score & source tags of the GenericFeature > objects I insert attached to RichSeqs into a biosql db are missing in > seqfeature_qualifier_value? > Are they somewhere else? > I?ve set them using Bio::SeqFeature::Generic::score() & source()... > Other tags I added using add_tag_value method are present... > > Do those to have special meaning? - Because source is also missing and > score becomes /note="score..." when writing the Objects directly to > genbank format... > > Thanks in advance, > Daniel > > -- > > Daniel Lang > University of Freiburg, Plant Biotechnology > Sonnenstr. 5, D-79104 Freiburg > phone: +49 761 203 6988 > homepage: http://www.plant-biotech.net/ > e-mail: daniel.lang@biologie.uni-freiburg.de > > ################################################# > >REALITY.SYS corrupted: Reboot universe? (Y/N/A) > ################################################# > > Join MOSS 2004 in Freiburg, Germany from September 12th - 15th: > registration and information @ http://www.plant-biotech.net/moss2004 > > > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From alexg at ebi.ac.uk Wed Apr 14 05:31:22 2004 From: alexg at ebi.ac.uk (Alex Gutteridge) Date: Wed Apr 14 05:36:43 2004 Subject: [Bioperl-l] distances from one atom to another in biological structures Message-ID: <7E44F009-8DF6-11D8-8B76-000A957E44DC@ebi.ac.uk> Hi, This can be done with the BioPerl structure modules. You don't say what your 'protein sites' actually are (residues, patches, co-ordinates, etc..?), but assuming you know the serial number of your active site atom and the xyz co-ordinates of your 'site' the following (untested) script would work. Just give it the PDB file as fist argument, active site atom serial as the second, and the x,y,z co-ords as the remaining arguments. Let me know if you need anymore help. use strict; use Bio::Structure::IO; my $file = shift; my $active_site_serial = shift; my ($other_site_x, $other_site_y, $other_site_z) = @_; my $structure = Bio::Structure::IO->new(-file => shift, -format => 'pdb')->next_structure; my ($x,$y,$z) = $structure->get_atom_by_serial($active_site_serial)->xyz; print distance($other_site_x,$other_site_y,$other_site_z, $x,$y,$z); sub distance { my ($x1,$y1,$z1,$x2,$y2,$z2) = @_; my $distance = sqrt((($x1 - $x2) * ($x1 - $x2)) + (($y1 - $y2) * ($y1 - $y2)) + (($z1 - $z2) * ($z1 - $z2))); return $distance; } Alex Gutteridge European Bioinformatics Institute Cambridge CB10 1SD UK Tel: 01223 492550 Email: alexg@ebi.ac.uk From zqchenupenn at hotmail.com Wed Apr 14 07:53:59 2004 From: zqchenupenn at hotmail.com (zqchenupenn) Date: Wed Apr 14 06:59:20 2004 Subject: [Bioperl-l] problem of installing bioperl 1.4: 404 NOT found Message-ID: <200404141153.59200.heikki@ebi.ac.uk> Hi, I have tried to install bioperl 1.4 in ActivePerl 5.8.3.809 by ppm. I use windows XP. It successfully installed libxml-perl Heap Graph then it have an Error: Failed to download URL http://www.bioperl.org/DIST/GD.ppd: 404 Not Found. I have tried several times, but it still does not work. Could you help me for this? Thanks a lot! Best Regards, John From sweety21benoit at hotmail.com Wed Apr 14 09:39:27 2004 From: sweety21benoit at hotmail.com (tanner) Date: Wed Apr 14 07:44:24 2004 Subject: [Bioperl-l] PR0ZAC on yourdoorstep. Anonymously. Message-ID: <1081949967-5450@excite.com> No one needs to know... http://sweety.aw3ede.com/s95/index.php?id=s95 eugene front242public tracy charlie1 beautifu miles china user1 aehchevy philip impala cynthia bird dirk Get off this list by writing to http://denali.pro-meds.net/sv/index.php?pid=eph9106 From omid at rogers.com Wed Apr 14 10:00:23 2004 From: omid at rogers.com (omid@rogers.com) Date: Wed Apr 14 10:05:32 2004 Subject: [Bioperl-l] Problems with installing bioperl using PPM3 Message-ID: <20040414140023.TFWM30980.fep02-mail.bloor.is.net.cable.rogers.com@localhost> Thanks for the Reply Chris... I managed to get things working for the time being. I am reading the the PPM instructions provided by the Activestate and getting a feel for how things work. I tried the first method you mentioned ie setting up a local repository: Here is what I did. 1) I run PPM3 at command prompt. 2) rep add my_local "E:/Perl/Local_rep/" I got this error message: "Can't locate object method "host" via package "URI::_foreign" (perhaps you forgot to load "URI::_foreign"?) at E:/Perl/site/lib/PPM/Repository/Local.pm line 18, line 3." I check to see if "URI" is installed (ie query *) and it was. I checked to see if there are any upgraded to URI and there was not one available. I don't know if you if have come across this type of errors in the past. Another question I had was can we use the CPAN module to download and install packages under a windows environment or are we restricted to using PPM from activestate? Many Thanks Omid > > From: Chris Fields > Date: 2004/04/09 Fri PM 09:53:08 EDT > To: > CC: > Subject: Re: [Bioperl-l] Problems with installing bioperl using PPM3 > > Not quite sure if this made the Bioperl-l list, so I'll repost the > general answer here. > > On Apr 8, 2004, at 7:58 AM, wrote: > > > Thanks for the reply Chris.. I installed perl 5.6.1 Build 635 and when > > using PPM3 I encountered a new set of problems. > > > > > > it seems that bioperl-1.4 does not work for for PPM3 on build 633 but > > I was able to install an ealier version of bioperl "Bioinformatics > > Toolkit". > > > > with build 635 it seems that ppm3 itself has problems installing some > > modules. some bioperl dependencies were able to be installed while > > others that worked with build 633 were not. > > > > Also, I encountered a problem installing "IO-String" > > with both versions. This module is one of the listed dependencies for > > bioperl. > > This may be due to the perl build failing during ActiveState's > automated packaging procedures. If you check the build status of the > IO-String module at ActiveState's PPM repository site (specifically, > http://ppm.activestate.com/BuildStatus/5.6-I.html), it lists it as > failing. However, the zipped PPM package is available from the same > website(http://ppm.activestate.com/PPMPackages/zips/6xx-builds-only/). > You can install this one of two ways: > > 1) Create a local repository from a directory ('rep add local_rep > "C:\Perl\local"' or something similar). Decompress the zipped archive > directly into the directory path listed (i.e. the file with the ppd > extension should not be in a subdirectory under the repository > directory; other files may be). Search the local directory and install > from there. > > 2) Decompress the archive into a temp directory. Run PPM3 ('ppm > IO-String') from a command prompt within the directory. > > I use the first method myself (only have to set up the directory once). > > > What I had to do in that case was download the IO-String module from > > CPAN in a temp directory and run nmake etc on it. Not sure if this is > > the proper way of doing things?? > > That works as well, but always make sure to run 'nmake test' to make > sure the module will work. Some modules (usually older, less > maintained ones) tend to fail for various reasons, mainly due to > included C source code that won't compile in the Windows environment. > Also, nmake has a tendency to sometimes crash even when it works, so it > may be hard to tell if you get success! > > The main reason to use PPM3 is b/c PPM3 makes it much easier to install > and upgrade modules (somewhat like a mini version of rpm in Linux, if > you're familiar with it). The program keeps track of installed modules > and is capable of producing nicely formatted HTML from POD; if you add > modules with nmake, PPM3 will not find them (although you might be able > to rebuild the PPM3 database). > > > Thanks > > Omid > > > > > > > > > > > >> > >> From: Chris Fields > >> Date: 2004/04/07 Wed PM 05:22:55 EDT > >> To: , > >> Subject: Re: [Bioperl-l] Problems with installing bioperl using PPM3 > >> > >> Everything works when using ActiveState Perl 5.8.3 Build 809, which > >> comes > >> with PPM3 as the default package manager. It may be due to the > >> earlier PPM > >> version. I checked the ActiveState web site documentation for > >> ActivePerl > >> 5.6.1 build 635 (the newest version of the 5.6.1 branch) and there is > >> a bug > >> fix listed for PPM3. > >> > >> The following link describes a problem very like yours and is from > >> the PPM > >> bug database > >> (http://bugs.activestate.com/show_bug.cgi?id=19749&submit=Go) > >> and is likely the bug that is fixed in 5.6.1 build 635, so you might > >> want > >> to upgrade to that version or to the newest 5.8.3 release for the fix. > >> > >> Chris > >> > >> At 02:08 PM 4/7/2004, omid@rogers.com wrote: > >>> Hello all, > >>> > >>> I have ActiveState perl 5.6.1 BUILD 633 installed on a local machine > >>> running windows 2000 and I do the following: > >>> > >>> I type "ppm3" at the command prompt > >>> then type "search bioperl" (the repository is set to > >>> http://www.bioperl.org/DIST/). > >>> > >>> a listing is displayed with numbers and when I attemp to issue the > >>> command > >>> "describe 20" or describe "package name" I get an error saying: > >>> > >>> Can't call method "name" without a package or object reference at > >>> E:\Perl\bin/ppm3-bin line 4265, <$__ANONIO__> line 9. > >>> > >>> I don't know what it means. I searched the bioperl site and looked at > >>> various installation documents but nothing seems to address this > >>> type of > >>> problem. > >>> > >>> Any help you are able to provide is greatly appreciated. > >>> Thanks > >>> Omid > >>> > >>> > >>> > >>> > >>> 1 > >>> > >>> _______________________________________________ > >>> Bioperl-l mailing list > >>> Bioperl-l@portal.open-bio.org > >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l > >> > >> __________________________________ > >> > >> Chris Fields - Postdoctoral Researcher > >> Lab of Dr. Robert Switzer > >> > >> Address: > >> > >> University of Illinois at Urbana-Champaign > >> Dept. of Biochemistry - 323 RAL > >> 600 S. Mathews Ave. > >> Urbana, IL 61801 > >> > >> Phone : (217) 333-7098 > >> Fax : (217) 244-5858 > >> > >> > > > > 1 > > > > > Chris Fields > Postdoctoral Reseacher - Dept. of Biochemistry > Laboratory of Dr. Robert Switzer > University of Illinois at Urbana-Champaign > > 1 From brian_osborne at cognia.com Wed Apr 14 22:26:47 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Wed Apr 14 10:21:58 2004 Subject: [Bioperl-l] Problems with installing bioperl using PPM3 In-Reply-To: <20040414140023.TFWM30980.fep02-mail.bloor.is.net.cable.rogers.com@localhost> Message-ID: Omid, >Another question I had was can we use the CPAN module to download and install packages >under a windows environment or are we restricted to using PPM from activestate? Yes, you can. Lincoln has made this point a couple of times when people expressed their frustrations with the ActiveState approach. In the Command Prompt, for example, you should be able to do: >perl -e shell -MCPAN And then things like: cpan>install IO::String It's been some time since I last used ActiveState, I use Cygwin instead, so someone should correct me if this is no longer the case. Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of omid@rogers.com Sent: Wednesday, April 14, 2004 10:00 AM To: Chris Fields Cc: Bioperl-l@bioperl.org Subject: Re: Re: [Bioperl-l] Problems with installing bioperl using PPM3 Thanks for the Reply Chris... I managed to get things working for the time being. I am reading the the PPM instructions provided by the Activestate and getting a feel for how things work. I tried the first method you mentioned ie setting up a local repository: Here is what I did. 1) I run PPM3 at command prompt. 2) rep add my_local "E:/Perl/Local_rep/" I got this error message: "Can't locate object method "host" via package "URI::_foreign" (perhaps you forgot to load "URI::_foreign"?) at E:/Perl/site/lib/PPM/Repository/Local.pm line 18, line 3." I check to see if "URI" is installed (ie query *) and it was. I checked to see if there are any upgraded to URI and there was not one available. I don't know if you if have come across this type of errors in the past. Another question I had was can we use the CPAN module to download and install packages under a windows environment or are we restricted to using PPM from activestate? Many Thanks Omid > > From: Chris Fields > Date: 2004/04/09 Fri PM 09:53:08 EDT > To: > CC: > Subject: Re: [Bioperl-l] Problems with installing bioperl using PPM3 > > Not quite sure if this made the Bioperl-l list, so I'll repost the > general answer here. > > On Apr 8, 2004, at 7:58 AM, wrote: > > > Thanks for the reply Chris.. I installed perl 5.6.1 Build 635 and when > > using PPM3 I encountered a new set of problems. > > > > > > it seems that bioperl-1.4 does not work for for PPM3 on build 633 but > > I was able to install an ealier version of bioperl "Bioinformatics > > Toolkit". > > > > with build 635 it seems that ppm3 itself has problems installing some > > modules. some bioperl dependencies were able to be installed while > > others that worked with build 633 were not. > > > > Also, I encountered a problem installing "IO-String" > > with both versions. This module is one of the listed dependencies for > > bioperl. > > This may be due to the perl build failing during ActiveState's > automated packaging procedures. If you check the build status of the > IO-String module at ActiveState's PPM repository site (specifically, > http://ppm.activestate.com/BuildStatus/5.6-I.html), it lists it as > failing. However, the zipped PPM package is available from the same > website(http://ppm.activestate.com/PPMPackages/zips/6xx-builds-only/). > You can install this one of two ways: > > 1) Create a local repository from a directory ('rep add local_rep > "C:\Perl\local"' or something similar). Decompress the zipped archive > directly into the directory path listed (i.e. the file with the ppd > extension should not be in a subdirectory under the repository > directory; other files may be). Search the local directory and install > from there. > > 2) Decompress the archive into a temp directory. Run PPM3 ('ppm > IO-String') from a command prompt within the directory. > > I use the first method myself (only have to set up the directory once). > > > What I had to do in that case was download the IO-String module from > > CPAN in a temp directory and run nmake etc on it. Not sure if this is > > the proper way of doing things?? > > That works as well, but always make sure to run 'nmake test' to make > sure the module will work. Some modules (usually older, less > maintained ones) tend to fail for various reasons, mainly due to > included C source code that won't compile in the Windows environment. > Also, nmake has a tendency to sometimes crash even when it works, so it > may be hard to tell if you get success! > > The main reason to use PPM3 is b/c PPM3 makes it much easier to install > and upgrade modules (somewhat like a mini version of rpm in Linux, if > you're familiar with it). The program keeps track of installed modules > and is capable of producing nicely formatted HTML from POD; if you add > modules with nmake, PPM3 will not find them (although you might be able > to rebuild the PPM3 database). > > > Thanks > > Omid > > > > > > > > > > > >> > >> From: Chris Fields > >> Date: 2004/04/07 Wed PM 05:22:55 EDT > >> To: , > >> Subject: Re: [Bioperl-l] Problems with installing bioperl using PPM3 > >> > >> Everything works when using ActiveState Perl 5.8.3 Build 809, which > >> comes > >> with PPM3 as the default package manager. It may be due to the > >> earlier PPM > >> version. I checked the ActiveState web site documentation for > >> ActivePerl > >> 5.6.1 build 635 (the newest version of the 5.6.1 branch) and there is > >> a bug > >> fix listed for PPM3. > >> > >> The following link describes a problem very like yours and is from > >> the PPM > >> bug database > >> (http://bugs.activestate.com/show_bug.cgi?id=19749&submit=Go) > >> and is likely the bug that is fixed in 5.6.1 build 635, so you might > >> want > >> to upgrade to that version or to the newest 5.8.3 release for the fix. > >> > >> Chris > >> > >> At 02:08 PM 4/7/2004, omid@rogers.com wrote: > >>> Hello all, > >>> > >>> I have ActiveState perl 5.6.1 BUILD 633 installed on a local machine > >>> running windows 2000 and I do the following: > >>> > >>> I type "ppm3" at the command prompt > >>> then type "search bioperl" (the repository is set to > >>> http://www.bioperl.org/DIST/). > >>> > >>> a listing is displayed with numbers and when I attemp to issue the > >>> command > >>> "describe 20" or describe "package name" I get an error saying: > >>> > >>> Can't call method "name" without a package or object reference at > >>> E:\Perl\bin/ppm3-bin line 4265, <$__ANONIO__> line 9. > >>> > >>> I don't know what it means. I searched the bioperl site and looked at > >>> various installation documents but nothing seems to address this > >>> type of > >>> problem. > >>> > >>> Any help you are able to provide is greatly appreciated. > >>> Thanks > >>> Omid > >>> > >>> > >>> > >>> > >>> 1 > >>> > >>> _______________________________________________ > >>> Bioperl-l mailing list > >>> Bioperl-l@portal.open-bio.org > >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l > >> > >> __________________________________ > >> > >> Chris Fields - Postdoctoral Researcher > >> Lab of Dr. Robert Switzer > >> > >> Address: > >> > >> University of Illinois at Urbana-Champaign > >> Dept. of Biochemistry - 323 RAL > >> 600 S. Mathews Ave. > >> Urbana, IL 61801 > >> > >> Phone : (217) 333-7098 > >> Fax : (217) 244-5858 > >> > >> > > > > 1 > > > > > Chris Fields > Postdoctoral Reseacher - Dept. of Biochemistry > Laboratory of Dr. Robert Switzer > University of Illinois at Urbana-Champaign > > 1 _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From cjfields at uiuc.edu Wed Apr 14 13:08:41 2004 From: cjfields at uiuc.edu (Chris Fields) Date: Wed Apr 14 13:15:37 2004 Subject: [Bioperl-l] Problems with installing bioperl using PPM3 In-Reply-To: References: <20040414140023.TFWM30980.fep02-mail.bloor.is.net.cable.rogers.com@localhost> Message-ID: <6.0.0.22.2.20040414102518.01beaa88@express.cites.uiuc.edu> At 09:26 PM 4/14/2004, Brian Osborne wrote: >Omid, > > >Another question I had was can we use the CPAN module to download and >install packages > >under a windows environment or are we restricted to using PPM from >activestate? > >Yes, you can. Lincoln has made this point a couple of times when people >expressed their frustrations with the ActiveState approach. In the Command >Prompt, for example, you should be able to do: > > >perl -e shell -MCPAN > >And then things like: > >cpan>install IO::String > >It's been some time since I last used ActiveState, I use Cygwin instead, so >someone should correct me if this is no longer the case. > > >Brian O. I have tried this before and it works fine. The only issues that I've seen come up are test failures when installing some modules that have C code included, upon which nmake crashes and the install fails. The reason to use PPM can be summed up in one word: simplicity. I think that some Perl users, myself included, have learned Perl and other higher level languages w/o experience in the intricacies of the programming process that one learns from C or C++ in a basic computer programming course (i.e. plan program -> type program -> build (compile and link program) -> execute program). That's fine but becomes a problem when trying to install some modules w/o some background knowledge, such as how to use 'nmake' or 'make' in a Windows environment. I personally have a biochemistry and microbiology background and currently work as a postdoctoral researcher on RNA-binding proteins. I have since learned C and C++ for various other reasons, one being that I have an avid interest in programming. Learning the basics has helped me tremendously in picking out problems that I ran into before, such as how to compile a program in a Linux or Windows environment, using the proper header files, libraries, etc. It also has helped in learning a bit more about how Perl and how easy it is to use compared to C/C++. The advantage of using PPM is that it allows for easy installation and removal of packages w/o the need for building modules, and it also creates nicely HTML-formatted help pages from POD (something that pod2html can do as well). The biggest disadvantage with PPM is that it is somewhat like a using a calculator; it's quick and easy, but it's a 'black box' in that most people don't know how it works, but it does its job (sometimes). I'm now able to get around some of the problems of using PPM through a little detective work (reading the man pages!!!, web searches, etc) and learning a bit more about the programming process. I think most problems with PPM arise b/c some modules refuse to compile with Windows (for a list of the many failed builds from ActiveState automated build process, see http://ppm.activestate.com/). Randy Kobes has many PPM modules not available from ActiveState that have been tweaked for Windows, including GD (http://theoryx5.uwinnipeg.ca/), but many distributions still have problems. PDL is one distribution that comes to mind, which is required for the Transcription Factor Binding Site modules. My 2c chris >-----Original Message----- >From: bioperl-l-bounces@portal.open-bio.org >[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of omid@rogers.com >Sent: Wednesday, April 14, 2004 10:00 AM >To: Chris Fields >Cc: Bioperl-l@bioperl.org >Subject: Re: Re: [Bioperl-l] Problems with installing bioperl using PPM3 > >Thanks for the Reply Chris... > >I managed to get things working for the time being. > >I am reading the the PPM instructions provided by the Activestate and >getting a feel for how things work. > >I tried the first method you mentioned ie setting up a local repository: > >Here is what I did. > >1) I run PPM3 at command prompt. >2) rep add my_local "E:/Perl/Local_rep/" > >I got this error message: > >"Can't locate object method "host" via package "URI::_foreign" (perhaps you >forgot to load "URI::_foreign"?) at E:/Perl/site/lib/PPM/Repository/Local.pm >line 18, line 3." > > >I check to see if "URI" is installed (ie query *) and it was. I checked to >see if there are any upgraded to URI and there was not one available. > >I don't know if you if have come across this type of errors in the past. > > > >Another question I had was can we use the CPAN module to download and >install packages under a windows environment or are we restricted to using >PPM from activestate? > > >Many Thanks >Omid _________________________________ Chris Fields - Postdoctoral Researcher Lab of Dr. Robert Switzer Address: University of Illinois at Urbana-Champaign Dept. of Biochemistry - 323 RAL 600 S. Mathews Ave. Urbana, IL 61801 Phone : (217) 333-7098 Fax : (217) 244-5858 From bdirks at uclink.berkeley.edu Wed Apr 14 13:35:16 2004 From: bdirks at uclink.berkeley.edu (Bill Dirks) Date: Wed Apr 14 13:39:59 2004 Subject: [Bioperl-l] StandAloneBlast and Shell Variable Question Message-ID: Hello, I was wondering if there is a way to set BLASTDIR and BLASTDATADIR from inside a perl script instead of getting their values from the shell variables. Thanks, Bill From sanges at biogem.it Wed Apr 14 13:47:41 2004 From: sanges at biogem.it (Remo Sanges) Date: Wed Apr 14 13:52:24 2004 Subject: [Bioperl-l] StandAloneBlast and Shell Variable Question In-Reply-To: References: Message-ID: Hello Bill, you can try: $ENV{'BLASTDIR'} = 'path to the dir'; you must not user my. Remo On Apr 14, 2004, at 7:35 PM, Bill Dirks wrote: > Hello, > I was wondering if there is a way to set BLASTDIR and BLASTDATADIR > from inside a perl script instead of getting their values from the > shell variables. > Thanks, > Bill > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From jason at cgt.duhs.duke.edu Wed Apr 14 14:50:58 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed Apr 14 14:56:33 2004 Subject: [Bioperl-l] StandAloneBlast and Shell Variable Question In-Reply-To: References: Message-ID: BEGIN { $ENV{BLASTDIR} = '/some/path'; $ENV{BLASTDATADIR} = '/some/path'; } Make sure the go in BEFORE you have the use Bio::Tools::Run::StandAloneBlast; as the datadir values are done at include-time. Also I believe you can pass in the full path to the db you are searching $blastfactory->d('/path/to/db'); -jason On Wed, 14 Apr 2004, Bill Dirks wrote: > Hello, > I was wondering if there is a way to set BLASTDIR and BLASTDATADIR from inside a perl script > instead of getting their values from the shell variables. > Thanks, > Bill > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From tex at bioinformatics.rit.edu Tue Apr 13 23:48:42 2004 From: tex at bioinformatics.rit.edu (James Thompson) Date: Wed Apr 14 15:07:16 2004 Subject: [Bioperl-l] StandAloneBlast and Shell Variable Question In-Reply-To: Message-ID: One option would be to reset the environment variable within your perl script, like this: $ENV{'BLASTDATADIR'} = '/usr/share/ncbi/blastdb'; $ENV{'BLASTDIR'} = '/usr/share/ncbi/blast'; Tex Thompson On Wed, 14 Apr 2004, Bill Dirks wrote: > Hello, > I was wondering if there is a way to set BLASTDIR and BLASTDATADIR from inside a perl script > instead of getting their values from the shell variables. > Thanks, > Bill > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From pik at sindominio.net Thu Apr 15 06:13:20 2004 From: pik at sindominio.net (Mikel =?ISO-8859-1?B?RWdh?=) Date: Thu Apr 15 06:19:48 2004 Subject: [Bioperl-l] TreeIO problem Message-ID: <20040415121320.744b2bb1.pik@sindominio.net> Hello people; First of all, Bioperl is great. I have just started using it for one of my projects and I'm amazed. I have a problem with the TreeIO class. I just want to write a newick tree in SVG format, so I got this code from the api and put it in this little script: ------------------------------------------------------------------------ #!/usr/bin/perl use Bio::TreeIO; my $in = new Bio::TreeIO(-file => 'input', -format => 'newick'); my $out = new Bio::TreeIO(-file => '>output', -format => 'svggraph'); while( my $tree = $in->next_tree ) { my $svg_xml = $out->write_tree($tree); } ------------------------------------------------------------------------ And the following exception was given: ------------------------------------------------------------------------ MSG: Failed to load module Bio::TreeIO::svggraph. Can't locate SVG/Graph.pm in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.8.3 /usr/local/share/perl/5.8.3 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.8 /usr/share/perl/5.8 /usr/local/lib/site_perl .) at /usr/local/share/perl/5.8.3/Bio/TreeIO/svggraph.pm line 78. BEGIN failed--compilation aborted at /usr/local/share/perl/5.8.3/Bio/TreeIO/svggraph.pm line 78. Compilation failed in require at /usr/local/share/perl/5.8.3/Bio/Root/Root.pm line 394. STACK Bio::Root::Root::_load_module /usr/local/share/perl/5.8.3/Bio/Root/Root.pm:396 STACK (eval) /usr/local/share/perl/5.8.3/Bio/TreeIO.pm:227 STACK Bio::TreeIO::_load_format_module /usr/local/share/perl/5.8.3/Bio/TreeIO.pm:226 STACK Bio::TreeIO::new /usr/local/share/perl/5.8.3/Bio/TreeIO.pm:126 STACK toplevel ./svg.pl:6 ------------------------------------------------------------------------ So I have installed all the SVG related modules via CPAN but I receive the same error, and I cannot figure out what should I do next. Thank you for your time, Mikel Ega?a. PS: I'm using bioperl 1.4 in Debian Sarge. ------------------------------------------------- -->pik@lolita (Debian Sarge-Kernel 2.4.20) -->http://sindominio.net/~pik -->"Don Quijote se salva cuando se echa a los caminos a ser apaleado" (Francisco Umbral) ------------------------------------------------- From gabriele.bucci at ieo-research.it Thu Apr 15 06:21:13 2004 From: gabriele.bucci at ieo-research.it (gabriele bucci) Date: Thu Apr 15 06:25:59 2004 Subject: [Bioperl-l] any documentation on bioperl? Message-ID: <000201c422d3$61393740$0d6d5cd5@Gabriele7C> Dears, I'm seeking for a book guide to bioperl, but except for the embedded perldocs I was unable to find something. Does anybody knows or heard about any publication covering this useful tool? Thanks Gabriele Bucci Department of Experimental Oncology European Institute of Oncology Via Ripamonti, 435 20141 Milan, Italy Tel. 02-57489-864 Fax. 02-57489-851 e-mail: gabriele.bucci@ieo-research.it From brian_osborne at cognia.com Thu Apr 15 19:33:18 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Thu Apr 15 07:27:54 2004 Subject: [Bioperl-l] any documentation on bioperl? In-Reply-To: <000201c422d3$61393740$0d6d5cd5@Gabriele7C> Message-ID: Gabriele, Take a look at the bptutorial and the various HOWTOs (http://www.bioperl.org/Core/Latest/modules.html). There's also a chapter in Mastering Perl for Bioinformatics (http://www.oreilly.com/catalog/mperlbio/chapter/ch09.pdf). Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of gabriele bucci Sent: Thursday, April 15, 2004 6:21 AM To: bioperl-l@portal.open-bio.org Subject: [Bioperl-l] any documentation on bioperl? Dears, I'm seeking for a book guide to bioperl, but except for the embedded perldocs I was unable to find something. Does anybody knows or heard about any publication covering this useful tool? Thanks Gabriele Bucci Department of Experimental Oncology European Institute of Oncology Via Ripamonti, 435 20141 Milan, Italy Tel. 02-57489-864 Fax. 02-57489-851 e-mail: gabriele.bucci@ieo-research.it _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From sanges at biogem.it Thu Apr 15 09:30:55 2004 From: sanges at biogem.it (Remo Sanges) Date: Thu Apr 15 09:35:46 2004 Subject: [Bioperl-l] any documentation on bioperl? In-Reply-To: <000201c422d3$61393740$0d6d5cd5@Gabriele7C> References: <000201c422d3$61393740$0d6d5cd5@Gabriele7C> Message-ID: <1FBD8BBD-8EE1-11D8-9934-000A95B95F88@biogem.it> Hi Gabriele, you can find: pdocs and howtos at http://doc.bioperl.org/ tutorial at http://www.bioperl.org/Core/Latest/bptutorial.html a bioperl course at http://www.pasteur.fr/recherche/unites/sis/formation/bioperl/ There's some books about perl for bioinformatics, but the bioperl section are very little http://www.oreilly.com/catalog/begperlbio/ http://www.oreilly.com/catalog/mperlbio/ If you are looking for more or for specific problem I think you can ask in this mailing list Remo On Apr 15, 2004, at 12:21 PM, gabriele bucci wrote: > Dears, > I'm seeking for a book guide to bioperl, but except for the embedded > perldocs I was unable to find something. > Does anybody knows or heard about any publication covering this useful > tool? > > Thanks > > > Gabriele Bucci > Department of Experimental Oncology > European Institute of Oncology > Via Ripamonti, 435 > 20141 Milan, Italy > Tel. 02-57489-864 > Fax. 02-57489-851 > e-mail: gabriele.bucci@ieo-research.it > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From iain.wallace at ucd.ie Thu Apr 15 09:44:49 2004 From: iain.wallace at ucd.ie (Iain Wallace) Date: Thu Apr 15 09:56:50 2004 Subject: [Bioperl-l] AlignIO: Sequence length appended to name in output Message-ID: <1082036689.21391.22.camel@dhcp-892b8d7e.ucd.ie> Hi I am using the AlignIO module to manipulate alignments. I noticed that every time I write out an alignment the sequence length gets appended to the name of the sequence e.g. >1srya becomes >1srya/1-311 Does anyone know how I can turn this feature off? Thanks for your help again Iain From heikki at nildram.co.uk Thu Apr 15 12:23:06 2004 From: heikki at nildram.co.uk (Heikki Lehvaslaiho) Date: Thu Apr 15 11:29:16 2004 Subject: [Bioperl-l] AlignIO: Sequence length appended to name in output In-Reply-To: <1082036689.21391.22.camel@dhcp-892b8d7e.ucd.ie> References: <1082036689.21391.22.camel@dhcp-892b8d7e.ucd.ie> Message-ID: <200404151623.07975.heikki@nildram.co.uk> Iain, See the pod documentation for reasons for that. You can this feature on oand off using methods set_displayname_flat() and set_displayname_normal(). -Heikki On Thursday 15 Apr 2004 13:44, Iain Wallace wrote: > Hi > > I am using the AlignIO module to manipulate alignments. I noticed that > every time I write out an alignment the sequence length gets appended to > the name of the sequence > e.g. >1srya becomes >1srya/1-311 > > Does anyone know how I can turn this feature off? > > Thanks for your help again > > Iain > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From laurence.amilhat at biogemma.com Wed Apr 14 03:43:08 2004 From: laurence.amilhat at biogemma.com (laurence.amilhat@biogemma.com) Date: Thu Apr 15 12:04:49 2004 Subject: [Bioperl-l] Error message when parsing Blast report Message-ID: Hi everybody, I tried to parse a blast report using the BioPerl modules. I have this error message: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: no data for midline ........................done STACK: Error::throw STACK: Bio::Root::Root::throw /usr/lib/perl-5.6.0/lib/site_perl/5.6.0/Bio/Root/Root.pm:328 STACK: Bio::SearchIO::blast::next_result /usr/lib/perl-5.6.0/lib/site_perl/5.6.0/Bio/SearchIO/blast.pm:1151 STACK: blast_retour4.pl:96 ----------------------------------------------------------- When I parse another Blast report I don't have this message. My Blast report must have something wrong, do you have an idea of what ? Thanks, Sincerely, Laurence Amilhat From barry.moore at genetics.utah.edu Wed Apr 14 20:21:25 2004 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Thu Apr 15 12:04:51 2004 Subject: [Bioperl-l] problem of installing bioperl 1.4: 404 NOT found In-Reply-To: <200404141153.59200.heikki@ebi.ac.uk> References: <200404141153.59200.heikki@ebi.ac.uk> Message-ID: <407DD585.10809@genetics.utah.edu> John- The INSTALL.WIN document on the bioperl website (http://bioperl.org/Core/Latest/INSTALL.WIN) that step 2 in installing BioPerl on Windows is to install external modules. GD is one of those - there are other as well (i.e. see http://www.bioperl.org/Core/external.shtml). You can install GD with ppm: ppm> search GD If you don't see GD on the list returned by search add Randy Kobes respository which has it: ppm> rep add Kobes http://theoryx5.uwinnipeg.ca/ppms/ The search for GD again. Chose and install a version above 2.0 (I think). This has other dependencies that you may or may not already have. Installation on Windows can be a challenge, but there is an end to the trouble, and it does work. Keep at it and you'll get there. Barry zqchenupenn (by way of Heikki Lehvaslaiho ) wrote: >Hi, > I have tried to install bioperl 1.4 in ActivePerl 5.8.3.809 by ppm. I use > windows XP. It successfully installed > libxml-perl > Heap > Graph >then it have an Error: Failed to download URL >http://www.bioperl.org/DIST/GD.ppd: 404 Not Found. > > I have tried several times, but it still does not work. Could you help me > for this? Thanks a lot! Best Regards, >John > > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Barry Moore Dept. of Human Genetics University of Utah Salt Lake City, UT From babenko at ncbi.nlm.nih.gov Thu Apr 15 10:37:52 2004 From: babenko at ncbi.nlm.nih.gov (Babenko, Vladimir (NIH/NLM/NCBI)) Date: Thu Apr 15 12:04:53 2004 Subject: [Bioperl-l] tiling hits to multiple alignment Message-ID: <69BA0F938FAC6A4CBEF49461720696F2032418CB@nihexchange16.nih.gov> I wonder if there is any optimal way/template to arrange the blast hits separately along the query in a form of multiple alignment? I have no problems in pairwise AlignIO object creation from blast output, thanks to SearchIO, but as for the whole hit set I have no clear idea. Could there be some ?natural? way to do that? Thanks, Vladimir From dhoworth at mrc-lmb.cam.ac.uk Thu Apr 15 12:10:59 2004 From: dhoworth at mrc-lmb.cam.ac.uk (Dave Howorth) Date: Thu Apr 15 12:15:57 2004 Subject: [Bioperl-l] bioperl-db make test errors Message-ID: <407EB413.5050802@mrc-lmb.cam.ac.uk> I'm trying to set up bioperl-db and getting some errors in the make test (full log is below). I just downloaded bioperl-db and biosql, and just upgraded mysql (from 3.23.49). MySQL appears to run OK with some existing databases. I just created a database (biosql_test) for the tests and loaded the biosqldb-mysql.sql schema. I'm using: bioperl 1.4 bioperl-db (the README says "README,v 1.17 2003/08/22 12:44:23") biosql (the README says "README,v 1.4 2003/09/21 05:01:23") Perl 5.6.1 MySQL 4.0.18 Debian woody with many backports Does anybody have any idea what is causing the errors? Cheers, Dave ---- bioperl-db$ make test PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib/perl/5.6.1 -I/usr/share/perl/5.6.1 -e 'use Test::Harness qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/*.t t/cluster.......ok 155/160 -------------------- WARNING --------------------- MSG: failed to store one or more child objects for an instance of class Bio::Cluster::UniGene (PK=1) --------------------------------------------------- t/cluster.......ok t/comment.......ok t/dbadaptor.....ok t/dblink........ok t/ensembl.......ok t/fuzzy2........ok t/genbank.......ok t/locuslink.....NOK 24Can't call method "as_text" on an undefined value at t/locuslink.t line 122, line 1. t/locuslink.....FAILED tests 24, 29-110 Failed 83/110 tests, 24.55% okay t/ontology......ok t/query.........ok t/remove........ok t/seqfeature....ok t/simpleseq.....ok t/species.......ok 5/65 ------------- EXCEPTION ------------- MSG: Unique key query in Bio::DB::BioSQL::SpeciesAdaptor returned 2 rows instead of 1. Query was [name_class="scientific name",binomial="Homo sapiens"] STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:960 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:856 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:183 STACK Bio::DB::Persistent::PersistentObject::create blib/lib/Bio/DB/Persistent/PersistentObject.pm:243 STACK toplevel t/species.t:35 -------------------------------------- t/species.......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-65 Failed 60/65 tests, 7.69% okay t/swiss.........ok Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/locuslink.t 110 83 75.45% 24 29-110 t/species.t 255 65280 65 120 184.62% 6-65 Failed 2/15 test scripts, 86.67% okay. 143/930 subtests failed, 84.62% okay. make: *** [test_dynamic] Error 11 From jurgen.pletinckx at algonomics.com Thu Apr 15 12:35:56 2004 From: jurgen.pletinckx at algonomics.com (Jurgen Pletinckx) Date: Thu Apr 15 12:26:59 2004 Subject: [Bioperl-l] tiling hits to multiple alignment In-Reply-To: <69BA0F938FAC6A4CBEF49461720696F2032418CB@nihexchange16.nih.gov> Message-ID: If you are looking to generate a multiple alignment from a blast report, Nigel Brown's Mview is worth looking into - see http://mathbio.nimr.mrc.ac.uk/~nbrown/mview/ He gives some background on the tiling process in http://mathbio.nimr.mrc.ac.uk/~nbrown/mview/blast/index.html -- Jurgen Pletinckx AlgoNomics NV From jason at cgt.duhs.duke.edu Thu Apr 15 12:44:14 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Thu Apr 15 12:49:47 2004 Subject: [Bioperl-l] TreeIO problem In-Reply-To: <20040415121320.744b2bb1.pik@sindominio.net> References: <20040415121320.744b2bb1.pik@sindominio.net> Message-ID: And you did install SVG::Graph... which pulls in a bunch of dependancies: Math::Derivative Math::Spline Tree::DAG_Node What does 'perldoc SVG::Graph' report? If I do the install via the cpan shell I get all the dependancies too. -jason On Thu, 15 Apr 2004, Mikel [ISO-8859-1] Ega wrote: > Hello people; > > First of all, Bioperl is great. I have just started using it for one of > my projects and I'm amazed. > > I have a problem with the TreeIO class. I just want to write a newick > tree in SVG format, so I got this code from the api and put it in this > little script: > > ------------------------------------------------------------------------ > #!/usr/bin/perl > > use Bio::TreeIO; > > my $in = new Bio::TreeIO(-file => 'input', -format => 'newick'); > my $out = new Bio::TreeIO(-file => '>output', -format => 'svggraph'); > > while( my $tree = $in->next_tree ) { > my $svg_xml = $out->write_tree($tree); > } > > ------------------------------------------------------------------------ > > And the following exception was given: > > ------------------------------------------------------------------------ > MSG: Failed to load module Bio::TreeIO::svggraph. Can't locate > SVG/Graph.pm in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.8.3 > /usr/local/share/perl/5.8.3 /usr/lib/perl5 /usr/share/perl5 > /usr/lib/perl/5.8 /usr/share/perl/5.8 /usr/local/lib/site_perl .) at > /usr/local/share/perl/5.8.3/Bio/TreeIO/svggraph.pm line 78. BEGIN > failed--compilation aborted at > /usr/local/share/perl/5.8.3/Bio/TreeIO/svggraph.pm line 78. Compilation > failed in require at /usr/local/share/perl/5.8.3/Bio/Root/Root.pm line > 394. > > STACK Bio::Root::Root::_load_module > /usr/local/share/perl/5.8.3/Bio/Root/Root.pm:396 STACK (eval) > /usr/local/share/perl/5.8.3/Bio/TreeIO.pm:227 STACK > Bio::TreeIO::_load_format_module > /usr/local/share/perl/5.8.3/Bio/TreeIO.pm:226 STACK Bio::TreeIO::new > /usr/local/share/perl/5.8.3/Bio/TreeIO.pm:126 STACK toplevel ./svg.pl:6 > ------------------------------------------------------------------------ > > So I have installed all the SVG related modules via CPAN but I receive > the same error, and I cannot figure out what should I do next. > > Thank you for your time, > > Mikel Egaña. > > PS: I'm using bioperl 1.4 in Debian Sarge. > > ------------------------------------------------- > -->pik@lolita (Debian Sarge-Kernel 2.4.20) > > -->http://sindominio.net/~pik > > -->"Don Quijote se salva cuando se echa a > los caminos a ser apaleado" (Francisco Umbral) > ------------------------------------------------- > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From barry.moore at genetics.utah.edu Thu Apr 15 14:09:13 2004 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Thu Apr 15 14:13:54 2004 Subject: [Bioperl-l] tiling hits to multiple alignment In-Reply-To: References: Message-ID: <407ECFC9.4030407@genetics.utah.edu> Vladimir, If you are looking for a graphical alignment of hits, see also the Graphics HOWTO http://bioperl.org/HOWTOs/html/Graphics-HOWTO.html. Barry Jurgen Pletinckx wrote: >If you are looking to generate a multiple alignment from >a blast report, Nigel Brown's Mview is worth looking into - >see http://mathbio.nimr.mrc.ac.uk/~nbrown/mview/ > >He gives some background on the tiling process in >http://mathbio.nimr.mrc.ac.uk/~nbrown/mview/blast/index.html > > > -- Barry Moore Dept. of Human Genetics University of Utah Salt Lake City, UT From hlapp at gnf.org Thu Apr 15 15:31:05 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Thu Apr 15 15:35:53 2004 Subject: [Bioperl-l] Re: ComparableI stuff In-Reply-To: <407E5DB5.4020105@egenetics.com> Message-ID: <6FD44B24-8F13-11D8-A5EA-000A959EB4C4@gnf.org> I was going to write a more detailed response but probably won't be getting to it before Monday due to painful deadlines. Generally, I have a number of issues with this. - On a very general level, basing equality on equal hash keys is dangerous because it violates the standard definition of a hash key. You construct it as a string most of the time and hence comparing keys is meant as a short-cut for comparing objects, but I really would not call it hash keys and at the same time assume equal objects iff equal hash keys. - Defining object equality for complex objects is more a matter of subjective judgment rather than having objective criteria that we can define and impose on everybody. In fact, I think doing so is dangerous, because it creates the false impression of obviating people's need to make their own appropriate decision on when to call objects equal and when not to. As an example, your hashkey() on SeqFeatureI uses the positional information but leaves out the sequence on which it sits, leaves out the source_tag(), and in fact leaves out the entire tag system. It also leaves out a feature's annotation. This definition of equality may be fine in some cases, but may also be completely inappropriate in others. In biosql, as an example, it is completely inappropriate; biosql defines two SeqFeature entries as equal that are on the same sequence, have the same primary_tag, same source_tag, and are in the same position in the sequence's feature array. The features' display_name is irrelevant, as is the positional information. If I compared two seqfeatures using the ComparableI interface, they may compare as unequal and yet if I store them I'd get thrown out with a unique key failure. Chado I believe has a slightly different definition of the unique key and may take the positional information into account. As another example, for genbank/embl features it is also inappropriate because it doesn't test for equality of attached annotations. Note that you may define equality of two feature table entries in a genbank record by them containing the same annotation regardless of the annotations' order of appearance. I.e., comparing the annotation arrays element by element would be too strict then. My point here is not that I would urge you to add all these properties to the SeqFeatureI->diff implementation, because there may be use cases for which your current implementation is perfectly fine. My point is rather, I don't see the value of having one definition of equality implemented in a way that doesn't allow others to coexist when the one that is implemented is going to serve only a third of all use cases. I guess one of my key problems is that in fact I don't understand what the exact use case is. Apart from that, the implementation doesn't seem to allow for multiple use cases, which will unequivocally result in different implementations of equality having to peacefully co-exist. What I could rather envision as being useful is a design along 'schemes', where you can swap in one 'equality scheme' for another depending on what your needs are, and in which somebody who has a need for a yet-unimplemented definition could add that implementation and then swap it in. -hilmar On Thursday, April 15, 2004, at 03:02 AM, Peter van Heusden wrote: > [...] > Any comments on the ComparableI interface? Can this be checked into > CVS? > > Thanks, > Peter > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From hlapp at gnf.org Thu Apr 15 15:58:05 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Thu Apr 15 16:02:51 2004 Subject: [Bioperl-l] bioperl-db make test errors In-Reply-To: <407EB413.5050802@mrc-lmb.cam.ac.uk> Message-ID: <35D1CA9A-8F17-11D8-A5EA-000A959EB4C4@gnf.org> Both tests pass for me, running against mysql and both the development trunk and the 1.4 branch of bioperl. To exclude the obvious: - did you make sure that innodb is enabled in mysql? You have to edit the config file to do that. On the mysql prompt, insert a record into biodatabase, then issue a rollback. Is the record that you inserted still there? There may have been fixes to the 1.4 branch from me or somebody else after the 1.4.0 release that may fix your problems. Try the latest download from cvs of the 1.4 branch. If this doesn't help, run the locuslink.t test in verbose mode and send the result to me. You do this by $ make test_locuslink TEST_VERBOSE=1 I suspect the species test failure is caused by the previous one (although it actually shouldn't; that's why I also suspect that maybe you don't have innodb enabled). Make sure your database is empty and then run the species test again individually: $ make test_species TEST_VERBOSE=1 Let me know what the result is. -hilmar On Thursday, April 15, 2004, at 09:10 AM, Dave Howorth wrote: > I'm trying to set up bioperl-db and getting some errors in the make > test (full log is below). I just downloaded bioperl-db and biosql, > and just upgraded mysql (from 3.23.49). MySQL appears to run OK with > some existing databases. I just created a database (biosql_test) for > the tests and loaded the biosqldb-mysql.sql schema. > > I'm using: > bioperl 1.4 > bioperl-db (the README says "README,v 1.17 2003/08/22 12:44:23") > biosql (the README says "README,v 1.4 2003/09/21 05:01:23") > Perl 5.6.1 > MySQL 4.0.18 > Debian woody with many backports > > Does anybody have any idea what is causing the errors? > > Cheers, Dave > > ---- > > bioperl-db$ make test > PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib > -I/usr/lib/perl/5.6.1 -I/usr/share/perl/5.6.1 -e 'use Test::Harness > qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/*.t > t/cluster.......ok 155/160 > -------------------- WARNING --------------------- > MSG: failed to store one or more child objects for an instance of > class Bio::Cluster::UniGene (PK=1) > --------------------------------------------------- > t/cluster.......ok > t/comment.......ok > t/dbadaptor.....ok > t/dblink........ok > t/ensembl.......ok > t/fuzzy2........ok > t/genbank.......ok > t/locuslink.....NOK 24Can't call method "as_text" on an undefined > value at t/locuslink.t line 122, line 1. > t/locuslink.....FAILED tests 24, 29-110 > Failed 83/110 tests, 24.55% okay > t/ontology......ok > t/query.........ok > t/remove........ok > t/seqfeature....ok > t/simpleseq.....ok > t/species.......ok 5/65 > ------------- EXCEPTION ------------- > MSG: Unique key query in Bio::DB::BioSQL::SpeciesAdaptor returned 2 > rows instead of 1. Query was [name_class="scientific > name",binomial="Homo sapiens"] > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key > blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:960 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key > blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:856 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create > blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:183 > STACK Bio::DB::Persistent::PersistentObject::create > blib/lib/Bio/DB/Persistent/PersistentObject.pm:243 > STACK toplevel t/species.t:35 > > -------------------------------------- > t/species.......dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 6-65 > Failed 60/65 tests, 7.69% okay > t/swiss.........ok > Failed Test Stat Wstat Total Fail Failed List of Failed > ----------------------------------------------------------------------- > -------- > t/locuslink.t 110 83 75.45% 24 29-110 > t/species.t 255 65280 65 120 184.62% 6-65 > Failed 2/15 test scripts, 86.67% okay. 143/930 subtests failed, 84.62% > okay. > make: *** [test_dynamic] Error 11 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From muratem at eng.uah.edu Thu Apr 15 18:01:54 2004 From: muratem at eng.uah.edu (Mike Muratet) Date: Thu Apr 15 18:06:40 2004 Subject: [Bioperl-l] tiling hits to multiple alignment In-Reply-To: Message-ID: Greetings All Does anyone know how to reach Nigel? I had a question about MView (I use it quite a bit and find it very useful) but all of the email addresses on the web site were bouncing for 'user unknown'. Thanks Mike On Thu, 15 Apr 2004, Jurgen Pletinckx wrote: > If you are looking to generate a multiple alignment from > a blast report, Nigel Brown's Mview is worth looking into - > see http://mathbio.nimr.mrc.ac.uk/~nbrown/mview/ > > He gives some background on the tiling process in > http://mathbio.nimr.mrc.ac.uk/~nbrown/mview/blast/index.html > > -- > Jurgen Pletinckx > AlgoNomics NV > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From allenday at ucla.edu Thu Apr 15 19:50:02 2004 From: allenday at ucla.edu (Allen Day) Date: Thu Apr 15 20:54:43 2004 Subject: [Bioperl-l] TreeIO problem In-Reply-To: <20040415221900.283cb722.pik@sindominio.net> References: <20040415121320.744b2bb1.pik@sindominio.net> <20040415194540.58cfb2bd.pik@sindominio.net> <20040415214029.69225583.pik@sindominio.net> <20040415221900.283cb722.pik@sindominio.net> Message-ID: there is a problem with your newick input, or its interaction with the TreeIO subsystem. from the bioperl cvs, this code works: #!/usr/bin/perl -w use strict; use lib '.'; use Bio::TreeIO; use Data::Dumper; use SVG::Graph; my $in = new Bio::TreeIO(-file => './t/data/cysprot1b.newick', -format => 'newick'); my $out = new Bio::TreeIO(-file => '>pik_svg', -format => 'svggraph'); while( my $tree = $in->next_tree ) { warn $tree; my $svg_xml = $out->write_tree($tree); } however using the newick data you provide below, the while loop is never entered. here is the data i am using from the bioperl regression tests. ( CATH_RAT:0.31356, ( CATL_HUMAN:0.13938, CATL_RAT:0.12788) :0.18794, PAPA_CARPA:0.34410); -Allen On Thu, 15 Apr 2004, Mikel Ega wrote: > At the end I have produced a Dummy simple tree to see if distances > affected in anything: > > (A,(B,C),(D,E)) > > And it doesn't work either. > > The original tree was: > > (Pf-CNP4:0.07786,(((Tr-CNP3:1.04017,Hs-CNP:0.90128):0.58396, > ((((Tr-CNP1:0.20253,(Pf-CNP1:0.15012,(Om-CNP:0.12547, > Ol-CNP1:0.25526):0.03512):0.08989):0.14887,Omy-CNP1:0.36290):0.47164, > (Ol-CNP2:0.39033,Tr-CNP2:0.31133):0.71930):0.19555, > (Tr-BNP:0.20983,(Pf-BNP:0.15777,Om-BNP:0.17203):0.09696):0.98657):0.372 > 19):0.64073, Ol-CNP4:0.18286):0.10371,Tr-CNP4:0.09927) > > Find attached the file, > > Thanks > > ------------------------------------------------- > -->pik@lolita (Debian Sarge-Kernel 2.4.20) > > -->http://sindominio.net/~pik > > -->"Don Quijote se salva cuando se echa a > los caminos a ser apaleado" (Francisco Umbral) > ------------------------------------------------- > > > On Thu, 15 Apr 2004 11:45:39 -0700 (PDT) > Allen Day wrote: > > > send me your input file and i will try to replicate it here. > > > > On Thu, 15 Apr 2004, Mikel Ega wrote: > > > > > I have tried it with > > > > > > use SVG::Graph > > > > > > and the script works, but the input is void (the pik_svg file). > > > Perhaps I'm doing wrong something really obvious....here is the > > > script again: > > > > > > ------------------------------------------------------------------- > > > -----#!/usr/bin/perl -w > > > > > > use strict; > > > use SVG::Graph; > > > use Bio::TreeIO; > > > > > > my $in = new Bio::TreeIO(-file => 'pik_tree', -format => 'newick'); > > > my $out = new Bio::TreeIO(-file => '>pik_svg', -format => > > > 'svggraph'); > > > > > > while( my $tree = $in->next_tree ) { > > > my $svg_xml = $out->write_tree($tree); > > > } > > > ------------------------------------------------------------------- > > > ----- > > > > > > > > > Regards > > > > > > ------------------------------------------------- > > > -->pik@lolita (Debian Sarge-Kernel 2.4.20) > > > > > > -->http://sindominio.net/~pik > > > > > > -->"Don Quijote se salva cuando se echa a > > > los caminos a ser apaleado" (Francisco Umbral) > > > ------------------------------------------------- > > > > > > > > > On Thu, 15 Apr 2004 10:40:13 -0700 (PDT) > > > Allen Day wrote: > > > > > > > it looks like you need to in your script include SVG::Graph, a la > > > > > > > > use strict; > > > > use Bio::TreeIO; > > > > use SVG::Graph; > > > > #... > > > > > > > > if this works let me know. you shouldn't have to do this and i'll > > > > fix it in cvs. > > > > > > > > -allen > > > > > > > > > > > > On Thu, 15 Apr 2004, Jason Stajich wrote: > > > > > > > > > I don't really know - this is Allen's baby so he'll have to > > > > > chime in. > > > > > > > > > > -jason > > > > > On Thu, 15 Apr 2004, Mikel [ISO-8859-1] Ega)`)t1^Y^Q! wrote: > > > > > > > > > > > Yes, that's right; > > > > > > > > > > > > I forgot to install SVG::Graph, I have installed it and the > > > > > > script works... but the output file is void! > > > > > > > > > > > > the -w option doesn't give any clues. > > > > > > > > > > > > I have been having a brief look into SVG::Graph and > > > > > > Bio::TreeIO::svggraph and I cannot figure out what should be > > > > > > wrong. > > > > > > > > > > > > Regards. > > > > > > > > > > > > On Thu, 15 Apr 2004 12:44:14 -0400 (EDT) > > > > > > Jason Stajich wrote: > > > > > > > > > > > > > And you did install SVG::Graph... which pulls in a bunch of > > > > > > > dependancies: > > > > > > > > > > > > > > Math::Derivative > > > > > > > Math::Spline > > > > > > > Tree::DAG_Node > > > > > > > > > > > > > > > > > > > > > What does 'perldoc SVG::Graph' report? > > > > > > > > > > > > > > If I do the install via the cpan shell I get all the > > > > > > > dependancies too.-jason > > > > > > > > > > > > > > On Thu, 15 Apr 2004, Mikel [ISO-8859-1] Ega wrote: > > > > > > > > > > > > > > > Hello people; > > > > > > > > > > > > > > > > First of all, Bioperl is great. I have just started using > > > > > > > > it for one of my projects and I'm amazed. > > > > > > > > > > > > > > > > I have a problem with the TreeIO class. I just want to > > > > > > > > write a newick tree in SVG format, so I got this code from > > > > > > > > the api and put it in this little script: > > > > > > > > > > > > > > > > --------------------------------------------------------- > > > > > > > > ---------------#!/usr/bin/perl > > > > > > > > > > > > > > > > use Bio::TreeIO; > > > > > > > > > > > > > > > > my $in = new Bio::TreeIO(-file => 'input', -format => > > > > > > > > 'newick'); my $out = new Bio::TreeIO(-file => '>output', > > > > > > > > -format =>'svggraph'); > > > > > > > > > > > > > > > > while( my $tree = $in->next_tree ) { > > > > > > > > my $svg_xml = $out->write_tree($tree); > > > > > > > > } > > > > > > > > > > > > > > > > --------------------------------------------------------- > > > > > > > > --------------- > > > > > > > > > > > > > > > > And the following exception was given: > > > > > > > > > > > > > > > > --------------------------------------------------------- > > > > > > > > --------------- MSG: Failed to load module > > > > > > > > Bio::TreeIO::svggraph. Can't locate SVG/Graph.pm in @INC > > > > > > > > (@INC contains: > > > > > > > > /etc/perl/usr/local/lib/perl/5.8.3/usr/local/share/perl/5 > > > > > > > > .8.3/usr/lib/perl5/usr/share/perl5/usr/lib/perl/5.8 > > > > > > > > /usr/share/perl/5.8/usr/local/lib/site_perl .) > > > > > > > > at/usr/local/share/perl/5.8.3/Bio/TreeIO/svggraph.pm line > > > > > > > > 78. BEGIN failed--compilation aborted > > > > > > > > at/usr/local/share/perl/5.8.3/Bio/TreeIO/svggraph.pm line > > > > > > > > 78. Compilation failed in require at > > > > > > > > /usr/local/share/perl/5.8.3/Bio/Root/Root.pm line 394. > > > > > > > > > > > > > > > > STACK Bio::Root::Root::_load_module > > > > > > > > /usr/local/share/perl/5.8.3/Bio/Root/Root.pm:396 STACK > > > > > > > > (eval)/usr/local/share/perl/5.8.3/Bio/TreeIO.pm:227 STACK > > > > > > > > Bio::TreeIO::_load_format_module > > > > > > > > /usr/local/share/perl/5.8.3/Bio/TreeIO.pm:226 STACK > > > > > > > > Bio::TreeIO::new/usr/local/share/perl/5.8.3/Bio/TreeIO.pm > > > > > > > > :126 STACK > > > > > > > > toplevel./svg.pl:6--------------------------------------- > > > > > > > > --------------------------------- > > > > > > > > > > > > > > > > So I have installed all the SVG related modules via CPAN > > > > > > > > but I receive the same error, and I cannot figure out what > > > > > > > > should I do next. > > > > > > > > > > > > > > > > Thank you for your time, > > > > > > > > > > > > > > > > Mikel Ega?a. > > > > > > > > > > > > > > > > PS: I'm using bioperl 1.4 in Debian Sarge. > > > > > > > > > > > > > > > > ------------------------------------------------- > > > > > > > > -->pik@lolita (Debian Sarge-Kernel 2.4.20) > > > > > > > > > > > > > > > > -->http://sindominio.net/~pik > > > > > > > > > > > > > > > > -->"Don Quijote se salva cuando se echa a > > > > > > > > los caminos a ser apaleado" (Francisco Umbral) > > > > > > > > ------------------------------------------------- > > > > > > > > _______________________________________________ > > > > > > > > Bioperl-l mailing list > > > > > > > > Bioperl-l@portal.open-bio.org > > > > > > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > Jason Stajich > > > > > > > Duke University > > > > > > > jason at cgt.mc.duke.edu > > > > > > > > > > > > > > _______________________________________________ > > > > > > > Bioperl-l mailing list > > > > > > > Bioperl-l@portal.open-bio.org > > > > > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > > > > > > > > > ------------------------------------------------- > > > > > > -->pik@lolita (Debian Sarge-Kernel 2.4.20) > > > > > > > > > > > > -->http://sindominio.net/~pik > > > > > > > > > > > > -->"Don Quijote se salva cuando se echa a > > > > > > los caminos a ser apaleado" (Francisco Umbral) > > > > > > ------------------------------------------------- > > > > > > > > > > > > > > > > -- > > > > > Jason Stajich > > > > > Duke University > > > > > jason at cgt.mc.duke.edu > > > > > > > > > > > > > > ------------------------------------------------- > > > -->pik@lolita (Debian Sarge-Kernel 2.4.20) > > > > > > -->http://sindominio.net/~pik > > > > > > -->"Don Quijote se salva cuando se echa a > > > los caminos a ser apaleado" (Francisco Umbral) > > > ------------------------------------------------- > > > > > > ------------------------------------------------- > -->pik@lolita (Debian Sarge-Kernel 2.4.20) > > -->http://sindominio.net/~pik > > -->"Don Quijote se salva cuando se echa a > los caminos a ser apaleado" (Francisco Umbral) > ------------------------------------------------- > From lawuson_36 at hotmail.com Thu Apr 15 23:47:57 2004 From: lawuson_36 at hotmail.com (bradford) Date: Thu Apr 15 23:51:43 2004 Subject: [Bioperl-l] medications without perscriptions for you! Message-ID: <1082087277-9719@excite.com> mike1 buffy gofish hanna kathy jeanette james1 septembe dirk We've got the cheapest medications around!! http://informix.base4ds.com/s95/index.php?id=s95 cherry robinhoo utopia obiwan camping space tiffany abby ricky sbdc tiffany fugazi hazel promethe valhalla ruth jordan23 justin1 gray mailman percy garnet dolphins energy front242 nuggethello1 lady abby public research bach charity doom2 lloyd gofish prof tequila eugene No more updates: http://jeff.hotspringprices.com/mm/chair.php From dhoworth at mrc-lmb.cam.ac.uk Fri Apr 16 06:12:09 2004 From: dhoworth at mrc-lmb.cam.ac.uk (Dave Howorth) Date: Fri Apr 16 06:17:05 2004 Subject: [Bioperl-l] bioperl-db make test errors In-Reply-To: <35D1CA9A-8F17-11D8-A5EA-000A959EB4C4@gnf.org> References: <35D1CA9A-8F17-11D8-A5EA-000A959EB4C4@gnf.org> Message-ID: <407FB179.6070405@mrc-lmb.cam.ac.uk> Hilmar Lapp wrote: > To exclude the obvious: > - did you make sure that innodb is enabled in mysql? You have to > edit the config file to do that. On the mysql prompt, insert a record > into biodatabase, then issue a rollback. Is the record that you > inserted still there? Hi Hilmar, Never underestimate the stupidity of the general public :) I had modified the config file but forgotten to restart the server. Now it works. Thanks! I was curious as to why I got no warnings when I created the database so I looked in the logs in case my memory was playing tricks. No warnings there either. So I RTFM and discovered that MySQL silently reverts to MyISAM if it isn't configured for the table type you request (for version < 4.1.1). Perhaps it's worth adding your rollback test to the test suite or even to Bio::DB startup to protect fools against themselves? (I'll code the test if you wish). Thanks again, Dave -- Dave Howorth MRC Centre for Protein Engineering Hills Road, Cambridge, CB2 2QH 01223 252960 From dhoworth at mrc-lmb.cam.ac.uk Fri Apr 16 06:16:02 2004 From: dhoworth at mrc-lmb.cam.ac.uk (Dave Howorth) Date: Fri Apr 16 06:20:45 2004 Subject: [Bioperl-l] TreeIO problem In-Reply-To: References: <20040415121320.744b2bb1.pik@sindominio.net> <20040415194540.58cfb2bd.pik@sindominio.net> <20040415214029.69225583.pik@sindominio.net> <20040415221900.283cb722.pik@sindominio.net> Message-ID: <407FB262.8030408@mrc-lmb.cam.ac.uk> Allen Day wrote: > there is a problem with your newick input, or its interaction with the > TreeIO subsystem. from the bioperl cvs, this code works: The most obvious difference is that there is no semicolon at the end of both of Mikel's examples. That's an error and I believe that will be enough to stop it working. Cheers, Dave > > however using the newick data you provide below, the while loop is never > entered. here is the data i am using from the bioperl regression tests. > > ( > CATH_RAT:0.31356, > ( > CATL_HUMAN:0.13938, > CATL_RAT:0.12788) > :0.18794, > PAPA_CARPA:0.34410); > > -Allen > > On Thu, 15 Apr 2004, Mikel Ega wrote: > > >>At the end I have produced a Dummy simple tree to see if distances >>affected in anything: >> >>(A,(B,C),(D,E)) >> >>And it doesn't work either. >> >>The original tree was: >> >>(Pf-CNP4:0.07786,(((Tr-CNP3:1.04017,Hs-CNP:0.90128):0.58396, >>((((Tr-CNP1:0.20253,(Pf-CNP1:0.15012,(Om-CNP:0.12547, >>Ol-CNP1:0.25526):0.03512):0.08989):0.14887,Omy-CNP1:0.36290):0.47164, >>(Ol-CNP2:0.39033,Tr-CNP2:0.31133):0.71930):0.19555, >>(Tr-BNP:0.20983,(Pf-BNP:0.15777,Om-BNP:0.17203):0.09696):0.98657):0.372 >>19):0.64073, Ol-CNP4:0.18286):0.10371,Tr-CNP4:0.09927) -- Dave Howorth MRC Centre for Protein Engineering Hills Road, Cambridge, CB2 2QH 01223 252960 From josie21buttons at hotmail.com Fri Apr 16 19:47:39 2004 From: josie21buttons at hotmail.com (walter) Date: Fri Apr 16 06:47:16 2004 Subject: [Bioperl-l] Anonymous Valium, Soma, VIA-GRA. Message-ID: <1082159259-1241@excite.com> New OFFSHORE PHARMACY - Not a single medical question asked, guaranteed or it's free. Relaxants, Pain Relievers, & Anti-Depressants delivered discreetly in non-despcript packaging to your door, QUICKLY! 100% Private & NO QUESTIONS. Click here: http://homebrew.base4ds.com/s95/index.php?id=s95 No one needs to know but you. suzuki josiepromethe dodgers turbo arizona jan fun zenith jeanettecarolina safety whitney sapphire xxxx dasha From dhoworth at mrc-lmb.cam.ac.uk Fri Apr 16 10:57:24 2004 From: dhoworth at mrc-lmb.cam.ac.uk (Dave Howorth) Date: Fri Apr 16 11:02:07 2004 Subject: [Bioperl-l] bioperl-db & biosql documentation Message-ID: <407FF454.3000800@mrc-lmb.cam.ac.uk> I've just installed bioperl-db and thought I'd offer some comments about my experience as a contribution to the project. The installation went well (with the exception of a self-inflicted test failure) so my thoughts are centred around the documentation. There seem to be lots of (fairly) small files that describe different aspects of bioperl-db and biosql, particularly installation. They are all incomplete and all give slightly different instructions (e.g for the version of MySQL 3.23.? that is required). Most of them don't have dates or version numbers or authors or any other indication of their name or origin. It would be better to condense them into a smaller number of more comprehensive documents, IMO. From the point of view of a bioperl user, it isn't clear why it's necessary to go to three/four sites, download separate tarballs etc and read as many sets of documentation (biosql, bioperl-db, bioperl, cpan, mysql) to do what from the user's point of view should in an ideal world all have been transparently installed when 'bioperl' was installed. The current distribution mechanism seems to be designed more for the developers' convenience than the users'. Files ----- bioperl-db/INSTALL bioperl-db/README bioperl-db/README-MYSQL bioperl-db/docs/HOWTO-MySQL.html bioperl-db/docs/HOWTO-make_test.pod biosql-schema/INSTALL biosql-schema/README biosql-schema/doc/README biosql-schema/doc/biosql-ERD.pdf biosql-schema/doc/biosql.html biosql-schema/doc/schema-overview.txt biosql-schema/sql/README biosql-schema/sql/biosql-ora/README biosql-schema/sql/biosql-ora/INSTALL http://bioperl.org/Core/Latest/biodatabases.html Version numbers --------------- Why aren't there explicit version numbers? (in the name of the tar file, for example, or explicitly stated in the README or INSTALL files) The docs have a number of places where small improvements might be made: bioperl-db/INSTALL ------------------ 1/ Doesn't actually say how to install bioperl-db (ideally make Makefile.PL; make; make test; make install but in reality more complicated because the schema is shipped separately) 2/ It mentions DBHarness.markerdb.conf but it's not clear why. This file doesn't appear to be mentioned elsewhere. 3/ Within the conf scripts, these lines mystified me # The name of the database within bioperl-db # There is right now only one possible value: # 'biosql' for the biosql adaptors 'database' => 'biosql', It wasn't clear what the difference is from the previous dbname line. I changed the dbname to biosql_test (which is what I had created) and left database as biosql, and that worked but I don't know why. 4/ Refers to MySQL 3.23.52 5/ Discusses whether a pre-existing database should be used for testing. Allowing the bioperl-db test script to create a temporary database seems dangerous since it requires the user be given wide-ranging powers over any database (unless there's a way to allow a user to just create a database named '_test_*'). bioperl-db/docs/HOWTO-MySQL.html -------------------------------- 1/ Full marks for author, date and version number! 2/ Document is excellent at creating a warm fuzzy feeling so I understood what was going on. 3/ Refers to MySQL 3.23.41, which apparently worked!!! 4/ It does list 'make Makefile.PL; make; make install', but it omits 'make test'! (which would be after step 7, I guess) bioperl-db/docs/HOWTO-make_test.pod ----------------------------------- 1/ This says to copy the conf file to the bioperl-db home directory, whilst the INSTALL doc says to leave them in the bioperl-db/t directory (and that works) 2/ This file should be deleted and the content incorporated in the INSTALL doc, IMO. The point about a user name is a useful reminder. biosql-schema/INSTALL --------------------- 1/ Lots of good stuff about biosql 2/ Also includes stuff about bioperl, including hints about preloading the taxonomy tables that isn't available in the bioperl docs themselves as far as I can see. biosql-schema/README -------------------- 1/ Full marks for author, date and version number! 2/ Refers to MySQL 3.23.50 biosql-schema/doc/README ------------------------ 1/ This seems just to be a note about how the (obsolete) biosql.html was generated, so should be deleted (or stated directly in an updated version of biosql.html) biosql-schema/doc/biosql-ERD.pdf -------------------------------- 1/ A very useful document. 2/ I'm not sure how the version number ties in with that of the biosqldb-mysql.sql script, for example. biosql-schema/doc/biosql.html ----------------------------- 1/ This would be a useful document but it appears to be obsolete (again, no version number, but it's inconsistent with the SQL) biosql-schema/doc/schema-overview.txt ------------------------------------- 1/ This is a very useful file because it provides design description and rationale not found anywhere else. 2/ It appears to be obsolete though still useful (no version number) 3/ It could be improved, IMO, if the section headings matched those of the coloured blocks in the ERD and if diagrams of the relevant subsets of the ERD were used to illustrate it. biosql-schema/sql/README ------------------------ 1/ This file is short and contains some useful information; it's not clear why it isn't simply part of biosql-schema/README. http://bioperl.org/Core/Latest/biodatabases.html ------------------------------------------------ 1/ A useful overview. 2/ The link below is broken (the full stop shouldn't be part of the link): http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/?cvsroot=bioperl. 3/ The links to the Bio::DB::SQL::SeqAdaptor manpage, the Bio::DB::SQL::QueryConstraint manpage, the Bio::DB::SQL::CommentAdaptor manpage, and the Bio::DB::SQL::BioQuery manpage don't work. Just to be clear that this is meant to be constructive suggestions: a big thank you to everybody who has put in effort on these great projects. Thanks and regards, Dave -- Dave Howorth MRC Centre for Protein Engineering Hills Road, Cambridge, CB2 2QH 01223 252960 From brian_osborne at cognia.com Fri Apr 16 11:36:37 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Fri Apr 16 11:43:40 2004 Subject: [Bioperl-l] bioperl-db & biosql documentation In-Reply-To: <407FF454.3000800@mrc-lmb.cam.ac.uk> Message-ID: Dave, Very good suggestions, thank you. In fact my basic response to all this documentation was the same as yours. I will try to do what I can to simplify this collection of files but it may be that a single HOWTO is also part of the solution. Unfortunately I'm not the best person to do this because I'm not a regular user of these packages but I could do a decent first pass by trans-splicing existing files, then an expert/user would have to step in. Like you! ;-) Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Dave Howorth Sent: Friday, April 16, 2004 10:57 AM To: BioPerl Subject: [Bioperl-l] bioperl-db & biosql documentation I've just installed bioperl-db and thought I'd offer some comments about my experience as a contribution to the project. The installation went well (with the exception of a self-inflicted test failure) so my thoughts are centred around the documentation. There seem to be lots of (fairly) small files that describe different aspects of bioperl-db and biosql, particularly installation. They are all incomplete and all give slightly different instructions (e.g for the version of MySQL 3.23.? that is required). Most of them don't have dates or version numbers or authors or any other indication of their name or origin. It would be better to condense them into a smaller number of more comprehensive documents, IMO. From the point of view of a bioperl user, it isn't clear why it's necessary to go to three/four sites, download separate tarballs etc and read as many sets of documentation (biosql, bioperl-db, bioperl, cpan, mysql) to do what from the user's point of view should in an ideal world all have been transparently installed when 'bioperl' was installed. The current distribution mechanism seems to be designed more for the developers' convenience than the users'. Files ----- bioperl-db/INSTALL bioperl-db/README bioperl-db/README-MYSQL bioperl-db/docs/HOWTO-MySQL.html bioperl-db/docs/HOWTO-make_test.pod biosql-schema/INSTALL biosql-schema/README biosql-schema/doc/README biosql-schema/doc/biosql-ERD.pdf biosql-schema/doc/biosql.html biosql-schema/doc/schema-overview.txt biosql-schema/sql/README biosql-schema/sql/biosql-ora/README biosql-schema/sql/biosql-ora/INSTALL http://bioperl.org/Core/Latest/biodatabases.html Version numbers --------------- Why aren't there explicit version numbers? (in the name of the tar file, for example, or explicitly stated in the README or INSTALL files) The docs have a number of places where small improvements might be made: bioperl-db/INSTALL ------------------ 1/ Doesn't actually say how to install bioperl-db (ideally make Makefile.PL; make; make test; make install but in reality more complicated because the schema is shipped separately) 2/ It mentions DBHarness.markerdb.conf but it's not clear why. This file doesn't appear to be mentioned elsewhere. 3/ Within the conf scripts, these lines mystified me # The name of the database within bioperl-db # There is right now only one possible value: # 'biosql' for the biosql adaptors 'database' => 'biosql', It wasn't clear what the difference is from the previous dbname line. I changed the dbname to biosql_test (which is what I had created) and left database as biosql, and that worked but I don't know why. 4/ Refers to MySQL 3.23.52 5/ Discusses whether a pre-existing database should be used for testing. Allowing the bioperl-db test script to create a temporary database seems dangerous since it requires the user be given wide-ranging powers over any database (unless there's a way to allow a user to just create a database named '_test_*'). bioperl-db/docs/HOWTO-MySQL.html -------------------------------- 1/ Full marks for author, date and version number! 2/ Document is excellent at creating a warm fuzzy feeling so I understood what was going on. 3/ Refers to MySQL 3.23.41, which apparently worked!!! 4/ It does list 'make Makefile.PL; make; make install', but it omits 'make test'! (which would be after step 7, I guess) bioperl-db/docs/HOWTO-make_test.pod ----------------------------------- 1/ This says to copy the conf file to the bioperl-db home directory, whilst the INSTALL doc says to leave them in the bioperl-db/t directory (and that works) 2/ This file should be deleted and the content incorporated in the INSTALL doc, IMO. The point about a user name is a useful reminder. biosql-schema/INSTALL --------------------- 1/ Lots of good stuff about biosql 2/ Also includes stuff about bioperl, including hints about preloading the taxonomy tables that isn't available in the bioperl docs themselves as far as I can see. biosql-schema/README -------------------- 1/ Full marks for author, date and version number! 2/ Refers to MySQL 3.23.50 biosql-schema/doc/README ------------------------ 1/ This seems just to be a note about how the (obsolete) biosql.html was generated, so should be deleted (or stated directly in an updated version of biosql.html) biosql-schema/doc/biosql-ERD.pdf -------------------------------- 1/ A very useful document. 2/ I'm not sure how the version number ties in with that of the biosqldb-mysql.sql script, for example. biosql-schema/doc/biosql.html ----------------------------- 1/ This would be a useful document but it appears to be obsolete (again, no version number, but it's inconsistent with the SQL) biosql-schema/doc/schema-overview.txt ------------------------------------- 1/ This is a very useful file because it provides design description and rationale not found anywhere else. 2/ It appears to be obsolete though still useful (no version number) 3/ It could be improved, IMO, if the section headings matched those of the coloured blocks in the ERD and if diagrams of the relevant subsets of the ERD were used to illustrate it. biosql-schema/sql/README ------------------------ 1/ This file is short and contains some useful information; it's not clear why it isn't simply part of biosql-schema/README. http://bioperl.org/Core/Latest/biodatabases.html ------------------------------------------------ 1/ A useful overview. 2/ The link below is broken (the full stop shouldn't be part of the link): http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/?cvsroot=bioperl. 3/ The links to the Bio::DB::SQL::SeqAdaptor manpage, the Bio::DB::SQL::QueryConstraint manpage, the Bio::DB::SQL::CommentAdaptor manpage, and the Bio::DB::SQL::BioQuery manpage don't work. Just to be clear that this is meant to be constructive suggestions: a big thank you to everybody who has put in effort on these great projects. Thanks and regards, Dave -- Dave Howorth MRC Centre for Protein Engineering Hills Road, Cambridge, CB2 2QH 01223 252960 _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From skirov at utk.edu Fri Apr 16 13:00:13 2004 From: skirov at utk.edu (Stefan Kirov) Date: Fri Apr 16 13:04:57 2004 Subject: [Bioperl-l] small change to Bio::Align::Utilities Message-ID: <4080111D.9040604@utk.edu> Jason, Hope this does not break anything else... Just introduced "." as a possible gap character to be expected along with "-" in aa_to_dna_aln. -- Stefan Kirov From keh13 at po.cwru.edu Fri Apr 16 15:46:48 2004 From: keh13 at po.cwru.edu (Karen Hayden) Date: Fri Apr 16 15:51:29 2004 Subject: [Bioperl-l] blastz parser Message-ID: <40803828.70400@po.cwru.edu> Hello all, Is there a module to parse blastz output? Thanks, Karen -- Karen E. Hayden Dept. of Genetics/BRB 747A School of Medicine Case Western Reserve University 10900 Euclid Ave.(BUT FOR COURIER SERVICES USE: 2109 Adelbert Rd.) Cleveland, OH 44106-4955 phone: 216 368 1887 From jason at cgt.duhs.duke.edu Fri Apr 16 16:08:08 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Fri Apr 16 16:12:51 2004 Subject: [Bioperl-l] blastz parser In-Reply-To: <40803828.70400@po.cwru.edu> References: <40803828.70400@po.cwru.edu> Message-ID: Karen - You can convert the blastz lav output to axt or psl with Jim Kent's lavToPsl or lavToAxt. Bio::SearchIO can parse psl or axt, Bio::Tools::Blat can also parse psl output. (I think there is an off-by-one error in SearchIO::psl that Elliot M reported but it hasn't been fixed yet). -jason On Fri, 16 Apr 2004, Karen Hayden wrote: > Hello all, > Is there a module to parse blastz output? > > Thanks, > Karen > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From allenday at ucla.edu Sat Apr 17 04:31:49 2004 From: allenday at ucla.edu (Allen Day) Date: Sat Apr 17 05:36:27 2004 Subject: [Bioperl-l] new module: Bio::Tools::WebBlat Message-ID: added a new module to bioperl-live for running BLAT jobs from a UCSC CGI script. i didn't want to go to the hassle of setting up my own BLAT server, so here you go. Docs below, enjoy. -Allen NAME Bio::Tools::WebBlat - Run BLAT on UCSC CGI script SYNOPSIS my $webblat = Bio::Tools::WebBlat->new(); my $seq = Bio::Seq->new(display_id => 'foo' , seq => 'aataataat'); my $searchio = $webblat->create_searchio($seq); while(my $result = $searchio->next_result){ #process Bio::SearchIO::ResultI } DESCRIPTION Run BLAT at UCSC. The useful method in this class after instantiation is create_searchio. This factory method takes a Bio::Seq object as input, reformats it as Fasta, and sends it off to a CGI script running at www.genome.ucsc.edu. The resultant PSL embedded in HTML is HTML-stripped and used to construct a Bio::SearchIO, which is passed back to the user. AUTHOR Allen Day From dhoworth at mrc-lmb.cam.ac.uk Mon Apr 19 05:54:52 2004 From: dhoworth at mrc-lmb.cam.ac.uk (Dave Howorth) Date: Mon Apr 19 05:59:37 2004 Subject: [Bioperl-l] load_ontology/GO error Message-ID: <4083A1EC.7070708@mrc-lmb.cam.ac.uk> Hello again, I tried to use my shiny new bioperl_db installation to load GO but it failed with the error message below. I'm afraid it doesn't mean very much to me and my searches haven't turned up anything that demystified it, so I'd be grateful for any explanation or suggestions on how to fix the problem. Thanks, Dave biosql$ perl load_ontology.pl --dbname biosql_1 --dbuser bioperl --driver mysql --namespace "Gene Ontology" --format goflat --fmtargs "-defs_file,GO.defs" function.ontology process.ontology component.ontology Parsing input ... Loading ontology Gene Ontology: ... terms -------------------- WARNING --------------------- MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed, values were ("BBD_pathwayID:C1cyc","","","") FKs (1) Column 'name' cannot be null --------------------------------------------------- Could not store BBD_pathwayID:C1cyc (): ------------- EXCEPTION ------------- MSG: create: object (Bio::Ontology::GOterm) failed to insert or to be found by unique key STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/share/perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:207 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/share/perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:253 STACK Bio::DB::Persistent::PersistentObject::store /usr/local/share/perl/5.6.1/Bio/DB/Persistent/PersistentObject.pm:270 STACK (eval) load_ontology.pl:508 STACK toplevel load_ontology.pl:490 -------------------------------------- -- Dave Howorth MRC Centre for Protein Engineering Hills Road, Cambridge, CB2 2QH 01223 252960 From pvh at egenetics.com Mon Apr 19 06:10:38 2004 From: pvh at egenetics.com (Peter van Heusden) Date: Mon Apr 19 06:15:17 2004 Subject: [Bioperl-l] Re: ComparableI stuff In-Reply-To: <6FD44B24-8F13-11D8-A5EA-000A959EB4C4@gnf.org> References: <6FD44B24-8F13-11D8-A5EA-000A959EB4C4@gnf.org> Message-ID: <4083A59E.50505@egenetics.com> Hilmar Lapp wrote: > I was going to write a more detailed response but probably won't be > getting to it before Monday due to painful deadlines. Generally, I > have a number of issues with this. > > - On a very general level, basing equality on equal hash keys is > dangerous because it violates the standard definition of a hash key. > You construct it as a string most of the time and hence comparing keys > is meant as a short-cut for comparing objects, but I really would not > call it hash keys and at the same time assume equal objects iff equal > hash keys. > > - Defining object equality for complex objects is more a matter of > subjective judgment rather than having objective criteria that we can > define and impose on everybody. In fact, I think doing so is > dangerous, because it creates the false impression of obviating > people's need to make their own appropriate decision on when to call > objects equal and when not to. > > As an example, your hashkey() on SeqFeatureI uses the positional > information but leaves out the sequence on which it sits, leaves out > the source_tag(), and in fact leaves out the entire tag system. It > also leaves out a feature's annotation. This definition of equality > may be fine in some cases, but may also be completely inappropriate in > others. > Ok, valid criticism. But the I just noticed that the hashkey() documentation is wrong. I shouldn't say that hashkey() can stand in for equality, it can't. That's the job of the diff() method. The hashkey() method is just used to order SeqFeatureI objects so that the comparison of feature lists can be done. Probably a bad name for the method (a result of development history). > In biosql, as an example, it is completely inappropriate; biosql > defines two SeqFeature entries as equal that are on the same sequence, > have the same primary_tag, same source_tag, and are in the same > position in the sequence's feature array. The features' display_name > is irrelevant, as is the positional information. If I compared two > seqfeatures using the ComparableI interface, they may compare as > unequal and yet if I store them I'd get thrown out with a unique key > failure. Chado I believe has a slightly different definition of the > unique key and may take the positional information into account. > > As another example, for genbank/embl features it is also inappropriate > because it doesn't test for equality of attached annotations. Note > that you may define equality of two feature table entries in a genbank > record by them containing the same annotation regardless of the > annotations' order of appearance. I.e., comparing the annotation > arrays element by element would be too strict then. > Wait a sec... I compare annotations at the sequence level by comparing the (sorted) annotation lists. The process of sorting is meant to deal with the problem of order. > My point here is not that I would urge you to add all these properties > to the SeqFeatureI->diff implementation, because there may be use > cases for which your current implementation is perfectly fine. My > point is rather, I don't see the value of having one definition of > equality implemented in a way that doesn't allow others to coexist > when the one that is implemented is going to serve only a third of all > use cases. > > I guess one of my key problems is that in fact I don't understand what > the exact use case is. Apart from that, the implementation doesn't > seem to allow for multiple use cases, which will unequivocally result > in different implementations of equality having to peacefully co-exist. > > What I could rather envision as being useful is a design along > 'schemes', where you can swap in one 'equality scheme' for another > depending on what your needs are, and in which somebody who has a need > for a yet-unimplemented definition could add that implementation and > then swap it in. > Firstly, I think the question of the use case is the hub of our misunderstanding. The reason I wrote this stuff is that I want a way to check that what SeqIO reads off disk is complete and correct. My understanding is that a sequence file in a particular format unambigously defines what a sequence (with its associated annotations) is. Two formats with the same power (e.g. genbank and embl) describing the same entry should turn into the same sequence object. And secondly, if a sequence is read from disk and then written to disk again, the resulting sequence file should parse into the same sequence information. (At the moment this is not the case for Bioperl) This is all useful to me because I'm trying to write a set of tests to prove: does Bioperl do what it claims that it does? The current SeqIO tests focus on comparing values parsed from a given file against a set of 'known good values'. I feel that is a dangerous way to test because it focusses on a small number of test cases as opposed to a large range of possible real world data. So I decided to try and set a standard for how sequence parsing should behave, and that standard in my mind is that for a given format, a given set of attributes should be parseable and writeable in a predictable way. Ultimately this is all towards developing some way of 'validating' Bioperl, i.e. giving a kind of guarantee that where the documentation says it does this, it actually does do it. To do that, I need a way to enumerate as much as possible the expected behaviour, to put some kind of bounds on it in a fairly general sense. Does this make sense? Your idea about 'equality schemes' is interesting. So in this case you'd apply a scheme (a singleton object, I assume) to two sequences, and get a particular result? So the diff() methods I've written thus far would be within this class? Its another possible approach, I guess. I'd like to hear other people's ideas. Peter From pik at sindominio.net Thu Apr 15 13:50:03 2004 From: pik at sindominio.net (Mikel =?ISO-8859-1?B?RWdhYTlwZW4tYg==?=) Date: Mon Apr 19 06:55:16 2004 Subject: [Bioperl-l] TreeIO problem In-Reply-To: References: <20040415121320.744b2bb1.pik@sindominio.net> Message-ID: <20040415195003.02d2ace9.pik@sindominio.net> Yes, that's right; I forgot to install SVG::Graph, I have installed it and the script works... but the output file is void! the -w option doesn't give any clues. I have been having a brief look into SVG::Graph and Bio::TreeIO::svggraph and I cannot figure out what should be wrong. Regards. On Thu, 15 Apr 2004 12:44:14 -0400 (EDT) Jason Stajich wrote: > And you did install SVG::Graph... which pulls in a bunch of > dependancies: > > Math::Derivative > Math::Spline > Tree::DAG_Node > > > What does 'perldoc SVG::Graph' report? > > If I do the install via the cpan shell I get all the dependancies too. > -jason > > On Thu, 15 Apr 2004, Mikel [ISO-8859-1] Ega wrote: > > > Hello people; > > > > First of all, Bioperl is great. I have just started using it for one > > of my projects and I'm amazed. > > > > I have a problem with the TreeIO class. I just want to write a > > newick tree in SVG format, so I got this code from the api and put > > it in this little script: > > > > ------------------------------------------------------------------- > > -----#!/usr/bin/perl > > > > use Bio::TreeIO; > > > > my $in = new Bio::TreeIO(-file => 'input', -format => 'newick'); > > my $out = new Bio::TreeIO(-file => '>output', -format => > > 'svggraph'); > > > > while( my $tree = $in->next_tree ) { > > my $svg_xml = $out->write_tree($tree); > > } > > > > ------------------------------------------------------------------- > > ----- > > > > And the following exception was given: > > > > ------------------------------------------------------------------- > > ----- MSG: Failed to load module Bio::TreeIO::svggraph. Can't locate > > SVG/Graph.pm in @INC (@INC contains: /etc/perl > > /usr/local/lib/perl/5.8.3/usr/local/share/perl/5.8.3 /usr/lib/perl5 > > /usr/share/perl5/usr/lib/perl/5.8 /usr/share/perl/5.8 > > /usr/local/lib/site_perl .) > > at/usr/local/share/perl/5.8.3/Bio/TreeIO/svggraph.pm line 78. BEGIN > > failed--compilation aborted > > at/usr/local/share/perl/5.8.3/Bio/TreeIO/svggraph.pm line 78. > > Compilation failed in require at > > /usr/local/share/perl/5.8.3/Bio/Root/Root.pm line 394. > > > > STACK Bio::Root::Root::_load_module > > /usr/local/share/perl/5.8.3/Bio/Root/Root.pm:396 STACK (eval) > > /usr/local/share/perl/5.8.3/Bio/TreeIO.pm:227 STACK > > Bio::TreeIO::_load_format_module > > /usr/local/share/perl/5.8.3/Bio/TreeIO.pm:226 STACK Bio::TreeIO::new > > /usr/local/share/perl/5.8.3/Bio/TreeIO.pm:126 STACK toplevel > > ./svg.pl:6--------------------------------------------------------- > > --------------- > > > > So I have installed all the SVG related modules via CPAN but I > > receive the same error, and I cannot figure out what should I do > > next. > > > > Thank you for your time, > > > > Mikel Ega?a. > > > > PS: I'm using bioperl 1.4 in Debian Sarge. > > > > ------------------------------------------------- > > -->pik@lolita (Debian Sarge-Kernel 2.4.20) > > > > -->http://sindominio.net/~pik > > > > -->"Don Quijote se salva cuando se echa a > > los caminos a ser apaleado" (Francisco Umbral) > > ------------------------------------------------- > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l ------------------------------------------------- -->pik@lolita (Debian Sarge-Kernel 2.4.20) -->http://sindominio.net/~pik -->"Don Quijote se salva cuando se echa a los caminos a ser apaleado" (Francisco Umbral) ------------------------------------------------- -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040415/728dd1e4/attachment.bin From anunberg at oriongenomics.com Fri Apr 16 17:54:49 2004 From: anunberg at oriongenomics.com (Andrew Nunberg) Date: Mon Apr 19 06:55:18 2004 Subject: [Bioperl-l] Problem with Bio::Assembly::IO::ace Message-ID: When forcing reads into an empty assembly, which happens if you are assembly a single clone(genomic or ests) The contig names are not the normal Contig1 etc.., but instead are derived from read names eg. Trace_name-Contig The parser breaks on these contigs so I made the following change to Bio::Assembly::IO::ace.pm line 138 from (/^CO Contig(\d+) (\d+) (\d+) (\d+) (\w+)/) && do ... To ((/^CO Contig(\d+) (\d+) (\d+) (\d+) (\w+)/) or (/^CO (\S+)-Contig (\d+) (\d+) (\d+) (\w+)/)) && do ... This makes the contig the string (\S+) instead of the number (Contig(\d+) that follows Contig. Not sure what that will do downstream but for what I am doing seems to work -- Andrew Nunberg Bioinformagician Orion Genomics (314)-615-6989 www.oriongenomics.com From zhouyuwhu at hotmail.com Sat Apr 17 09:09:30 2004 From: zhouyuwhu at hotmail.com (Zhou Yu) Date: Mon Apr 19 06:55:21 2004 Subject: [Bioperl-l] how to use pipe in perl script? Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040417/5f0591d9/attachment.htm From avilella at ebi.ac.uk Mon Apr 19 07:27:29 2004 From: avilella at ebi.ac.uk (avilella) Date: Mon Apr 19 07:32:45 2004 Subject: [Bioperl-l] small change to Bio::Align::Utilities In-Reply-To: <4080111D.9040604@utk.edu> References: <4080111D.9040604@utk.edu> Message-ID: <1082374049.2520.63.camel@localhost.localdomain> On Fri, 2004-04-16 at 18:00, Stefan Kirov wrote: > Jason, > Hope this does not break anything else... Just introduced "." as a > possible gap character to be expected along with "-" in aa_to_dna_aln. Just to mention that, in some file formats, "." means "the same character as the first sequence", Albert. From paulo.david at netvisao.pt Mon Apr 19 07:30:48 2004 From: paulo.david at netvisao.pt (Paulo Almeida) Date: Mon Apr 19 07:33:26 2004 Subject: [Bioperl-l] how to use pipe in perl script? In-Reply-To: References: Message-ID: <4083B868.6040606@netvisao.pt> You can use the 'system' command to do something like this: system("program1 -infile filename | program2"); If that doesn't work for some reason, you could write the output of the first program to a file, and then open it with the second program. system("program1 -infile filename > output"); system ("program2 < output"); I hope that's what you wanted, I'm not sure I understood... -Paulo Almeida Zhou Yu wrote: > Hi, > > How to use pipe in a script, like redirecting the output of a program > to another program in a script? > > For example, I use this command "program1 -infile filename | program2" > in the command line, and how can I to do this in a script? > > Thanks! > * > Yu Zhou* > From ak at ebi.ac.uk Mon Apr 19 07:54:48 2004 From: ak at ebi.ac.uk (Andreas Kahari) Date: Mon Apr 19 07:59:32 2004 Subject: [Bioperl-l] how to use pipe in perl script? In-Reply-To: <4083B868.6040606@netvisao.pt> References: <4083B868.6040606@netvisao.pt> Message-ID: <20040419115448.GA2794@ebi.ac.uk> Another solution for another interpetation of the problem: If you want to do something like script1.pl | script2.pl Then script1.pl should write it's results to standard output (, the default for e.g. print()), and script2.pl should read its input from standard input (). And that's all there is to it. Andreas On Mon, Apr 19, 2004 at 12:30:48PM +0100, Paulo Almeida wrote: > You can use the 'system' command to do something like this: > > system("program1 -infile filename | program2"); > > If that doesn't work for some reason, you could write the output of the > first program to a file, and then open it with the second program. > > system("program1 -infile filename > output"); > system ("program2 < output"); > > I hope that's what you wanted, I'm not sure I understood... > -Paulo Almeida > > Zhou Yu wrote: > > >Hi, > > > >How to use pipe in a script, like redirecting the output of a program > >to another program in a script? > > > >For example, I use this command "program1 -infile filename | program2" > >in the command line, and how can I to do this in a script? > > > >Thanks! > >* > >Yu Zhou* > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- |}{}{| Andreas K?h?ri EMBL, European Bioinformatics Institute |{}{}| Wellcome Trust Genome Campus |}{}{| Ensembl Developer Hinxton, Cambridgeshire, CB10 1SD |{}{}| DAS Project Leader United Kingdom From MAILER-DAEMON at email.seznam.cz Mon Apr 19 08:58:26 2004 From: MAILER-DAEMON at email.seznam.cz (MAILER-DAEMON@email.seznam.cz) Date: Mon Apr 19 09:03:06 2004 Subject: [Bioperl-l] failure notice Message-ID: <200404191303.i3JD326B028091@portal.open-bio.org> Hi. This is the qmail-send program at email.seznam.cz. I'm afraid I wasn't able to deliver your message to the following addresses. This is a permanent error; I've given up. Sorry it didn't work out. : User "bcc_petr.farnik" does not exist! --- Below this line is a copy of the message. Return-Path: Received: (qmail 14626 invoked from network); 19 Apr 2004 12:58:10 -0000 Received: from unknown (HELO seznam.cz) (193.226.53.30) by fenix.go.seznam.cz with SMTP; 19 Apr 2004 12:58:10 -0000 From: bioperl-l@bioperl.org To: bcc_petr.farnik@seznam.cz Subject: Re: Your bill Date: Fri, 9 Apr 2004 13:52:03 +0300 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0012_00007C89.0000614C" X-Priority: 3 X-MSMail-Priority: Normal This is a multi-part message in MIME format. ------=_NextPart_000_0012_00007C89.0000614C Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit Your document is attached. ------=_NextPart_000_0012_00007C89.0000614C Content-Type: application/octet-stream; name="your_bill.pif" Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="your_bill.pif" TVqQAAMAAAAEAAAA//8AALgAAAAAAAAAQAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 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nQSDIIqydwsgfLJxCyBGslsLML/kv9O+TTxTgWZutKBxmg2EUmbJjois48bT+XgcjqZ1tJ0/ sdjqX2MUyXWmLE6acGlHkqwtTVSMO2Nj3MkmplwvmhxpMKYsXJnUfiRl0/xNbsQ08MlwfSz7 fz49BPhyFfXx9qQMSPiIZRqfZ8XE3TF6BMh1doIETVQqNQGEvUIJFEfBeRRsFn547B1OZY/x xFE54uglgybqlwj1svdOgrfzuO0VD956k8kDfS4OFv14//p9CPtKxSwqAtjS1+j+RTV9MoAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ------=_NextPart_000_0012_00007C89.0000614C-- From szhan at uoguelph.ca Mon Apr 19 09:28:22 2004 From: szhan at uoguelph.ca (szhan@uoguelph.ca) Date: Mon Apr 19 09:32:56 2004 Subject: [Bioperl-l] parse bl2seq report Message-ID: <1082381302.4083d3f69455c@webmail.uoguelph.ca> Hello, Bioperl experts: I want to parse an array of pairwise protein sequences alingments with BLAST bl2seq (standlone) in a loop. When there is no any "subject" (hit) in a bl2seq report, the program halted. Could you please help me catch the error and continue the loop? Your help will be highly appreciated! The partial code like this: @lucsarr is array of protein sequence objects for(my $k=0; $k<=$#lucsarr; $k++){ for(my $l=$k+1; $l<=$#lucsarr; $l++){ if($k<$l && $l<=$#lucsarr){ my $input1= $lucsarr[$k]; # take translated protein as an object my $input2= $lucsarr[$l]; # create local factory object my $factory = Bio::Tools::Run::StandAloneBlast->new('outfile' => 'bl2seq.out'); my $prgm='blastp'; # set parameter p for blastp $factory->p($prgm); # call executale bl2seq my $blast_report=$factory->bl2seq($input1, $input2); # retrieve the outputs from blast_report output file: bl2seq.out $blast_report->sbjctName; $blast_report->sbjctLength; print "Score\tBits\tID_percent\tE_value\tMatch\tPositive\tLength\n"; while(my $hsp = $blast_report->next_feature) {# get all alignments print $hsp->score, "\t"; print $hsp->bits, "\t"; print $hsp->percent, "\t"; print $hsp->P, "\t"; print $hsp->match, "\t"; print $hsp->positive, "\t"; print $hsp->length, "\n"; } } } } The output messages as follows: Score Bits ID_percent E_value Match Positive Length Can't call method "nextHSP" on unblessed reference at C:/Perl/site/lib/Bio/Tools /BPbl2seq.pm line 236, line 36. Again thank you in advance! Joshua From john.herbert at clinical-pharmacology.oxford.ac.uk Mon Apr 19 10:29:19 2004 From: john.herbert at clinical-pharmacology.oxford.ac.uk (john herbert) Date: Mon Apr 19 10:34:17 2004 Subject: [Bioperl-l] Primer3.pm problems. Message-ID: Hello Bioperlers I have been trying to use the BioPerl-run Primer3.pm module to run primer3. In doing so I think I have found 2 bugs that prevent it from working properly (I hope this is the right place to ask this). The line my $executable = $self->{'program_dir'}.$self->{'program'}; I think should be my $executable = $self->{'program_dir'}.$self->{'program_name'}; otherwise the primer3 executable is never found using the -path option in a call to the constructor my $primer3 = Bio::Tools::Run::Primer3->new(-path=>'/usr/mbin/primer3_core',-seq=>$seq, -outfile=>"temp.out"); The second is beyond my ability in BioPerl. basically the line my ($temphandle, $tempfile)=$self->io->tempfile; The temporary file never has any data in it. If you add the line `cat $tempfile`; following the line print $temphandle join "\n", @{$self->{'primer3_input'}}, "=\n"; The tempfile is empty but the variable @{$self->{'primer3_input'}} does contain data. I proved this by putting a crude temporary fix in with the lines $tempfile = "/tmp/primer3_temp_file.$$"; open(FH,">$tempfile") or die; print FH join "\n", @{$self->{'primer3_input'}}, "=\n"; close FH; Then everything works fine. I hope it is ok to point these out and please correct me if I am missing something. Kind regards, John. From skirov at utk.edu Mon Apr 19 10:40:28 2004 From: skirov at utk.edu (Stefan Kirov) Date: Mon Apr 19 10:45:01 2004 Subject: [Bioperl-l] small change to Bio::Align::Utilities In-Reply-To: <1082374049.2520.63.camel@localhost.localdomain> References: <4080111D.9040604@utk.edu> <1082374049.2520.63.camel@localhost.localdomain> Message-ID: <4083E4DC.2000302@utk.edu> Hi Albert, This certainly can be a problem. Actually I believe this problem should be handled by Bio::AlignIO, where each format specific parser will convert the gap character to a standard, "-" for example in the resulting Bio::Align::AliignI object.. And also account for cases like the one you mentioned. Then we can take my correction out. In any case aa_to_dna_aln did not care about . so you would end up with a shortened sequence. Stefan avilella wrote: >On Fri, 2004-04-16 at 18:00, Stefan Kirov wrote: > > >>Jason, >>Hope this does not break anything else... Just introduced "." as a >>possible gap character to be expected along with "-" in aa_to_dna_aln. >> >> > >Just to mention that, in some file formats, "." means "the same >character as the first sequence", > > Albert. > > > From hlapp at gmx.net Mon Apr 19 10:41:01 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon Apr 19 10:46:16 2004 Subject: [Bioperl-l] load_ontology/GO error In-Reply-To: <4083A1EC.7070708@mrc-lmb.cam.ac.uk> Message-ID: <9425F594-920F-11D8-8E20-000A959EB4C4@gmx.net> This is due to a bug in bioperl introduced shortly before the 1.4 release series. It is fixed on both main trunk and the 1.4 branch, but you need to get a cvs snapshot (of the branch, if you have 1.4 installed) because 1.4.1 has not been released yet. -holmar On Monday, April 19, 2004, at 02:54 AM, Dave Howorth wrote: > Hello again, > > I tried to use my shiny new bioperl_db installation to load GO but it > failed with the error message below. I'm afraid it doesn't mean very > much to me and my searches haven't turned up anything that demystified > it, so I'd be grateful for any explanation or suggestions on how to > fix the problem. > > Thanks, Dave > > biosql$ perl load_ontology.pl --dbname biosql_1 --dbuser bioperl > --driver mysql --namespace "Gene Ontology" --format goflat --fmtargs > "-defs_file,GO.defs" function.ontology process.ontology > component.ontology > Parsing input ... > Loading ontology Gene Ontology: > ... terms > > -------------------- WARNING --------------------- > MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed, values > were ("BBD_pathwayID:C1cyc","","","") FKs (1) > Column 'name' cannot be null > --------------------------------------------------- > Could not store BBD_pathwayID:C1cyc (): > > ------------- EXCEPTION ------------- > MSG: create: object (Bio::Ontology::GOterm) failed to insert or to be > found by unique key > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create > /usr/local/share/perl/5.6.1/Bio/DB/BioSQL/> BasePersistenceAdaptor.pm:207 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store > /usr/local/share/perl/5.6.1/Bio/DB/BioSQL/> BasePersistenceAdaptor.pm:253 > STACK Bio::DB::Persistent::PersistentObject::store > /usr/local/share/perl/5.6.1/Bio/DB/Persistent/PersistentObject.pm:270 > STACK (eval) load_ontology.pl:508 > STACK toplevel load_ontology.pl:490 > > -------------------------------------- > > -- > Dave Howorth > MRC Centre for Protein Engineering > Hills Road, Cambridge, CB2 2QH > 01223 252960 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From gll_21 at hotmail.com Mon Apr 19 16:51:08 2004 From: gll_21 at hotmail.com (harold) Date: Mon Apr 19 17:56:17 2004 Subject: [Bioperl-l] Prescr`ip`tion drugs without the p:re'sc`ri`pt'ion! (ymojdd) Message-ID: <1082407868-20371@excite.com> Best Prices on Painkillers like Ult`ram! Great Deals on Vali`um! Stop smoking with ZYBAN!! Click here to learn more about each: http://velvet.ty65trg.com/s95/index.php?id=s95 gambit jimbo user1 canced surf sunbird dan valentin buttons niki express alfred tina angels xxxx button impala mission katie vermont corrado trek christop oranges jared gordon From szhan at uoguelph.ca Mon Apr 19 21:59:26 2004 From: szhan at uoguelph.ca (szhan@uoguelph.ca) Date: Mon Apr 19 22:03:59 2004 Subject: [Bioperl-l] How to parse bl2seq report? Message-ID: <1082426366.408483fe1a650@webmail.uoguelph.ca> Hello, Bioperl experts: I want to parse an array of pairwise protein sequences alingments with BLAST bl2seq (standlone) in a loop. When there is no any "subject" (hit) in a bl2seq report, the program halted. Could you please help me catch the error and continue the loop? Your help will be highly appreciated! The partial code like this: @lucsarr is array of protein sequence objects for(my $k=0; $k<=$#lucsarr; $k++){ for(my $l=$k+1; $l<=$#lucsarr; $l++){ if($k<$l && $l<=$#lucsarr){ my $input1= $lucsarr[$k]; # take translated protein as an object my $input2= $lucsarr[$l]; # create local factory object my $factory = Bio::Tools::Run::StandAloneBlast->new('outfile' => 'bl2seq.out'); my $prgm='blastp'; # set parameter p for blastp $factory->p($prgm); # call executale bl2seq my $blast_report=$factory->bl2seq($input1, $input2); # retrieve the outputs from blast_report output file: bl2seq.out $blast_report->sbjctName; $blast_report->sbjctLength; print "Score\tBits\tID_percent\tE_value\tMatch\tPositive\tLength\n"; while(my $hsp = $blast_report->next_feature) {# get all alignments print $hsp->score, "\t"; print $hsp->bits, "\t"; print $hsp->percent, "\t"; print $hsp->P, "\t"; print $hsp->match, "\t"; print $hsp->positive, "\t"; print $hsp->length, "\n"; } } } } The output messages as follows: Score Bits ID_percent E_value Match Positive Length Can't call method "nextHSP" on unblessed reference at C:/Perl/site/lib/Bio/Tools /BPbl2seq.pm line 236, line 36. Again thank you in advance! Joshua From venkat at calmail.berkeley.edu Tue Apr 20 04:03:10 2004 From: venkat at calmail.berkeley.edu (Venky Nandagopal) Date: Tue Apr 20 04:07:41 2004 Subject: [Bioperl-l] Ensembl and Bio::DB::GFF Message-ID: Does anyone have experience (and scripts, maybe) to convert Ensembl mysql dumps to Bio::DB::GFF (and gbrowse) compatible GFFs or databases? Is there an easy way to do this? The genbank and embl files I found on the Ensembl ftp site dont have the annotations I want, so bp_genbank2gff.pl doesnt serve. I'm trying to get at the Anopheles genome in particular, though I think all their dumps have the same structure. Thanks for your time! Venky -- ___ Venky Nandagopal Graduate Student Eisen Lab UC Berkeley From matth at unsw.edu.au Tue Apr 20 04:55:37 2004 From: matth at unsw.edu.au (Matt Hope) Date: Tue Apr 20 05:00:12 2004 Subject: [Bioperl-l] Bioperl 1.4 on Debian In-Reply-To: <20040331002444.GG14934@iastate.edu> References: <404E10F4.5010300@burnham.org> <20040309190612.GB9004@bioinfo.ucr.edu> <20040331002444.GG14934@iastate.edu> Message-ID: <1082451337.8972.20.camel@uruk-hai.bioinformatics.unsw.edu.au> On Wed, 2004-03-31 at 10:24, D. Joe Anderson wrote: > I've filed a wishlist bug against the Debian bioperl package, in hopes that > the Debian maintainer can find the time to get 1.4 in: > > http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=241146 > > What would be especially sweet is if it makes it into sarge before it goes > stable. Thanks for (forcibly) bringing this to my attention. I was working on an updated package before. I'll have a sample ready, available for testing, on http://debian.bioinformatics.unsw.edu.au/ [ Most likely http://debian.bioinformatics.unsw.edu.au/pool/main/b/bioperl/ ] later this evening. -- Matt Hope Bioinformatics System Administrator University of New South Wales From paulo.david at netvisao.pt Tue Apr 20 05:03:55 2004 From: paulo.david at netvisao.pt (Paulo Almeida) Date: Tue Apr 20 05:06:28 2004 Subject: [Bioperl-l] How to parse bl2seq report? In-Reply-To: <1082426366.408483fe1a650@webmail.uoguelph.ca> References: <1082426366.408483fe1a650@webmail.uoguelph.ca> Message-ID: <4084E77B.8020006@netvisao.pt> Try enclosing the assignment of $blast_report in an 'if': if (my $blast_report=$factory->bl2seq($input1, $input2)){ while $blast_report->next_feature{ print hsp->score; } -Paulo Almeida szhan@uoguelph.ca wrote: >Hello, Bioperl experts: >I want to parse an array of pairwise protein sequences alingments with BLAST >bl2seq (standlone) in a loop. When there is no any "subject" (hit) in a bl2seq >report, the program halted. Could you please help me catch the error and >continue the loop? >Your help will be highly appreciated! > >The partial code like this: >@lucsarr is array of protein sequence objects >for(my $k=0; $k<=$#lucsarr; $k++){ > for(my $l=$k+1; $l<=$#lucsarr; $l++){ > if($k<$l && $l<=$#lucsarr){ > > my $input1= $lucsarr[$k]; # take translated protein as an object > my $input2= $lucsarr[$l]; > > # create local factory object > my $factory = Bio::Tools::Run::StandAloneBlast->new('outfile' >=> 'bl2seq.out'); > my $prgm='blastp'; # set parameter p for blastp > $factory->p($prgm); > # call executale bl2seq > my $blast_report=$factory->bl2seq($input1, $input2); > > # retrieve the outputs from blast_report output file: bl2seq.out > $blast_report->sbjctName; > $blast_report->sbjctLength; > >print "Score\tBits\tID_percent\tE_value\tMatch\tPositive\tLength\n"; > > while(my $hsp = $blast_report->next_feature) {# get all >alignments > print $hsp->score, "\t"; > print $hsp->bits, "\t"; > print $hsp->percent, "\t"; > print $hsp->P, "\t"; > print $hsp->match, "\t"; > print $hsp->positive, "\t"; > print $hsp->length, "\n"; > } > > } > } >} > >The output messages as follows: >Score Bits ID_percent E_value Match Positive Length >Can't call method "nextHSP" on unblessed reference at >C:/Perl/site/lib/Bio/Tools >/BPbl2seq.pm line 236, line 36. > >Again thank you in advance! >Joshua > From heikki at ebi.ac.uk Tue Apr 20 06:42:08 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Tue Apr 20 05:47:27 2004 Subject: [Bioperl-l] how to use pipe in perl script? In-Reply-To: <20040419115448.GA2794@ebi.ac.uk> References: <4083B868.6040606@netvisao.pt> <20040419115448.GA2794@ebi.ac.uk> Message-ID: <200404201042.08611.heikki@ebi.ac.uk> Zhou, My guess is that Andreas answered the right question but did not give enough details. I remember being confused on how to read from STDIN in perl. Here is an example oneliner that demonstates it. It helps if you remember that structure while(<>){...} can be invoked by using -n to perl: perl -le 'for (1..10) {print $_}' | perl -nle 'print "item $_"' -Heikki On Monday 19 Apr 2004 11:54, Andreas Kahari wrote: > Another solution for another interpetation of the problem: > > If you want to do something like > > script1.pl | script2.pl > > Then script1.pl should write it's results to standard output > (, the default for e.g. print()), and script2.pl should > read its input from standard input (). And that's all > there is to it. > > > Andreas > > On Mon, Apr 19, 2004 at 12:30:48PM +0100, Paulo Almeida wrote: > > You can use the 'system' command to do something like this: > > > > system("program1 -infile filename | program2"); > > > > If that doesn't work for some reason, you could write the output of the > > first program to a file, and then open it with the second program. > > > > system("program1 -infile filename > output"); > > system ("program2 < output"); > > > > I hope that's what you wanted, I'm not sure I understood... > > -Paulo Almeida > > > > Zhou Yu wrote: > > >Hi, > > > > > >How to use pipe in a script, like redirecting the output of a program > > >to another program in a script? > > > > > >For example, I use this command "program1 -infile filename | program2" > > >in the command line, and how can I to do this in a script? > > > > > >Thanks! > > >* > > >Yu Zhou* > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From sivan_online at yahoo.co.in Tue Apr 20 07:09:44 2004 From: sivan_online at yahoo.co.in (=?iso-8859-1?q?Sivakumar.K.C?=) Date: Tue Apr 20 07:14:19 2004 Subject: [Bioperl-l] Compilation error Message-ID: <20040420110944.47339.qmail@web8206.mail.in.yahoo.com> Dear Sir, i have downloaded current_run_stable.tar.gz from the site and followed the instructions in the file README. After that i tried to run a programme Clustalw.pl from bioperl-run-1.4/examples/pise show some error like...this.. Can't locate Bio/Root/Root.pm in @INC (@INC contains: /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/AnalysisFactory/Pise.pm line 148. BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/AnalysisFactory/Pise.pm line 148. Compilation failed in require at clustalw.pl line 2. BEGIN failed--compilation aborted at clustalw.pl line 2. Sir, please help me in rectifying the problem... hoping for a early reply.. with regards Sivakumar ===== ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Sivakumar K.C Bioinformatics Consultant Center for Bioinformatics and Computational biology Soundarya Buildings,Thiruvananthapuram, Kerala - 695001 ~~~~~~~~~~~~~~~ ________________________________________________________________________ Yahoo! India Matrimony: Find your partner online. http://yahoo.shaadi.com/india-matrimony/ From brian_osborne at cognia.com Tue Apr 20 07:35:15 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Tue Apr 20 07:41:51 2004 Subject: [Bioperl-l] Compilation error In-Reply-To: <20040420110944.47339.qmail@web8206.mail.in.yahoo.com> Message-ID: Sivakumar, Have you installed the bioperl package as well as the bioperl-run package? Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Sivakumar.K.C Sent: Tuesday, April 20, 2004 7:10 AM To: bioperl-l@bioperl.org Subject: [Bioperl-l] Compilation error Dear Sir, i have downloaded current_run_stable.tar.gz from the site and followed the instructions in the file README. After that i tried to run a programme Clustalw.pl from bioperl-run-1.4/examples/pise show some error like...this.. Can't locate Bio/Root/Root.pm in @INC (@INC contains: /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/AnalysisFactory/Pise.pm line 148. BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/AnalysisFactory/Pise.pm line 148. Compilation failed in require at clustalw.pl line 2. BEGIN failed--compilation aborted at clustalw.pl line 2. Sir, please help me in rectifying the problem... hoping for a early reply.. with regards Sivakumar ===== ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Sivakumar K.C Bioinformatics Consultant Center for Bioinformatics and Computational biology Soundarya Buildings,Thiruvananthapuram, Kerala - 695001 ~~~~~~~~~~~~~~~ ________________________________________________________________________ Yahoo! India Matrimony: Find your partner online. http://yahoo.shaadi.com/india-matrimony/ _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From heikki at ebi.ac.uk Tue Apr 20 08:41:00 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Tue Apr 20 07:46:18 2004 Subject: [Bioperl-l] Compilation error In-Reply-To: <20040420110944.47339.qmail@web8206.mail.in.yahoo.com> References: <20040420110944.47339.qmail@web8206.mail.in.yahoo.com> Message-ID: <200404201241.00569.heikki@ebi.ac.uk> Sivakumar, It looks like you have not either installed bioperl-core which the run needs or added it into your PERL5LIB environmental variable. The core is at http://bioperl.org/DIST/current_core_stable.tar.gz Modify as needed and put one of the following into you shell initalization file: ~/.bash_profile: export PERL5LIB='$HOME/src/bioperl-core:$HOME/src/bioperl-run' ~/.cshrc: setenv PERL5LIB '$HOME/src/bioperl-core:$HOME/src/bioperl-run' Yours, -Heikki On Tuesday 20 Apr 2004 11:09, Sivakumar.K.C wrote: > Dear Sir, > > i have downloaded current_run_stable.tar.gz from the > site and followed the instructions in the file README. > After that i tried to run a programme Clustalw.pl from > bioperl-run-1.4/examples/pise show some error > like...this.. > > Can't locate Bio/Root/Root.pm in @INC (@INC contains: > /usr/lib/perl5/5.8.0/i386-linux-thread-multi > /usr/lib/perl5/5.8.0 > /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.0 > /usr/lib/perl5/site_perl > /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.0 > /usr/lib/perl5/vendor_perl .) at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/AnalysisFactory/Pise.pm > line 148. > BEGIN failed--compilation aborted at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/AnalysisFactory/Pise.pm > line 148. > Compilation failed in require at clustalw.pl line 2. > BEGIN failed--compilation aborted at clustalw.pl line > 2. > > > Sir, please help me in rectifying the problem... > > hoping for a early reply.. > > with regards > Sivakumar > > > ===== > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > Sivakumar K.C > Bioinformatics Consultant > Center for Bioinformatics and Computational biology > Soundarya Buildings,Thiruvananthapuram, > Kerala - 695001 > ~~~~~~~~~~~~~~~ > > ________________________________________________________________________ > Yahoo! India Matrimony: Find your partner online. > http://yahoo.shaadi.com/india-matrimony/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From covitzp at mail.nih.gov Mon Apr 19 15:59:35 2004 From: covitzp at mail.nih.gov (Covitz, Peter (NIH/NCI)) Date: Tue Apr 20 07:57:17 2004 Subject: [Bioperl-l] caBIOperl Message-ID: <27C204BD76CBC142BA1AE46D62A8548E0A3BDA54@nihexchange9.nih.gov> Dear bioperl, I'd like to let you know that a new Perl API to the NCI's caBIO data management system has been released. Called "caBIOperl", it was designed with bioperl style in mind. At some point we'd like to contribute it directly to bioperl. caBIOperl is essentially a Perl version of the caBIO Java API. You can instantiate caBIO data objects directly as Perl objects, just like you can when working with caBIO in Java. Under the hood caBIOperl uses the caBIO SOAP-XML interface, but it parses all the XML and populates objects with data for you, so you don't have to deal with XML parsing. caBIOperl was developed by Shan Jiang, an SAIC employee working at the NCI Center for Bioinformatics. You can find caBIOperl on the caBIO section of the NCICB Download site: http://ncicb.nci.nih.gov/download Support requests for caBIOperl can be sent to ncicb@pop.nci.nih.gov . General discussion about caBIO, including caBIOperl, is conducted on this mailing list: http://list.nih.gov/archives/cabio_users.html Hope you like it, and we'd love to hear any feedback you may have. Sincerely, Peter Peter A. Covitz, Ph.D. Director, Bioinformatics Core Infrastructure NCI Center for Bioinformatics 6116 Executive Blvd. Suite 403 Rockville, MD 20852 Tel. 301-451-4385 covitzp@mail.nih.gov http://ncicb.nci.nih.gov From zhouyuwhu at hotmail.com Tue Apr 20 08:04:44 2004 From: zhouyuwhu at hotmail.com (Zhou Yu) Date: Tue Apr 20 08:09:15 2004 Subject: [Bioperl-l] how to use pipe in perl script? Message-ID: Thankls to all! I know what to do with your help!
Best wishes!

Yu Zhou
>From: Heikki Lehvaslaiho <heikki@ebi.ac.uk> >To: Paulo Almeida <paulo.david@netvisao.pt>, Zhou Yu <zhouyuwhu@hotmail.com>, bioperl-l@bioperl.org >Subject: Re: [Bioperl-l] how to use pipe in perl script? >Date: Tue, 20 Apr 2004 10:42:08 +0000 > >Zhou, > >My guess is that Andreas answered the right question but did not give enough >details. > >I remember being confused on how to read from STDIN in perl. Here is an >example oneliner that demonstates it. It helps if you remember that structure >while(<>){...} can be invoked by using -n to perl: > >perl -le 'for (1..10) {print $_}' | perl -nle 'print "item $_"' > > -Heikki > >On Monday 19 Apr 2004 11:54, Andreas Kahari wrote: > > Another solution for another interpetation of the problem: > > > > If you want to do something like > > > > script1.pl | script2.pl > > > > Then script1.pl should write it's results to standard output > > (<STDOUT>, the default for e.g. print()), and script2.pl should > > read its input from standard input (<STDIN>). And that's all > > there is to it. > > > > > > Andreas > > > > On Mon, Apr 19, 2004 at 12:30:48PM +0100, Paulo Almeida wrote: > > > You can use the 'system' command to do something like this: > > > > > > system("program1 -infile filename | program2"); > > > > > > If that doesn't work for some reason, you could write the output of the > > > first program to a file, and then open it with the second program. > > > > > > system("program1 -infile filename > output"); > > > system ("program2 < output"); > > > > > > I hope that's what you wanted, I'm not sure I understood... > > > -Paulo Almeida > > > > > > Zhou Yu wrote: > > > >Hi, > > > > > > > >How to use pipe in a script, like redirecting the output of a program > > > >to another program in a script? > > > > > > > >For example, I use this command "program1 -infile filename | program2" > > > >in the command line, and how can I to do this in a script? > > > > > > > >Thanks! > > > >* > > > >Yu Zhou* > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l@portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > >-- >______ _/ _/_____________________________________________________ > _/ _/ http://www.ebi.ac.uk/mutations/ > _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk > _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute > _/ _/ _/ Wellcome Trust Genome Campus, Hinxton > _/ _/ _/ Cambs. CB10 1SD, United Kingdom > _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 >___ _/_/_/_/_/________________________________________________________ >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l _________________________________________________________________ ÏíÓÃÊÀ½çÉÏ×î´óµÄµç×ÓÓʼþϵͳ¡ª MSN Hotmail¡£ http://www.hotmail.com From hlapp at gmx.net Tue Apr 20 11:58:01 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue Apr 20 12:02:38 2004 Subject: [Bioperl-l] failures on the stable branch Message-ID: <8010C371-92E3-11D8-9AE2-000A959EB4C4@gmx.net> On the latest update of the stable branch if you run the test suite you get a number of failures, some of them looking troubling to the uninitiated. Given that we point people at downloading the current stable branch as a means of getting bug fixes early, in my opinion we should not aim any lower than that on the stable branch *all* tests pass at *any* time, with no exceptions. Also, modules should not be added on the stable branch, let alone an API be altered. If you feel your module is warranted for being added to the branch as an exception, please *always* ask on the mailing list before adding it to the branch. -hilmar -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- The failures: Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------ ------- t/AlignIO.t 2 512 80 10 12.50% 76-80 t/DB.t 78 9 11.54% 79-87 t/SearchIO.t 1145 9 0.79% 1146-1154 t/cigarstring.t 255 65280 3 6 200.00% 1-3 I fixed the AlignIO failure by removing the failing format as it is an added one, as opposed to adding the missing module on the branch. I also fixed the SearchIO failures by fixing the number of tests. DB.t fails because it encounters more tests than announced. I don't know whether this is due to a query response having changed, or due to the connection failures. Note that unlike before these connection failures are reproducible and not intermittent. ok 62 # could not connect to Genbank ok 63 # could not connect to Genbank ok 64 # could not connect to Genbank ok 65 # could not connect to Genbank ok 66 # could not connect to Genbank ok 67 # could not connect to Genbank ok 68 # could not connect to Genbank ok 69 # could not connect to Genbank ok 70 # could not connect to Genbank ok 71 # could not connect to Genbank ok 72 # could not connect to Genbank ok 73 # could not connect to Genbank ok 74 # could not connect to Genbank ok 75 # could not connect to Genbank ok 76 # could not connect to Genbank ok 77 # could not connect to Genbank ok 78 # could not connect to Genbank t/AlignIO....................ok 75/80Bio::AlignIO: largemultifasta cannot be found Exception ------------- EXCEPTION ------------- MSG: Failed to load module Bio::AlignIO::largemultifasta. Can't locate Bio/Seq/LargeLocatableSeq.pm in @INC (@INC contains: t blib/arch blib/lib /System/Library/Perl/darwin /System/Library/Perl /sw/lib/perl5/5.6.0/darwin /sw/lib/perl5/5.6.0 /sw/lib/perl5/darwin /sw/lib/perl5 /Library/Perl/darwin /Library/Perl /Network/Library/Perl/darwin /Network/Library/Perl .) at blib/lib/Bio/AlignIO/largemultifasta.pm line 69, line 28. BEGIN failed--compilation aborted at blib/lib/Bio/AlignIO/largemultifasta.pm line 69, line 28. Compilation failed in require at blib/lib/Bio/Root/Root.pm line 394, line 28. STACK Bio::Root::Root::_load_module blib/lib/Bio/Root/Root.pm:396 STACK (eval) blib/lib/Bio/AlignIO.pm:420 STACK Bio::AlignIO::_load_format_module blib/lib/Bio/AlignIO.pm:419 STACK Bio::AlignIO::new blib/lib/Bio/AlignIO.pm:347 STACK toplevel t/AlignIO.t:283 -------------------------------------- For more information about the AlignIO system please see the AlignIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "next_aln" on an undefined value at t/AlignIO.t line 285, line 28. t/AlignIO....................dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 76-80 Failed 5/80 tests, 93.75% okay t/cigarstring................Can't use an undefined value as an ARRAY reference at blib/lib/Bio/Search/Hit/GenericHit.pm line 409, line 434. t/cigarstring................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-3 Failed 3/3 tests, 0.00% okay (* note: these are only warnings, although they don't leave you with comfort *) t/GFF........................ok 1/32Filehandle Symbol::GEN0 opened only for output at blib/lib/Bio/Root/IO.pm line 440. t/GFF........................ok 2/32Filehandle Symbol::GEN1 opened only for output at blib/lib/Bio/Root/IO.pm line 440. t/GFF........................ok t/GeneCoordinateMapper.......ok 71/113 -------------------- WARNING --------------------- MSG: sorted sublocation array requested but root location doesn't define seq_id (at least one sublocation does!) --------------------------------------------------- -------------------- WARNING --------------------- MSG: sorted sublocation array requested but root location doesn't define seq_id (at least one sublocation does!) --------------------------------------------------- t/GeneCoordinateMapper.......ok 98/113Use of uninitialized value in concatenation (.) at blib/lib/Bio/Coordinate/GeneMapper.pm line 814. t/GeneCoordinateMapper.......ok From jason at cgt.duhs.duke.edu Tue Apr 20 12:52:56 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Apr 20 12:57:47 2004 Subject: [Bioperl-l] failures on the stable branch In-Reply-To: <8010C371-92E3-11D8-9AE2-000A959EB4C4@gmx.net> References: <8010C371-92E3-11D8-9AE2-000A959EB4C4@gmx.net> Message-ID: On Tue, 20 Apr 2004, Hilmar Lapp wrote: > On the latest update of the stable branch if you run the test suite you > get a number of failures, some of them looking troubling to the > uninitiated. > > Given that we point people at downloading the current stable branch as > a means of getting bug fixes early, in my opinion we should not aim any > lower than that on the stable branch *all* tests pass at *any* time, > with no exceptions. Also, modules should not be added on the stable > branch, let alone an API be altered. > > If you feel your module is warranted for being added to the branch as > an exception, please *always* ask on the mailing list before adding it > to the branch. > > -hilmar > -- > ------------------------------------------------------------- > Hilmar Lapp email: lapp at gnf.org > GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 > ------------------------------------------------------------- > I'll take a look at some of these this week. I might have inadvertantly caused some of them, not sure. > The failures: > > Failed Test Stat Wstat Total Fail Failed List of Failed > ------------------------------------------------------------------------ > ------- > t/AlignIO.t 2 512 80 10 12.50% 76-80 > t/DB.t 78 9 11.54% 79-87 > t/SearchIO.t 1145 9 0.79% 1146-1154 > t/cigarstring.t 255 65280 3 6 200.00% 1-3 > > I fixed the AlignIO failure by removing the failing format as it is an > added one, as opposed to adding the missing module on the branch. I > also fixed the SearchIO failures by fixing the number of tests. > > DB.t fails because it encounters more tests than announced. I don't > know whether this is due to a query response having changed, or due to > the connection failures. Note that unlike before these connection > failures are reproducible and not intermittent. > > ok 62 # could not connect to Genbank > ok 63 # could not connect to Genbank > ok 64 # could not connect to Genbank > ok 65 # could not connect to Genbank > ok 66 # could not connect to Genbank > ok 67 # could not connect to Genbank > ok 68 # could not connect to Genbank > ok 69 # could not connect to Genbank > ok 70 # could not connect to Genbank > ok 71 # could not connect to Genbank > ok 72 # could not connect to Genbank > ok 73 # could not connect to Genbank > ok 74 # could not connect to Genbank > ok 75 # could not connect to Genbank > ok 76 # could not connect to Genbank > ok 77 # could not connect to Genbank > ok 78 # could not connect to Genbank > > > t/AlignIO....................ok 75/80Bio::AlignIO: largemultifasta > cannot be found > Exception > ------------- EXCEPTION ------------- > MSG: Failed to load module Bio::AlignIO::largemultifasta. Can't locate > Bio/Seq/LargeLocatableSeq.pm in @INC (@INC contains: t blib/arch > blib/lib /System/Library/Perl/darwin /System/Library/Perl > /sw/lib/perl5/5.6.0/darwin /sw/lib/perl5/5.6.0 /sw/lib/perl5/darwin > /sw/lib/perl5 /Library/Perl/darwin /Library/Perl > /Network/Library/Perl/darwin /Network/Library/Perl .) at > blib/lib/Bio/AlignIO/largemultifasta.pm line 69, line 28. > BEGIN failed--compilation aborted at > blib/lib/Bio/AlignIO/largemultifasta.pm line 69, line 28. > Compilation failed in require at blib/lib/Bio/Root/Root.pm line 394, > line 28. > > STACK Bio::Root::Root::_load_module blib/lib/Bio/Root/Root.pm:396 > STACK (eval) blib/lib/Bio/AlignIO.pm:420 > STACK Bio::AlignIO::_load_format_module blib/lib/Bio/AlignIO.pm:419 > STACK Bio::AlignIO::new blib/lib/Bio/AlignIO.pm:347 > STACK toplevel t/AlignIO.t:283 > > -------------------------------------- > > For more information about the AlignIO system please see the AlignIO > docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "next_aln" on an undefined value at t/AlignIO.t line > 285, line 28. > t/AlignIO....................dubious > Test returned status 2 (wstat 512, 0x200) > DIED. FAILED tests 76-80 > Failed 5/80 tests, 93.75% okay > > t/cigarstring................Can't use an undefined value as an ARRAY > reference at blib/lib/Bio/Search/Hit/GenericHit.pm line 409, > line 434. > t/cigarstring................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-3 > Failed 3/3 tests, 0.00% okay > > > > (* note: these are only warnings, although they don't leave you with > comfort *) > t/GFF........................ok 1/32Filehandle Symbol::GEN0 opened only > for output at blib/lib/Bio/Root/IO.pm line 440. > t/GFF........................ok 2/32Filehandle Symbol::GEN1 opened only > for output at blib/lib/Bio/Root/IO.pm line 440. > t/GFF........................ok I've tried to fix these - but perl doesn't let you ask if an already opened filehandle is opened for reading - I have a fix on the main trunk which traps the error though. > > t/GeneCoordinateMapper.......ok 71/113 > -------------------- WARNING --------------------- > MSG: sorted sublocation array requested but root location doesn't > define seq_id (at least one sublocation does!) > --------------------------------------------------- > > -------------------- WARNING --------------------- > MSG: sorted sublocation array requested but root location doesn't > define seq_id (at least one sublocation does!) > --------------------------------------------------- > t/GeneCoordinateMapper.......ok 98/113Use of uninitialized value in > concatenation (.) at blib/lib/Bio/Coordinate/GeneMapper.pm line 814. > t/GeneCoordinateMapper.......ok > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From electric21kramer at hotmail.com Wed Apr 21 10:22:39 2004 From: electric21kramer at hotmail.com (chang) Date: Tue Apr 20 21:22:05 2004 Subject: [Bioperl-l] Muscle Relaxers, Pain Relief and more.. Check it out! Message-ID: <1082557359-27535@excite.com> New OFFSHORE PHARMACY - Not a single medical question asked, guaranteed or it's free. Relaxants, Pain Relievers, & Anti-Depressants delivered discreetly in non-despcript packaging to your door, QUICKLY! 100% Private & NO QUESTIONS. Click here: http://arizona.ty65trg.com/s95/index.php?id=s95 No one needs to know but you. easter abbyswimming theatre love tigre bmw river midori racoontintin rugby groovy dexter genius lloyd From avilella at ebi.ac.uk Wed Apr 21 05:07:58 2004 From: avilella at ebi.ac.uk (avilella) Date: Wed Apr 21 05:13:27 2004 Subject: [Bioperl-l] Bio::AlignIO::phylip write_aln ignores line_length Message-ID: <1082538478.2492.10.camel@localhost.localdomain> Hi, I would like to confirm that the write_aln method in phylip doesn't take into account the value of line_length parameter. Is that right? Thanks, Albert. From malatorr at genoma.ciencias.uchile.cl Tue Apr 20 10:32:47 2004 From: malatorr at genoma.ciencias.uchile.cl (mariano latorre) Date: Wed Apr 21 07:37:20 2004 Subject: [Bioperl-l] bio::graphics problem Message-ID: <4085348F.8070004@genoma.ciencias.uchile.cl> I installed bioperl because I'm interested on using bio::graphics. The first time I try to install bioperl it says I have problems installing bio::graphics because I probably don't have GD or Text::Shellwords. It was not specific. Later I try installing GD: perl-GD-1.41-0.rh90.dag.i386.rpm And then Text-Shellwords-1.06 Then I tried again installing bioperl 1.4 using perl Make.PL make make install etc It said bio:graphics installed ok! But I still having problems...When I try the first example (****render_blast1.pl on http://bioperl.org/HOWTOs/html/Graphics-HOWTO.html**) with "perl -d" on a blast report I get this error: /[malatorr@myserver]$ cat blastX_report.txt | ./test.pl Loading DB routines from perl5db.pl version 1.19 Editor support available. Enter h or `h h' for help, or `man perldebug' for more help. main::(./test.pl:8): my $panel = Bio::Graphics::Panel->new(-length => 1000,-width => 800); /What could be wrong? Thank you. Mariano Latorre Universidad de Chile / / From bioperl at email.com Tue Apr 20 10:52:27 2004 From: bioperl at email.com (cr cd) Date: Wed Apr 21 07:37:22 2004 Subject: [Bioperl-l] bioperl-run on windows XP Message-ID: <20040420145227.319231536DC@ws3-1.us4.outblaze.com> An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040420/0d47dce0/attachment.htm From s.paul at surrey.ac.uk Tue Apr 20 19:36:31 2004 From: s.paul at surrey.ac.uk (S.Paul) Date: Wed Apr 21 07:37:24 2004 Subject: [Bioperl-l] statistics of sequences Message-ID: <06ae01c42730$50903cc0$2b6fe383@LTCEP1SP> Hi Everybody: I am pretty new to bioperl and am trying to find the statistics of the polarity of amino acids in the protein sequence eg. how many are polar, hydrophobic etc. I tried using the SeqStats to calculate the mol wt and the number of A and C but cannot calculate the number of hydrophobic acids present. I am enclosing the portion of the code. I would appreciate if anybody can offer any suggestions in this regard. ***************************************************************************************************************************** my $seq_stats = Bio::Tools::SeqStats->new($seq); my $weight = $seq_stats->get_mol_wt(); #note $weight is an array print " the weight is ", $$weight[0], "\n"; my $monomer_ref = $seq_stats->count_monomers(); print "Number of A\'s in sequence is $$monomer_ref{'A'} \n"; print "Number of C\'s in sequence is $$monomer_ref{'C'} \n"; print "Number of T\'s in sequence is $$monomer_ref{'T'} \n"; print "Number of G\'s in sequence is $$monomer_ref{'G'} \n"; print "\-----------------------------------------------\n"; my $oddcode_obj = Bio::Tools::OddCodes->new(-seq =>$seq); #returns the reference my $output1 = $oddcode_obj->charge(); my $output2 = $oddcode_obj->structural(); my $output3 = $oddcode_obj->chemical(); my $output4 = $oddcode_obj->functional(); my $output5= $oddcode_obj->hydrophobic(); #displays my $new_coding1 =$$output1; print "\nthe charge of the sequence is $new_coding1"; print "\-----------------------------------------------\n"; my $new_coding2 =$$output2; print "\nthe structural sequence $new_coding2"; print "\-----------------------------------------------\n"; my $new_coding3 =$$output3; print "\n the chemical structure is : $new_coding3"; print "\-----------------------------------------------\n"; my $new_coding4 =$$output4; print "\n the functional nature of the protein: $new_coding4"; print "\-----------------------------------------------\n"; my $new_coding5 =$$output5; print "\n the hydrophobic nature of the protein: $new_coding5"; ********************************************************************************************************************** Thanks Sujoy Paul Sujoy Paul, PRISE Centre, UniS, s.paul@surrey.ac.uk From heikki at ebi.ac.uk Wed Apr 21 08:35:52 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Wed Apr 21 07:41:18 2004 Subject: [Bioperl-l] Re: Bio::AlignIO::phylip write_aln ignores line_length In-Reply-To: <1082538478.2492.10.camel@localhost.localdomain> References: <1082538478.2492.10.camel@localhost.localdomain> Message-ID: <200404211235.54284.heikki@ebi.ac.uk> Albert, You are right, of course. Go ahead and commit your enhancements. -Heikki On Wednesday 21 Apr 2004 09:07, avilella wrote: > Hi, > > I would like to confirm that the write_aln method in phylip doesn't take > into account the value of line_length parameter. Is that right? > > Thanks, > > Albert. -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From pvh at egenetics.com Wed Apr 21 08:01:00 2004 From: pvh at egenetics.com (Peter van Heusden) Date: Wed Apr 21 08:05:38 2004 Subject: [Bioperl-l] Most used parts of Bioperl Message-ID: <4086627C.3090800@egenetics.com> Does anyone have a sense of what the most-used parts of Bioperl are? I imagine SeqIO, the core Seq object, but these are all guesses. I've had some ideas of trying to look for module names in the mailing list archives, or parsing info from the CVS repository, or looking at the Bugzilla database, but nothing definite. Any ideas welcome. Thanks, Peter From jason at cgt.duhs.duke.edu Wed Apr 21 08:34:01 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed Apr 21 08:38:36 2004 Subject: [Bioperl-l] Most used parts of Bioperl In-Reply-To: <4086627C.3090800@egenetics.com> References: <4086627C.3090800@egenetics.com> Message-ID: Bio::Root::Root and Bio::Root::IO are of course used very heavily, but not directly by users. I would say Bio::SearchIO, Bio::SeqIO, Bio::AlignIO are all used very heavily. I guess CVS + bugs might help you correlate how worked on a module is- but not clear what you want to do with the information. -jason On Wed, 21 Apr 2004, Peter van Heusden wrote: > Does anyone have a sense of what the most-used parts of Bioperl are? I > imagine SeqIO, the core Seq object, but these are all guesses. I've had > some ideas of trying to look for module names in the mailing list > archives, or parsing info from the CVS repository, or looking at the > Bugzilla database, but nothing definite. Any ideas welcome. > > Thanks, > Peter > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From dhoworth at mrc-lmb.cam.ac.uk Wed Apr 21 09:04:45 2004 From: dhoworth at mrc-lmb.cam.ac.uk (Dave Howorth) Date: Wed Apr 21 09:09:50 2004 Subject: [Bioperl-l] failures on the stable branch Message-ID: <4086716D.3090805@mrc-lmb.cam.ac.uk> On Tue, 20 Apr 2004, Hilmar Lapp wrote: >>On the latest update of the stable branch if you run the test suite you >>get a number of failures, some of them looking troubling to the >>uninitiated. I was the one having trouble. As previously discussed, I've just installed bioperl-db/biosql with my existing bioperl 1.4 installation and am trying to load the GO data. It failed because of problems in 1.4 and Hilmar advised me to get branch-1-4 from cvs. Yesterday Hilmar very kindly helped me through the process, because I'm a newbie to it, but it failed with the errors he described. I've just updated from CVS and unfortunately now get a different set of errors: Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/DB.t 78 9 11.54% 79-87 t/RestrictionIO.t 14 1 7.14% 10 t/TreeIO.t 41 1 2.44% 42 t/cigarstring.t 255 65280 3 6 200.00% 1-3 121 subtests skipped. make: *** [test_dynamic] Error 11 (the full log is at the end) What I still don't know is whether the release as it stands will work for me or not. I don't want to break my existing installation but I can't get on with my current work until bioperl-db/biosql is working. Do the DB failures matter? RestrictionIO didn't fail yesterday. It does now. But I'm pretty sure I don't need it. TreeIO didn't fail yesterday. It does now. And I do have existing code that uses it. I don't use cigarstring presently, though may do in future (DAS). I don't know what "make: *** [test_dynamic] Error 11" at the end means. >>Given that we point people at downloading the current stable branch as >>a means of getting bug fixes early, in my opinion we should not aim any >>lower than that on the stable branch *all* tests pass at *any* time, >>with no exceptions. Also, modules should not be added on the stable >>branch, let alone an API be altered. I'd like to second this plea. My work intersects with bioperl - there are certain specific parts of bioperl that are relevant to my work on protein structure classification and huge tranches that are irrelevant. I don't want to have to understand the irrelevant bits of bioperl just so I can decide whether its safe to install a broken release. It just adds insult to injury if the broken release is a patch branch that should be clearing test failures, not introducing new ones! Jason Stajich wrote: > I'll take a look at some of these this week. I might have inadvertantly > caused some of them, not sure. That would be great; as I say, I'm stuck until I can get a working system. Thanks, Dave PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib/perl/5.6.1 -I/usr/share/perl/5.6.1 -e 'use Test::Harness qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/*.t t/AAChange...................ok ... ok snipped t/Chain......................ok t/cigarstring................Can't use an undefined value as an ARRAY reference at blib/lib/Bio/Search/Hit/GenericHit.pm line 409, line 434. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-3 Failed 3/3 tests, 0.00% okay t/ClusterIO..................ok ... t/DBCUTG.....................ok 20/22 skipped: tests which require remote servers - set env variable BIOPERLDEBUG to test t/DBFasta....................ok t/DB......................... FAILED tests 79-87 Failed 9/78 tests, 88.46% okay (less 1 skipped test: 68 okay, 87.18%) t/DNAMutation................ok t/Domcut.....................ok 22/25 skipped: tests which require remote servers - set env variable BIOPERLDEBUG to test t/ECnumber...................ok ... t/ESEfinder..................ok 10/12 skipped: tests which require remote servers - set env variable BIOPERLDEBUG to test t/est2genome.................ok ... t/GDB........................ok t/GeneCoordinateMapper....... -------------------- WARNING --------------------- MSG: sorted sublocation array requested but root location doesn't define seq_id (at least one sublocation does!) --------------------------------------------------- -------------------- WARNING --------------------- MSG: sorted sublocation array requested but root location doesn't define seq_id (at least one sublocation does!) --------------------------------------------------- Use of uninitialized value in concatenation (.) or string at blib/lib/Bio/Coordinate/GeneMapper.pm line 814. ok t/Geneid.....................ok t/Genewise...................ok 2/51 skipped: t/Genomewise.................ok t/Genpred....................ok t/GFF........................Filehandle Symbol::GEN0 opened only for output at blib/lib/Bio/Root/IO.pm line 440. Filehandle Symbol::GEN1 opened only for output at blib/lib/Bio/Root/IO.pm line 440. ok t/GOR4.......................ok 8/11 skipped: tests which require remote servers - set env variable BIOPERLDEBUG to test t/GOterm.....................ok t/GuessSeqFormat.............ok t/hmmer......................ok t/HNN........................ok 10/13 skipped: tests which require remote servers - set env variable BIOPERLDEBUG to test t/Index......................ok ... t/MitoProt...................ok 5/8 skipped: tests which require remote servers - set env variable BIOPERLDEBUG to test t/Molphy.....................ok ... t/RefSeq.....................ok 10/13 skipped: tests which require remote servers - set env variable BIOPERLDEBUG to test t/Registry...................DB_File and BerkeleyDB not found. Skipping DB_File tests ok t/Relationship...............ok t/RelationshipType...........ok t/RemoteBlast................ok 4/6 skipped: to avoid timeout t/RepeatMasker...............ok t/RestrictionAnalysis........ok t/RestrictionEnzyme..........ok t/RestrictionIO..............Use of uninitialized value in string eq at blib/lib/Bio/Restriction/IO/withrefm.pm line 130, line 13. Use of uninitialized value in string eq at blib/lib/Bio/Restriction/IO/withrefm.pm line 130, line 24. FAILED test 10 Failed 1/14 tests, 92.86% okay t/RNAChange..................ok ... t/SeqFeature.................ok 6/74 skipped: tests which need the Bio::DB::GenBank module t/SeqIO......................ok 3/235 skipped: t/SeqPattern.................ok ... t/Sopma......................ok 12/15 skipped: tests which require remote servers - set env variable BIOPERLDEBUG to test t/Species....................ok ... t/Taxonomy...................ok 7/8 skipped: to avoid blocking t/Tempfile...................ok t/Term.......................ok t/Tools......................ok t/TreeIO.....................FAILED test 42 Failed 1/41 tests, 97.56% okay (less 1 skipped test: 39 okay, 95.12%) t/Tree.......................ok t/trim.......................ok t/tutorial...................Use of uninitialized value in print at blib/lib/bptutorial.pl line 4042, line 934. ok t/UCSCParsers................ok t/Unflattener2...............ok t/Unflattener................ok t/UniGene....................ok t/Variation_IO...............ok t/WABA.......................ok t/XEMBL_DB...................ok Failed 4/180 test scripts, 97.78% okay. -6/8314 subtests failed, 100.07% okay. Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/DB.t 78 9 11.54% 79-87 t/RestrictionIO.t 14 1 7.14% 10 t/TreeIO.t 41 1 2.44% 42 t/cigarstring.t 255 65280 3 6 200.00% 1-3 121 subtests skipped. make: *** [test_dynamic] Error 11 -- Dave Howorth MRC Centre for Protein Engineering Hills Road, Cambridge, CB2 2QH 01223 252960 From heikki at ebi.ac.uk Wed Apr 21 10:53:50 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Wed Apr 21 09:59:07 2004 Subject: [Bioperl-l] statistics of sequences In-Reply-To: <06ae01c42730$50903cc0$2b6fe383@LTCEP1SP> References: <06ae01c42730$50903cc0$2b6fe383@LTCEP1SP> Message-ID: <200404211453.51337.heikki@ebi.ac.uk> Sujou, You are on the right track to use OddCodes. The OddCode methods give you back a refrence to a plain string. (which, BTW, you can store into a specialized sequence object of type Bio::Seq::Meta) that can be manipulated using standard perl functions. Here are two possibilities: # 1. works without knowing the characters my %hash; for (split / */, $new_coding5) { $hash{$_}++; } for (keys %hash) { print $_, ": ", $hash{$_}, "\n"; } #2. you have to know what you are looking for my ($O) = $new_coding5 =~ tr/O//; print "O: $O\n"; my ($I) = $new_coding5 =~ tr/I//; print "I: $I\n"; ### There are more ways of doing the same thing, all depends on what you want to do with the data. Yours, -Heikki On Tuesday 20 Apr 2004 23:36, S.Paul wrote: > Hi Everybody: > > I am pretty new to bioperl and am trying to find the statistics of the > polarity of amino acids in the protein sequence eg. how many are polar, > hydrophobic etc. I tried using the SeqStats to calculate the mol wt and > the number of A and C but cannot calculate the number of hydrophobic acids > present. I am enclosing the portion of the code. I would appreciate if > anybody can offer any suggestions in this regard. > > *************************************************************************** >************************************************** my $seq_stats = > Bio::Tools::SeqStats->new($seq); > my $weight = $seq_stats->get_mol_wt(); > #note $weight is an array > print " the weight is ", $$weight[0], "\n"; > my $monomer_ref = $seq_stats->count_monomers(); > print "Number of A\'s in sequence is $$monomer_ref{'A'} \n"; > print "Number of C\'s in sequence is $$monomer_ref{'C'} \n"; > print "Number of T\'s in sequence is $$monomer_ref{'T'} \n"; > print "Number of G\'s in sequence is $$monomer_ref{'G'} \n"; > > > print "\-----------------------------------------------\n"; > my $oddcode_obj = Bio::Tools::OddCodes->new(-seq =>$seq); > #returns the reference > > my $output1 = $oddcode_obj->charge(); > my $output2 = $oddcode_obj->structural(); > my $output3 = $oddcode_obj->chemical(); > my $output4 = $oddcode_obj->functional(); > > my $output5= $oddcode_obj->hydrophobic(); > > #displays > my $new_coding1 =$$output1; > print "\nthe charge of the sequence is $new_coding1"; > > print "\-----------------------------------------------\n"; > > my $new_coding2 =$$output2; > print "\nthe structural sequence $new_coding2"; > print "\-----------------------------------------------\n"; > my $new_coding3 =$$output3; > print "\n the chemical structure is : $new_coding3"; > print "\-----------------------------------------------\n"; > my $new_coding4 =$$output4; > print "\n the functional nature of the protein: $new_coding4"; > print "\-----------------------------------------------\n"; > > my $new_coding5 =$$output5; > print "\n the hydrophobic nature of the protein: $new_coding5"; > > *************************************************************************** >******************************************* > > Thanks > > Sujoy Paul > Sujoy Paul, PRISE Centre, UniS, s.paul@surrey.ac.uk -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From redwards at utmem.edu Wed Apr 21 09:56:38 2004 From: redwards at utmem.edu (Rob Edwards) Date: Wed Apr 21 10:01:12 2004 Subject: [Bioperl-l] failures on the stable branch In-Reply-To: <4086716D.3090805@mrc-lmb.cam.ac.uk> References: <4086716D.3090805@mrc-lmb.cam.ac.uk> Message-ID: There is a thread about RestrictionIO test 14 failing back in January. http://bioperl.org/pipermail/bioperl-l/2004-January/014487.html I couldn't repeat the error, and no one could identify why that test failed, so it wasn't chased down. If you or anyone else has any clues let me know. There is also not a bugzilla report for it. Rob On Apr 21, 2004, at 8:04 AM, Dave Howorth wrote: > On Tue, 20 Apr 2004, Hilmar Lapp wrote: >>> On the latest update of the stable branch if you run the test suite >>> you >>> get a number of failures, some of them looking troubling to the >>> uninitiated. > > I was the one having trouble. As previously discussed, I've just > installed bioperl-db/biosql with my existing bioperl 1.4 installation > and am trying to load the GO data. It failed because of problems in 1.4 > and Hilmar advised me to get branch-1-4 from cvs. > > Yesterday Hilmar very kindly helped me through the process, because I'm > a newbie to it, but it failed with the errors he described. I've just > updated from CVS and unfortunately now get a different set of errors: > > Failed Test Stat Wstat Total Fail Failed List of Failed > ----------------------------------------------------------------------- > -------- > t/DB.t 78 9 11.54% 79-87 > t/RestrictionIO.t 14 1 7.14% 10 > t/TreeIO.t 41 1 2.44% 42 > t/cigarstring.t 255 65280 3 6 200.00% 1-3 > 121 subtests skipped. > make: *** [test_dynamic] Error 11 > > (the full log is at the end) > > What I still don't know is whether the release as it stands will work > for me or not. I don't want to break my existing installation but I > can't get on with my current work until bioperl-db/biosql is working. > > Do the DB failures matter? > > RestrictionIO didn't fail yesterday. It does now. But I'm pretty sure I > don't need it. > > TreeIO didn't fail yesterday. It does now. And I do have existing code > that uses it. > > I don't use cigarstring presently, though may do in future (DAS). > > I don't know what "make: *** [test_dynamic] Error 11" at the end means. > > >>> Given that we point people at downloading the current stable branch >>> as >>> a means of getting bug fixes early, in my opinion we should not aim >>> any >>> lower than that on the stable branch *all* tests pass at *any* time, >>> with no exceptions. Also, modules should not be added on the stable >>> branch, let alone an API be altered. > > I'd like to second this plea. My work intersects with bioperl - there > are certain specific parts of bioperl that are relevant to my work on > protein structure classification and huge tranches that are irrelevant. > I don't want to have to understand the irrelevant bits of bioperl > just > so I can decide whether its safe to install a broken release. > > It just adds insult to injury if the broken release is a patch branch > that should be clearing test failures, not introducing new ones! > > Jason Stajich wrote: >> I'll take a look at some of these this week. I might have >> inadvertantly >> caused some of them, not sure. > > That would be great; as I say, I'm stuck until I can get a working > system. > > Thanks, Dave > > > PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib > -I/usr/lib/perl/5.6.1 -I/usr/share/perl/5.6.1 -e 'use Test::Harness > qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/*.t > t/AAChange...................ok > ... ok snipped > t/Chain......................ok > t/cigarstring................Can't use an undefined value as an ARRAY > reference at blib/lib/Bio/Search/Hit/GenericHit.pm line 409, > line > 434. > dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-3 > Failed 3/3 tests, 0.00% okay > t/ClusterIO..................ok > ... > t/DBCUTG.....................ok > 20/22 skipped: tests which require remote servers - set env > variable BIOPERLDEBUG to test > t/DBFasta....................ok > t/DB......................... > FAILED tests 79-87 > Failed 9/78 tests, 88.46% okay (less 1 skipped test: 68 okay, > 87.18%) > t/DNAMutation................ok > t/Domcut.....................ok > 22/25 skipped: tests which require remote servers - set env > variable BIOPERLDEBUG to test > t/ECnumber...................ok > ... > t/ESEfinder..................ok > 10/12 skipped: tests which require remote servers - set env > variable BIOPERLDEBUG to test > t/est2genome.................ok > ... > t/GDB........................ok > t/GeneCoordinateMapper....... > -------------------- WARNING --------------------- > MSG: sorted sublocation array requested but root location doesn't > define > seq_id (at least one sublocation does!) > --------------------------------------------------- > > -------------------- WARNING --------------------- > MSG: sorted sublocation array requested but root location doesn't > define > seq_id (at least one sublocation does!) > --------------------------------------------------- > Use of uninitialized value in concatenation (.) or string at > blib/lib/Bio/Coordinate/GeneMapper.pm line 814. > ok > t/Geneid.....................ok > t/Genewise...................ok > 2/51 skipped: > t/Genomewise.................ok > t/Genpred....................ok > t/GFF........................Filehandle Symbol::GEN0 opened only for > output at blib/lib/Bio/Root/IO.pm line 440. > Filehandle Symbol::GEN1 opened only for output at > blib/lib/Bio/Root/IO.pm line 440. > ok > t/GOR4.......................ok > 8/11 skipped: tests which require remote servers - set env > variable BIOPERLDEBUG to test > t/GOterm.....................ok > t/GuessSeqFormat.............ok > t/hmmer......................ok > t/HNN........................ok > 10/13 skipped: tests which require remote servers - set env > variable BIOPERLDEBUG to test > t/Index......................ok > ... > t/MitoProt...................ok > 5/8 skipped: tests which require remote servers - set env > variable BIOPERLDEBUG to test > t/Molphy.....................ok > ... > t/RefSeq.....................ok > 10/13 skipped: tests which require remote servers - set env > variable BIOPERLDEBUG to test > t/Registry...................DB_File and BerkeleyDB not found. Skipping > DB_File tests > ok > t/Relationship...............ok > t/RelationshipType...........ok > t/RemoteBlast................ok > 4/6 skipped: to avoid timeout > t/RepeatMasker...............ok > t/RestrictionAnalysis........ok > t/RestrictionEnzyme..........ok > t/RestrictionIO..............Use of uninitialized value in string eq at > blib/lib/Bio/Restriction/IO/withrefm.pm line 130, line 13. > Use of uninitialized value in string eq at > blib/lib/Bio/Restriction/IO/withrefm.pm line 130, line 24. > FAILED test 10 > Failed 1/14 tests, 92.86% okay > t/RNAChange..................ok > ... > t/SeqFeature.................ok > 6/74 skipped: tests which need the Bio::DB::GenBank module > t/SeqIO......................ok > 3/235 skipped: > t/SeqPattern.................ok > ... > t/Sopma......................ok > 12/15 skipped: tests which require remote servers - set env > variable BIOPERLDEBUG to test > t/Species....................ok > ... > t/Taxonomy...................ok > 7/8 skipped: to avoid blocking > t/Tempfile...................ok > t/Term.......................ok > t/Tools......................ok > t/TreeIO.....................FAILED test 42 > Failed 1/41 tests, 97.56% okay (less 1 skipped test: 39 okay, > 95.12%) > t/Tree.......................ok > t/trim.......................ok > t/tutorial...................Use of uninitialized value in print at > blib/lib/bptutorial.pl line 4042, line 934. > ok > t/UCSCParsers................ok > t/Unflattener2...............ok > t/Unflattener................ok > t/UniGene....................ok > t/Variation_IO...............ok > t/WABA.......................ok > t/XEMBL_DB...................ok > Failed 4/180 test scripts, 97.78% okay. -6/8314 subtests failed, > 100.07% > okay. > Failed Test Stat Wstat Total Fail Failed List of Failed > ----------------------------------------------------------------------- > -------- > t/DB.t 78 9 11.54% 79-87 > t/RestrictionIO.t 14 1 7.14% 10 > t/TreeIO.t 41 1 2.44% 42 > t/cigarstring.t 255 65280 3 6 200.00% 1-3 > 121 subtests skipped. > make: *** [test_dynamic] Error 11 > > > -- > Dave Howorth > MRC Centre for Protein Engineering > Hills Road, Cambridge, CB2 2QH > 01223 252960 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From redwards at utmem.edu Wed Apr 21 09:59:37 2004 From: redwards at utmem.edu (Rob Edwards) Date: Wed Apr 21 10:04:10 2004 Subject: [Bioperl-l] Primer3.pm problems. In-Reply-To: References: Message-ID: <208A9D00-939C-11D8-A31D-000A959E1622@utmem.edu> On Apr 19, 2004, at 9:29 AM, john herbert wrote: > Hello Bioperlers > I have been trying to use the BioPerl-run Primer3.pm module to run > primer3. In doing so I think I have found 2 bugs that prevent it from > working properly (I hope this is the right place to ask this). This is exactly the right place to ask this question > > The line > my $executable = $self->{'program_dir'}.$self->{'program'}; > I think should be > my $executable = $self->{'program_dir'}.$self->{'program_name'}; > otherwise the primer3 executable is never found using the -path option > in a call to the constructor > my $primer3 = > Bio::Tools::Run::Primer3->new(-path=>'/usr/mbin/primer3_core',- > seq=>$seq, > -outfile=>"temp.out"); Looking at the code it appears that I have used either program or program_name to mean the same things at various times. I will check through the whole thing and correct all of them. Totally my mistake! > > The second is beyond my ability in BioPerl. basically the line > my ($temphandle, $tempfile)=$self->io->tempfile; > > The temporary file never has any data in it. If you add the line > `cat $tempfile`; following the line > print $temphandle join "\n", @{$self->{'primer3_input'}}, "=\n"; > The tempfile is empty but the variable @{$self->{'primer3_input'}} does > contain data. > > I proved this by putting a crude temporary fix in with the lines > $tempfile = "/tmp/primer3_temp_file.$$"; > open(FH,">$tempfile") or die; > print FH join "\n", @{$self->{'primer3_input'}}, "=\n"; > close FH; Part of this is also because I lack a detailed knowledge of the bioperl IO structure as witnessed by the next lines: # I can't figure out how to use either of these to write the results out. # neither work, what am I doing wrong or missing in the docs? # $self->{output}=$self->_initialize_io(-file=>$self->{'outfile'}); # $self->{output}=$self->io; # OK, for now, I will just do it myself, because I need this to check the parser :) open (OUT, ">".$self->{'_outfilename'}) || $self->throw("Can't open ".$self->{'_outfilename'}." for writing"); I'll try and figure this out while I am looking through program and program_name, but if anyone has a suggestion about the IO approach I'd be glad to hear it. Rob > Then everything works fine. > > I hope it is ok to point these out and please correct me if I am > missing something. > > Kind regards, > > John. > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From jason at cgt.duhs.duke.edu Wed Apr 21 10:01:38 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed Apr 21 10:06:15 2004 Subject: [Bioperl-l] failures on the stable branch In-Reply-To: <8010C371-92E3-11D8-9AE2-000A959EB4C4@gmx.net> References: <8010C371-92E3-11D8-9AE2-000A959EB4C4@gmx.net> Message-ID: These are due to problems with Bio::DB::Query::GenBank setting the env variable BIOPERLDEBUG=1 will give more information. > ok 62 # could not connect to Genbank > ok 63 # could not connect to Genbank > ok 64 # could not connect to Genbank > ok 65 # could not connect to Genbank > ok 66 # could not connect to Genbank > ok 67 # could not connect to Genbank > ok 68 # could not connect to Genbank > ok 69 # could not connect to Genbank > ok 70 # could not connect to Genbank > ok 71 # could not connect to Genbank > ok 72 # could not connect to Genbank > ok 73 # could not connect to Genbank > ok 74 # could not connect to Genbank > ok 75 # could not connect to Genbank > ok 76 # could not connect to Genbank > ok 77 # could not connect to Genbank > ok 78 # could not connect to Genbank > > > t/AlignIO....................ok 75/80Bio::AlignIO: largemultifasta > cannot be found > Exception > ------------- EXCEPTION ------------- > MSG: Failed to load module Bio::AlignIO::largemultifasta. Can't locate > Bio/Seq/LargeLocatableSeq.pm in @INC (@INC contains: t blib/arch > blib/lib /System/Library/Perl/darwin /System/Library/Perl > /sw/lib/perl5/5.6.0/darwin /sw/lib/perl5/5.6.0 /sw/lib/perl5/darwin > /sw/lib/perl5 /Library/Perl/darwin /Library/Perl > /Network/Library/Perl/darwin /Network/Library/Perl .) at > blib/lib/Bio/AlignIO/largemultifasta.pm line 69, line 28. > BEGIN failed--compilation aborted at > blib/lib/Bio/AlignIO/largemultifasta.pm line 69, line 28. > Compilation failed in require at blib/lib/Bio/Root/Root.pm line 394, > line 28. > > STACK Bio::Root::Root::_load_module blib/lib/Bio/Root/Root.pm:396 > STACK (eval) blib/lib/Bio/AlignIO.pm:420 > STACK Bio::AlignIO::_load_format_module blib/lib/Bio/AlignIO.pm:419 > STACK Bio::AlignIO::new blib/lib/Bio/AlignIO.pm:347 > STACK toplevel t/AlignIO.t:283 > > -------------------------------------- > > For more information about the AlignIO system please see the AlignIO > docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "next_aln" on an undefined value at t/AlignIO.t line > 285, line 28. > t/AlignIO....................dubious > Test returned status 2 (wstat 512, 0x200) > DIED. FAILED tests 76-80 > Failed 5/80 tests, 93.75% okay > > t/cigarstring................Can't use an undefined value as an ARRAY > reference at blib/lib/Bio/Search/Hit/GenericHit.pm line 409, > line 434. > t/cigarstring................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-3 > Failed 3/3 tests, 0.00% okay > fixed > > > (* note: these are only warnings, although they don't leave you with > comfort *) > t/GFF........................ok 1/32Filehandle Symbol::GEN0 opened only > for output at blib/lib/Bio/Root/IO.pm line 440. > t/GFF........................ok 2/32Filehandle Symbol::GEN1 opened only > for output at blib/lib/Bio/Root/IO.pm line 440. > t/GFF........................ok > Added code from main trunk to quiet this local $^W=0; unless some has another way to see if fh is readable. > t/GeneCoordinateMapper.......ok 71/113 > -------------------- WARNING --------------------- > MSG: sorted sublocation array requested but root location doesn't > define seq_id (at least one sublocation does!) > --------------------------------------------------- > > -------------------- WARNING --------------------- > MSG: sorted sublocation array requested but root location doesn't > define seq_id (at least one sublocation does!) > --------------------------------------------------- > t/GeneCoordinateMapper.......ok 98/113Use of uninitialized value in > concatenation (.) at blib/lib/Bio/Coordinate/GeneMapper.pm line 814. > t/GeneCoordinateMapper.......ok fixed - this was a problem on main trunk too. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From jason at cgt.duhs.duke.edu Wed Apr 21 10:06:55 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed Apr 21 10:11:32 2004 Subject: [Bioperl-l] Primer3.pm problems. In-Reply-To: <208A9D00-939C-11D8-A31D-000A959E1622@utmem.edu> References: <208A9D00-939C-11D8-A31D-000A959E1622@utmem.edu> Message-ID: On Wed, 21 Apr 2004, Rob Edwards wrote: > > On Apr 19, 2004, at 9:29 AM, john herbert wrote: > > > Hello Bioperlers > > I have been trying to use the BioPerl-run Primer3.pm module to run > > primer3. In doing so I think I have found 2 bugs that prevent it from > > working properly (I hope this is the right place to ask this). > > This is exactly the right place to ask this question > > > > > The line > > my $executable = $self->{'program_dir'}.$self->{'program'}; > > I think should be > > my $executable = $self->{'program_dir'}.$self->{'program_name'}; > > otherwise the primer3 executable is never found using the -path option > > in a call to the constructor > > my $primer3 = > > Bio::Tools::Run::Primer3->new(-path=>'/usr/mbin/primer3_core',- > > seq=>$seq, > > -outfile=>"temp.out"); and rob - I think you want to call $self->program_dir and $self->program so they can overriden as well - that's why I set up the Base Class to have these methods. > > Looking at the code it appears that I have used either program or > program_name to mean the same things at various times. I will check > through the whole thing and correct all of them. Totally my mistake! > > > > > > The second is beyond my ability in BioPerl. basically the line > > my ($temphandle, $tempfile)=$self->io->tempfile; > > > > The temporary file never has any data in it. If you add the line > > `cat $tempfile`; following the line > > print $temphandle join "\n", @{$self->{'primer3_input'}}, "=\n"; > > The tempfile is empty but the variable @{$self->{'primer3_input'}} does > > contain data. > > > > I proved this by putting a crude temporary fix in with the lines > > $tempfile = "/tmp/primer3_temp_file.$$"; > > open(FH,">$tempfile") or die; > > print FH join "\n", @{$self->{'primer3_input'}}, "=\n"; > > close FH; > > Part of this is also because I lack a detailed knowledge of the bioperl > IO structure as witnessed by the next lines: > > # I can't figure out how to use either of these to write the results > out. > # neither work, what am I doing wrong or missing in the docs? > > # $self->{output}=$self->_initialize_io(-file=>$self->{'outfile'}); > # $self->{output}=$self->io; > > # OK, for now, I will just do it myself, because I need this to check > the parser :) > open (OUT, ">".$self->{'_outfilename'}) || $self->throw("Can't open > ".$self->{'_outfilename'}." for writing"); > > I'll try and figure this out while I am looking through program and > program_name, but if anyone has a suggestion about the IO approach I'd > be glad to hear it. > > Rob > > > > > Then everything works fine. > > > > I hope it is ok to point these out and please correct me if I am > > missing something. > > > > Kind regards, > > > > John. > > > > > > > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From brian_osborne at cognia.com Wed Apr 21 08:17:07 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Wed Apr 21 10:18:08 2004 Subject: [Bioperl-l] bioperl-run on windows XP In-Reply-To: <20040420145227.319231536DC@ws3-1.us4.outblaze.com> Message-ID: To whom it may concern, First, it doesn?t seem that you installed the bioperl package, you?ll need it in order to run the bioperl-run package. Second, the way that you installed bioperl-run, extracting and copying, doesn?t resemble any of the usual ways one would install bioperl, or perl and perl modules generally, my guess is that it?s more-or-less guaranteed that you?ll encounter various problems if you take this approach. I suggest that you take a look at the INSTALL.WIN file and choose one of the approaches described there. To answer your question, yes, you can run bioperl on XP. Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of cr cd Sent: Tuesday, April 20, 2004 10:52 AM To: bioperl-l@portal.open-bio.org Subject: [Bioperl-l] bioperl-run on windows XP Hi, all: This is my first time post, thank you for your attention and any suggestion is greatly appreciated. I just wonder if all modules of bioperl-run can work properly on wondows XP system. I tried ClustalW.pm, ProtPars.pm and ProtDist.pm. ClustalW module works fine after I copy clustalw.exe into my working folder. But ProtPars and ProtDist modules not work even if ProtPars.exe and ProtDist.exe works fine in my woking folder. Any suggestions? Thank you so much. Attached: A. Steps I took to install Bioperl-run: 1. download bioperl-run-1.4 (current_run_stable.tar.gz) from http://www.bioperl.org/Core/Latest/index.shtml. 2. Copy current_run_stable.tar.gz to my folder /bioperl_run and extract this gz file. 3. Copy \bioperl_run\bioperl-run-1.4\Bio\Tools\Run (folder) to C:\Perl\site\lib\Bio\Tools and replace the old folder Run, so that in current Run folder there are many new modules that I wish to use such as Alignment::TCoffee.pm. B. My code: use Bio::Tools::Run::Phylo::Phylip::ProtPars; my $tree_factory = Bio::Tools::Run::Phylo::Phylip::ProtPars->new(idlength=>30,threshold=>10); my $tree = $tree_factory->run("./folder/file.phy"); C. Error message: 'protpars.exe' is not recognized as an internal or external command, operable program or batch file. ------------- EXCEPTION ------------- MSG: Protpars did not create treefile correctly STACK Bio::Tools::Run::Phylo::Phylip::ProtPars::_run C:/Perl/site/lib/Bio/Tools/ Run/Phylo/Phylip/ProtPars.pm:348 STACK Bio::Tools::Run::Phylo::Phylip::ProtPars::run C:/Perl/site/lib/Bio/Tools/R un/Phylo/Phylip/ProtPars.pm:279 STACK toplevel Align_from_db.pl:169 -- __________________________________________________________ Sign-up for Ads Free at Mail.com http://www.mail.com/?sr=signup From andreas.boehm at virchow.uni-wuerzburg.de Wed Apr 21 10:16:22 2004 From: andreas.boehm at virchow.uni-wuerzburg.de (Andreas Boehm) Date: Wed Apr 21 10:20:53 2004 Subject: [Bioperl-l] bio::graphics problem In-Reply-To: <20040420145227.319231536DC@ws3-1.us4.outblaze.com> References: <20040420145227.319231536DC@ws3-1.us4.outblaze.com> Message-ID: <40868236.7050808@virchow.uni-wuerzburg.de> Marianno, > I get this error: this is not an error. > > /[malatorr@myserver]$ cat blastX_report.txt | ./test.pl > > Loading DB routines from perl5db.pl version 1.19 > Editor support available. > > Enter h or `h h' for help, or `man perldebug' for more help. > > main::(./test.pl:8): my $panel = Bio::Graphics::Panel->new(-length => 1000,-width => 800); > > /What could be wrong? You started perl with its integrated debugger, meaning perl waits for you to step through the program. That means, my $panel = Bio::Graphics::Panel->new(-length .. is your first executable statement in the script you started. In the debugger, you can step by entering "n" (without quotes) to the next statement or continue by entering "c". Enter "h" for more help or read one of the perl bibles, like the camel book. regards, Andreas M. Boehm Protein Mass Spectrometry and Functional Proteomics Group Rudolf-Virchow-Center for Experimental Biomedicine Versbacher Str. 9 97078 W?rzburg Tel. +49 (0) 931-201 48728 FAX. +49 (0) 931-201 48123 Email: andreas.boehm@virchow.uni-wuerzburg.de http://www.virchow-zentrum.uni-wuerzburg.de/ From pvh at egenetics.com Wed Apr 21 10:20:03 2004 From: pvh at egenetics.com (Peter van Heusden) Date: Wed Apr 21 10:24:56 2004 Subject: [Bioperl-l] Most used parts of Bioperl In-Reply-To: References: <4086627C.3090800@egenetics.com> Message-ID: <40868313.3010606@egenetics.com> Jason Stajich wrote: >Bio::Root::Root and Bio::Root::IO are of course used very heavily, but not >directly by users. > >I would say Bio::SearchIO, Bio::SeqIO, Bio::AlignIO are all used very >heavily. > >I guess CVS + bugs might help you correlate how worked on a module is- but >not clear what you want to do with the information. > > > The reason I want to know this stuff is to prioritise my work in the Bioperl software validation project I'm working on. Peter From dhoworth at mrc-lmb.cam.ac.uk Wed Apr 21 12:00:09 2004 From: dhoworth at mrc-lmb.cam.ac.uk (Dave Howorth) Date: Wed Apr 21 12:05:22 2004 Subject: [Bioperl-l] failures on the stable branch In-Reply-To: References: <8010C371-92E3-11D8-9AE2-000A959EB4C4@gmx.net> Message-ID: <40869A89.3070909@mrc-lmb.cam.ac.uk> Jason Stajich wrote: > These are due to problems with Bio::DB::Query::GenBank > > setting the env variable BIOPERLDEBUG=1 will give more information. > > >>ok 62 # could not connect to Genbank >>ok 63 # could not connect to Genbank >>ok 64 # could not connect to Genbank >>ok 65 # could not connect to Genbank >>ok 66 # could not connect to Genbank >>ok 67 # could not connect to Genbank >>ok 68 # could not connect to Genbank >>ok 69 # could not connect to Genbank >>ok 70 # could not connect to Genbank >>ok 71 # could not connect to Genbank >>ok 72 # could not connect to Genbank >>ok 73 # could not connect to Genbank >>ok 74 # could not connect to Genbank >>ok 75 # could not connect to Genbank >>ok 76 # could not connect to Genbank >>ok 77 # could not connect to Genbank >>ok 78 # could not connect to Genbank When I set BIOPERLDEBUG=1 I see: t/DB.........................Warning: Couldn't connect to complete GenBank query tests! ------------- EXCEPTION ------------- MSG: Error from Genbank: Range operation produced no results STACK Bio::DB::Query::GenBank::_parse_response Bio/DB/Query/GenBank.pm:267 STACK Bio::DB::Query::WebQuery::_run_query Bio/DB/Query/WebQuery.pm:268 STACK Bio::DB::Query::GenBank::count Bio/DB/Query/GenBank.pm:225 STACK (eval) t/DB.t:251 STACK toplevel t/DB.t:245 -------------------------------------- FAILED tests 79-87 Failed 9/78 tests, 88.46% okay (less 1 skipped test: 68 okay, 87.18%) I'm not sure why I see different results to you. I think what you're telling me is that I don't need to worry about this failure of db.t as long as I don't want to access GenBank. Is that right? Also, if I've understood you right, I'm not sure why the db.t test fails when BIOPERLDEBUG=0 when most (all?) other tests just skip the tests and output a warning like: t/DBCUTG.....................ok 20/22 skipped: tests which require remote servers - set env variable BIOPERLDEBUG to test Cheers, Dave -- Dave Howorth MRC Centre for Protein Engineering Hills Road, Cambridge, CB2 2QH 01223 252960 From khan at cshl.edu Wed Apr 21 11:50:18 2004 From: khan at cshl.edu (Khan, Sohail) Date: Wed Apr 21 12:14:29 2004 Subject: [Bioperl-l] Parsing a Genbank file to get the Comment line. Message-ID: <5F7E863301E72846B90A4CEBB15EAE661F5A8E@exch02> Hello Bioperl Experts, I have just started to use bioperl. I want to parse a Genbank flat file and retrieve only the comment line from each record. Any suggestion is greatly appreciated. Thanks Sohail Khan Scientific Programmer COLD SPRING HARBOR LABORATORY Genome Research Center 500 Sunnyside Boulevard Woodbury, NY 11797 (516)422-4076 From dhoworth at mrc-lmb.cam.ac.uk Wed Apr 21 12:22:12 2004 From: dhoworth at mrc-lmb.cam.ac.uk (Dave Howorth) Date: Wed Apr 21 12:32:34 2004 Subject: [Bioperl-l] Makefile.PL and cvs.bioperl.org Message-ID: <40869FB4.3040608@mrc-lmb.cam.ac.uk> Based on my experience, I'd like to suggest the following changes to make it easier for neophytes to patch a bioperl release: On http://cvs.bioperl.org ------------------------- At the bottom of the page, add an example on how to patch an existing installation. Or refer to somewhere else that does. Specifically give an example of the use of tags and explain where to find the upgrade/install instructions (I previously installed bioperl from CPAN so I had no idea how to use the cvs system. The page asks "Do you really want to be here?" to which my answer is "No, but I have to be because of bugs", and I think the page should address that audience). e.g.: "To patch an existing release, find the cvs tag of the appropriate branch (need to describe how!!) then type: cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/bioperl \ checkout -r branch-1-4 bioperl-live Then follow the normal install instructions in the INSTALL document in the top level directory (probably need more here!!!)" In Makefile.PL -------------- It picked up a missing dependency on GD::SVG and on SVG, but it failed to pick up on a dependency on SVG::Graph. I'd also suggest that where Makefile.PL prints out: "Enjoy the rest of bioperl, which you can use after going 'make install'" it could increase the warm fuzziness if it was expanded to say: "You can install the external packages now and then rerun 'make Makefile.PL' or just enjoy the rest of bioperl, which you can use after going 'make install'." Cheers, Dave -- Dave Howorth MRC Centre for Protein Engineering Hills Road, Cambridge, CB2 2QH 01223 252960 From jason at cgt.duhs.duke.edu Wed Apr 21 12:34:45 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed Apr 21 12:39:16 2004 Subject: [Bioperl-l] failures on the stable branch In-Reply-To: <40869A89.3070909@mrc-lmb.cam.ac.uk> References: <8010C371-92E3-11D8-9AE2-000A959EB4C4@gmx.net> <40869A89.3070909@mrc-lmb.cam.ac.uk> Message-ID: On Wed, 21 Apr 2004, Dave Howorth wrote: > Jason Stajich wrote: > > These are due to problems with Bio::DB::Query::GenBank > > > > setting the env variable BIOPERLDEBUG=1 will give more information. > > > > > >>ok 62 # could not connect to Genbank > >>ok 63 # could not connect to Genbank > >>ok 64 # could not connect to Genbank > >>ok 65 # could not connect to Genbank > >>ok 66 # could not connect to Genbank > >>ok 67 # could not connect to Genbank > >>ok 68 # could not connect to Genbank > >>ok 69 # could not connect to Genbank > >>ok 70 # could not connect to Genbank > >>ok 71 # could not connect to Genbank > >>ok 72 # could not connect to Genbank > >>ok 73 # could not connect to Genbank > >>ok 74 # could not connect to Genbank > >>ok 75 # could not connect to Genbank > >>ok 76 # could not connect to Genbank > >>ok 77 # could not connect to Genbank > >>ok 78 # could not connect to Genbank > > When I set BIOPERLDEBUG=1 I see: > > t/DB.........................Warning: Couldn't connect to complete > GenBank query tests! > > ------------- EXCEPTION ------------- > MSG: Error from Genbank: Range operation produced no results > STACK Bio::DB::Query::GenBank::_parse_response Bio/DB/Query/GenBank.pm:267 > STACK Bio::DB::Query::WebQuery::_run_query Bio/DB/Query/WebQuery.pm:268 > STACK Bio::DB::Query::GenBank::count Bio/DB/Query/GenBank.pm:225 > STACK (eval) t/DB.t:251 > STACK toplevel t/DB.t:245 > > -------------------------------------- > > > FAILED tests 79-87 > Failed 9/78 tests, 88.46% okay (less 1 skipped test: 68 okay, > 87.18%) > > > I'm not sure why I see different results to you. This is what I see as well. > > I think what you're telling me is that I don't need to worry about this > failure of db.t as long as I don't want to access GenBank. Is that right? > It works in general but for some reason the specific range query that is in the tests is failing. I will try and fix it at some point but I don't really have a burning desire to do it right now. Or maybe Lincoln will have a chance to look - presumably the date range query syntax changes at Entrez. > Also, if I've understood you right, I'm not sure why the db.t test fails > when BIOPERLDEBUG=0 when most (all?) other tests just skip the tests and > output a warning like: > > t/DBCUTG.....................ok > 20/22 skipped: tests which require remote servers - set env > variable BIOPERLDEBUG to test > not important, but if you want to know why its because those tests didn't implement a respect for this variable - no time to get into it - but that aspect of tests has not been standardized and some modules don't even have debugging code if you turn verbose on anyways. > Cheers, Dave > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From jason at cgt.duhs.duke.edu Wed Apr 21 12:35:59 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed Apr 21 12:40:29 2004 Subject: [Bioperl-l] Makefile.PL and cvs.bioperl.org In-Reply-To: <40869FB4.3040608@mrc-lmb.cam.ac.uk> References: <40869FB4.3040608@mrc-lmb.cam.ac.uk> Message-ID: On Wed, 21 Apr 2004, Dave Howorth wrote: > Based on my experience, I'd like to suggest the following changes to > make it easier for neophytes to patch a bioperl release: > > > On http://cvs.bioperl.org > ------------------------- > > At the bottom of the page, add an example on how to patch an existing > installation. Or refer to somewhere else that does. Specifically give an > example of the use of tags and explain where to find the upgrade/install > instructions (I previously installed bioperl from CPAN so I had no idea > how to use the cvs system. The page asks "Do you really want to be > here?" to which my answer is "No, but I have to be because of bugs", and > I think the page should address that audience). e.g.: > > "To patch an existing release, find the cvs tag of the appropriate > branch (need to describe how!!) then type: > cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/bioperl \ > checkout -r branch-1-4 bioperl-live > Then follow the normal install instructions in the INSTALL document > in the top level directory (probably need more here!!!)" > > > In Makefile.PL > -------------- > > It picked up a missing dependency on GD::SVG and on SVG, but it failed > to pick up on a dependency on SVG::Graph. > > I'd also suggest that where Makefile.PL prints out: > "Enjoy the rest of bioperl, which you can use after going > 'make install'" > it could increase the warm fuzziness if it was expanded to say: > "You can install the external packages now and then rerun > 'make Makefile.PL' or just enjoy the rest of bioperl, > which you can use after going 'make install'." Allen needs to add this to Makefile.PL and Chris needs to add it to Bundle::BioPerl. > > > Cheers, Dave > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From jason at cgt.duhs.duke.edu Wed Apr 21 12:37:02 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed Apr 21 12:41:59 2004 Subject: [Bioperl-l] Parsing a Genbank file to get the Comment line. In-Reply-To: <5F7E863301E72846B90A4CEBB15EAE661F5A8E@exch02> References: <5F7E863301E72846B90A4CEBB15EAE661F5A8E@exch02> Message-ID: See the HOWTO for Features and Annotation. Basically when you have a sequence from SeqIO you do: my @comments = $seq->annotation->get_Annotations('comment'); -jason On Wed, 21 Apr 2004, Khan, Sohail wrote: > Hello Bioperl Experts, > > I have just started to use bioperl. I want to parse a Genbank flat file and > retrieve only the comment line from each record. Any suggestion is greatly > appreciated. > > Thanks > > Sohail Khan > Scientific Programmer > COLD SPRING HARBOR LABORATORY > Genome Research Center > 500 Sunnyside Boulevard > Woodbury, NY 11797 > (516)422-4076 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From avilella at ebi.ac.uk Wed Apr 21 13:02:24 2004 From: avilella at ebi.ac.uk (avilella) Date: Wed Apr 21 13:07:17 2004 Subject: [Bioperl-l] Mapping between aligment position and reference (1st) sequence position for MAF files Message-ID: <1082566944.3381.46.camel@localhost.localdomain> Hi, I was wondering which is the best way to get a mapping between the alignment position of a MAF file and the reference sequence position, in that case for the first individual in the file. I would like to be able to associate the result of an analysis for a position in a MAF alignment to the reference sequence. If not being done before, which is the best place to implement that? Thanks, Albert. From jason at cgt.duhs.duke.edu Wed Apr 21 13:22:41 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed Apr 21 13:27:12 2004 Subject: [Bioperl-l] Mapping between aligment position and reference (1st) sequence position for MAF files In-Reply-To: <1082566944.3381.46.camel@localhost.localdomain> References: <1082566944.3381.46.camel@localhost.localdomain> Message-ID: If I understand your question correctly... I've added a method to Bio::Coordinate::Utils for getting the alignment position (column) for a specific position in the reference sequence. It is called from_seq_to_alignmentpos(). If you want to get the reverse - a reference position from the alignment you should just be able to do: my $seq = $aln->get_seq_by_pos(1); my $ref_loc = $se->location_from_column($column); # see what that position is: print $ref_loc->to_FTstring(),"\n"; -jason On Wed, 21 Apr 2004, avilella wrote: > Hi, > > I was wondering which is the best way to get a mapping between the > alignment position of a MAF file and the reference sequence position, in > that case for the first individual in the file. > > I would like to be able to associate the result of an analysis for a > position in a MAF alignment to the reference sequence. > > If not being done before, which is the best place to implement that? > > Thanks, > > Albert. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From avilella at lycos.es Wed Apr 21 14:11:02 2004 From: avilella at lycos.es (avilella) Date: Wed Apr 21 14:15:56 2004 Subject: [Bioperl-l] Mapping between aligment position and reference (1st) sequence position for MAF files In-Reply-To: References: <1082566944.3381.46.camel@localhost.localdomain> Message-ID: <1082571058.2637.4.camel@localhost.localdomain> On Wed, 2004-04-21 at 18:22, Jason Stajich wrote: > If I understand your question correctly... > > I've added a method to Bio::Coordinate::Utils for getting the alignment > position (column) for a specific position in the reference sequence. It > is called from_seq_to_alignmentpos(). > > If you want to get the reverse yes, this one, although the other one is also useful: getting into account that there is the offset in each piece of aln in the maf file... Thanks, Albert. PD: I can't update it from the cvs, but I suppose it's the lag in the server > - a reference position from the alignment > you should just be able to do: > my $seq = $aln->get_seq_by_pos(1); > my $ref_loc = $se->location_from_column($column); > > # see what that position is: > print $ref_loc->to_FTstring(),"\n"; > > -jason > > On Wed, 21 Apr 2004, avilella wrote: > > > Hi, > > > > I was wondering which is the best way to get a mapping between the > > alignment position of a MAF file and the reference sequence position, in > > that case for the first individual in the file. > > > > I would like to be able to associate the result of an analysis for a > > position in a MAF alignment to the reference sequence. > > > > If not being done before, which is the best place to implement that? > > > > Thanks, > > > > Albert. > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu From dag at sonsorol.org Wed Apr 21 14:41:42 2004 From: dag at sonsorol.org (Chris Dagdigian) Date: Wed Apr 21 14:46:14 2004 Subject: [Bioperl-l] Makefile.PL and cvs.bioperl.org In-Reply-To: References: <40869FB4.3040608@mrc-lmb.cam.ac.uk> Message-ID: <4086C066.7010002@sonsorol.org> I just uploaded a new Bundle::BioPerl to CPAN -- should be available within a few hours on search.cpan.org. Not sure how long it will take to filter out to all the CPAN mirrors, probably 24 hours or so. The new Bundle has "SVG::Graph" as an additional dependency. That module in turn depends on: Tree::DAG_Node SVG Statistics::Descriptive Math::Spline Math::Derivative SVG is in the Bundle::BioPerl but I left the others out. The CPAN script will follow the SVG::Graph dependency tree if the user allows -Chris > The uploaded file > > Bundle-BioPerl-2.1.5.tar.gz > > has entered CPAN as > > file: $CPAN/authors/id/C/CR/CRAFFI/Bundle-BioPerl-2.1.5.tar.gz > size: 3175 bytes > md5: fb3a5f1873b7c91f699de204aaad0277 > > No action is required on your part > Request entered by: CRAFFI (Chris Dagdigian) > Request entered on: Wed, 21 Apr 2004 18:29:55 GMT > Request completed: Wed, 21 Apr 2004 18:30:24 GMT Jason Stajich wrote: > On Wed, 21 Apr 2004, Dave Howorth wrote: > > >>Based on my experience, I'd like to suggest the following changes to >>make it easier for neophytes to patch a bioperl release: >> >> >>On http://cvs.bioperl.org >>------------------------- >> >>At the bottom of the page, add an example on how to patch an existing >>installation. Or refer to somewhere else that does. Specifically give an >>example of the use of tags and explain where to find the upgrade/install >>instructions (I previously installed bioperl from CPAN so I had no idea >>how to use the cvs system. The page asks "Do you really want to be >>here?" to which my answer is "No, but I have to be because of bugs", and >>I think the page should address that audience). e.g.: >> >> "To patch an existing release, find the cvs tag of the appropriate >> branch (need to describe how!!) then type: >> cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/bioperl \ >> checkout -r branch-1-4 bioperl-live >> Then follow the normal install instructions in the INSTALL document >>in the top level directory (probably need more here!!!)" >> >> >>In Makefile.PL >>-------------- >> >>It picked up a missing dependency on GD::SVG and on SVG, but it failed >>to pick up on a dependency on SVG::Graph. >> >>I'd also suggest that where Makefile.PL prints out: >> "Enjoy the rest of bioperl, which you can use after going >> 'make install'" >>it could increase the warm fuzziness if it was expanded to say: >> "You can install the external packages now and then rerun >> 'make Makefile.PL' or just enjoy the rest of bioperl, >> which you can use after going 'make install'." > > > > Allen needs to add this to Makefile.PL and Chris needs to add it to > Bundle::BioPerl. > > > >> >>Cheers, Dave From allenday at ucla.edu Wed Apr 21 14:13:23 2004 From: allenday at ucla.edu (Allen Day) Date: Wed Apr 21 15:17:53 2004 Subject: [Bioperl-l] Makefile.PL and cvs.bioperl.org In-Reply-To: References: <40869FB4.3040608@mrc-lmb.cam.ac.uk> Message-ID: done On Wed, 21 Apr 2004, Jason Stajich wrote: > On Wed, 21 Apr 2004, Dave Howorth wrote: > > > Based on my experience, I'd like to suggest the following changes to > > make it easier for neophytes to patch a bioperl release: > > > > > > On http://cvs.bioperl.org > > ------------------------- > > > > At the bottom of the page, add an example on how to patch an existing > > installation. Or refer to somewhere else that does. Specifically give an > > example of the use of tags and explain where to find the upgrade/install > > instructions (I previously installed bioperl from CPAN so I had no idea > > how to use the cvs system. The page asks "Do you really want to be > > here?" to which my answer is "No, but I have to be because of bugs", and > > I think the page should address that audience). e.g.: > > > > "To patch an existing release, find the cvs tag of the appropriate > > branch (need to describe how!!) then type: > > cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/bioperl \ > > checkout -r branch-1-4 bioperl-live > > Then follow the normal install instructions in the INSTALL document > > in the top level directory (probably need more here!!!)" > > > > > > In Makefile.PL > > -------------- > > > > It picked up a missing dependency on GD::SVG and on SVG, but it failed > > to pick up on a dependency on SVG::Graph. > > > > I'd also suggest that where Makefile.PL prints out: > > "Enjoy the rest of bioperl, which you can use after going > > 'make install'" > > it could increase the warm fuzziness if it was expanded to say: > > "You can install the external packages now and then rerun > > 'make Makefile.PL' or just enjoy the rest of bioperl, > > which you can use after going 'make install'." > > > Allen needs to add this to Makefile.PL and Chris needs to add it to > Bundle::BioPerl. > > > > > > > > Cheers, Dave > > > > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From cosmos21roxy at hotmail.com Thu Apr 22 06:16:11 2004 From: cosmos21roxy at hotmail.com (ervin) Date: Wed Apr 21 17:15:35 2004 Subject: [Bioperl-l] Muscle Relaxers, Pain Relief and more.. Check it out! Message-ID: <1082628971-18484@excite.com> New OFFSHORE PHARMACY - Not a single medical question asked, guaranteed or it's free. Relaxants, Pain Relievers, & Anti-Depressants delivered discreetly in non-despcript packaging to your door, QUICKLY! 100% Private & NO QUESTIONS. Click here: http://redrum.ty65trg.com/s95/index.php?id=s95 No one needs to know but you. cobra pedrogeorgia happyday pearl katie nimrod josh buffy supratrumpet gambit zenith sylvie republic canela From hlapp at gmx.net Wed Apr 21 23:43:15 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed Apr 21 23:47:53 2004 Subject: [Bioperl-l] failures on the stable branch In-Reply-To: Message-ID: <2FF003E7-940F-11D8-B26A-000A959EB4C4@gmx.net> Thanks for your fixes Jason. The DB.t failures were in fact sort-of my fault as I just realized, because I had forgotten to merge my fix for the range query from the main trunk to the branch (NCBI indeed changed the accepted date format). In fact I had hesitated because I hoped part of the fixes would be temporary only (any change to the query result caused by changed data in the databank will cause some of the tests to fail), but given that nobody has time to come up with a more permanent solution for testing the range query I guess it is better to at least get rid of the error for the time being. So, I just did that. DB.t passes for me on the branch. -hilmar On Wednesday, April 21, 2004, at 07:01 AM, Jason Stajich wrote: > These are due to problems with Bio::DB::Query::GenBank > > setting the env variable BIOPERLDEBUG=1 will give more information. > >> ok 62 # could not connect to Genbank >> ok 63 # could not connect to Genbank >> ok 64 # could not connect to Genbank >> ok 65 # could not connect to Genbank >> ok 66 # could not connect to Genbank >> ok 67 # could not connect to Genbank >> ok 68 # could not connect to Genbank >> ok 69 # could not connect to Genbank >> ok 70 # could not connect to Genbank >> ok 71 # could not connect to Genbank >> ok 72 # could not connect to Genbank >> ok 73 # could not connect to Genbank >> ok 74 # could not connect to Genbank >> ok 75 # could not connect to Genbank >> ok 76 # could not connect to Genbank >> ok 77 # could not connect to Genbank >> ok 78 # could not connect to Genbank >> >> >> t/AlignIO....................ok 75/80Bio::AlignIO: largemultifasta >> cannot be found >> Exception >> ------------- EXCEPTION ------------- >> MSG: Failed to load module Bio::AlignIO::largemultifasta. Can't locate >> Bio/Seq/LargeLocatableSeq.pm in @INC (@INC contains: t blib/arch >> blib/lib /System/Library/Perl/darwin /System/Library/Perl >> /sw/lib/perl5/5.6.0/darwin /sw/lib/perl5/5.6.0 /sw/lib/perl5/darwin >> /sw/lib/perl5 /Library/Perl/darwin /Library/Perl >> /Network/Library/Perl/darwin /Network/Library/Perl .) at >> blib/lib/Bio/AlignIO/largemultifasta.pm line 69, line 28. >> BEGIN failed--compilation aborted at >> blib/lib/Bio/AlignIO/largemultifasta.pm line 69, line 28. >> Compilation failed in require at blib/lib/Bio/Root/Root.pm line 394, >> line 28. >> >> STACK Bio::Root::Root::_load_module blib/lib/Bio/Root/Root.pm:396 >> STACK (eval) blib/lib/Bio/AlignIO.pm:420 >> STACK Bio::AlignIO::_load_format_module blib/lib/Bio/AlignIO.pm:419 >> STACK Bio::AlignIO::new blib/lib/Bio/AlignIO.pm:347 >> STACK toplevel t/AlignIO.t:283 >> >> -------------------------------------- >> >> For more information about the AlignIO system please see the AlignIO >> docs. >> This includes ways of checking for formats at compile time, not run >> time >> Can't call method "next_aln" on an undefined value at t/AlignIO.t line >> 285, line 28. >> t/AlignIO....................dubious >> Test returned status 2 (wstat 512, 0x200) >> DIED. FAILED tests 76-80 >> Failed 5/80 tests, 93.75% okay >> >> t/cigarstring................Can't use an undefined value as an ARRAY >> reference at blib/lib/Bio/Search/Hit/GenericHit.pm line 409, >> line 434. >> t/cigarstring................dubious >> Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 1-3 >> Failed 3/3 tests, 0.00% okay >> > fixed >> >> >> (* note: these are only warnings, although they don't leave you with >> comfort *) >> t/GFF........................ok 1/32Filehandle Symbol::GEN0 opened >> only >> for output at blib/lib/Bio/Root/IO.pm line 440. >> t/GFF........................ok 2/32Filehandle Symbol::GEN1 opened >> only >> for output at blib/lib/Bio/Root/IO.pm line 440. >> t/GFF........................ok >> > Added code from main trunk to quiet this > local $^W=0; > > unless some has another way to see if fh is readable. > >> t/GeneCoordinateMapper.......ok 71/113 >> -------------------- WARNING --------------------- >> MSG: sorted sublocation array requested but root location doesn't >> define seq_id (at least one sublocation does!) >> --------------------------------------------------- >> >> -------------------- WARNING --------------------- >> MSG: sorted sublocation array requested but root location doesn't >> define seq_id (at least one sublocation does!) >> --------------------------------------------------- >> t/GeneCoordinateMapper.......ok 98/113Use of uninitialized value in >> concatenation (.) at blib/lib/Bio/Coordinate/GeneMapper.pm line 814. >> t/GeneCoordinateMapper.......ok > > fixed - this was a problem on main trunk too. >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> > > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From mm65icallef at hotmail.com Thu Apr 22 01:13:20 2004 From: mm65icallef at hotmail.com (garrett) Date: Thu Apr 22 02:18:45 2004 Subject: [Bioperl-l] Prescr:ip`ti`on drug's wi:th`out the pre:scription! (etxhhr) Message-ID: <1082610800-17116@excite.com> Best Prices on Painkillers like Ultram! Gr:eat Deals on Vali`um! Stop smok'ing with ZYBAN!! Click here to learn more about each: http://jordan23.ty65trg.com/s95/index.php?id=s95 metallica meow sweety snuffy wolfMan oranges mike1 soccer1 miles ruth xxxx doom2 pookie1 chance symbol players sasha paula roy chevy pacers wanker mike1 trumpet nurse asterix From Sebastien.Moretti at igs.cnrs-mrs.fr Thu Apr 22 03:15:57 2004 From: Sebastien.Moretti at igs.cnrs-mrs.fr (Sebastien Moretti) Date: Thu Apr 22 03:20:27 2004 Subject: [Bioperl-l] [Structure of remote GenBank files] Message-ID: <200404220915.57334.Sebastien.Moretti@igs.cnrs-mrs.fr> Hello I use a BioPerl script to get GenBank and RefSeq files in GenBank flat file format. #!/usr/bin/perl -w use strict; use Bio::DB::GenBank; use Bio::DB::Query::GenBank; use Bio::SeqIO; my $acc=$ARGV[0] or die "\n\tThe accession number you seek for is missing.\n\tTry something like: ./update_estCDK.pl NM_178432\n\n"; $acc=$acc."[Accession]"; my $query_string = "$acc"; my $query = Bio::DB::Query::GenBank->new(-db=>'nucleotide', -query=>$query_string); my $gb = new Bio::DB::GenBank; my $stream = $gb->get_Stream_by_query($query); my $out=Bio::SeqIO->new(-format=>'genbank'); my $seq = $stream->next_seq(); my $result=$out->write_seq($seq); $result =~ s/^1.*$//; #print $out->write_seq($seq); print $result; exit; It works fine but I have two structures problems in my files: - the PUBMED fields are pasted with the JOURNAL fields line above: JOURNAL J. Biol. Chem. 278 (42), 40815-40828 (2003) PUBMED 12912980 or JOURNAL J. Cancer Res. Clin. Oncol. 129 (9), 498-502 (2003) PUBMED 12884029 or JOURNAL Am. J. Physiol. Heart Circ. Physiol. 284 (6), H1917-H1923 (2003) PUBMED 12742823 - the COMMENT fields haven't blank lines and \n, so COMMENT fields looks compact: COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The reference sequence was derived from Y00272.1 and BC014563.1. On Oct 22, 2001 this sequence version replaced gi:4502708. Summary: The protein encoded by this gene is a member of the Ser/Thr protein kinase family. This protein is a catalytic subunit of the highly conserved protein kinase complex known as M-phase promoting factor (MPF), which is essential for G1/S and G2/M phase transitions of eukaryotic cell cycle. Mitotic cyclins stably associate with this protein and function as regulatory subunits. The kinase activity of this protein is controlled by cyclin accumulation and destruction through the cell cycle. The phosphorylation and dephosphorylation of this protein also play important regulatory roles in cell cycle control. Transcript Variant: This variant (1) encodes the full length isoform. COMPLETENESS: complete on the 3' end. Does it come from my script ? Do you see the same thing ? Thanks -- Sebastien MORETTI CNRS - IGS 31 chemin Joseph Aiguier 13402 Marseille cedex 20, FRANCE tel. +33 (0)4 91 16 44 55 From dhoworth at mrc-lmb.cam.ac.uk Thu Apr 22 07:39:59 2004 From: dhoworth at mrc-lmb.cam.ac.uk (Dave Howorth) Date: Thu Apr 22 07:44:45 2004 Subject: [Bioperl-l] load_ontology and GO - progress! Message-ID: <4087AF0F.1080104@mrc-lmb.cam.ac.uk> Hi everybody, I'm very pleased to report that the upgraded branch-1-4 now passed its tests to an acceptable/understandable level and has installed. Furthermore, it has fixed the original trouble with the load_ontology program. So big thanks to everybody who has put effort into helping me, fixing problems and updating docs so quickly. There's always a gotcha, of course ... load_ontology is now failing with messages like this: Loading ontology Gene Ontology: ... terms -------------------- WARNING --------------------- MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed, values were ("GO:0001529","elastin","OBSOLETE (was not defined before being made obsolete).","X") FKs (2) Duplicate entry 'elastin-2' for key 2 --------------------------------------------------- Could not store GO:0001529 (elastin): ------------- EXCEPTION ------------- MSG: create: object (Bio::Ontology::GOterm) failed to insert or to be found by unique key STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/share/perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:207 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/share/perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:253 STACK Bio::DB::Persistent::PersistentObject::store /usr/local/share/perl/5.6.1/Bio/DB/Persistent/PersistentObject.pm:270 STACK (eval) load_ontology.pl:508 STACK toplevel load_ontology.pl:490 -------------------------------------- What appears to be happening is that the GO.defs file defines two terms called 'elastin' (0001528 and 0001529), one of which is used in component.ontology and the other in function.ontology. Both are declared OBSOLETE. This isn't an isolated case; it occurs for 'collagen' as well, for example. Neither is it new in this release of the files; I found it in an old copy I had. The GO flat file definition format document isn't very helpful in describing what should be in the file, so my question is whether this duplication is a legitimate occurence in GO? That is, is there a bug in the GO distribution (duplicate IDs) or a bug in the biosql model (each of the three GO ontologies needs a separate ontology ID)? Also of interest would be any ideas for a workaround :) Cheers, Dave -- Dave Howorth MRC Centre for Protein Engineering Hills Road, Cambridge, CB2 2QH 01223 252960 From postmaster at ebi.ac.uk Thu Apr 22 07:51:49 2004 From: postmaster at ebi.ac.uk (MailScanner) Date: Thu Apr 22 07:56:15 2004 Subject: [Bioperl-l] Warning: E-mail containing attachment(s) blocked Message-ID: <200404221151.i3MBpn820195@maui.ebi.ac.uk> Our MailScanner has blocked a message that you sent:- To: support@ebi.ac.uk Subject: Re: Your product Date: Thu Apr 22 12:51:49 2004 This is because it contains one or more attachments that we do not allow. Please rename any attachments to be in the form: filename.clean and resend the message (don't forget to tell the recipient the attachment type). If you have not actually sent this email it is possible that it has been forged (so that it appeared to be from you). MailScanner Report: Shortcuts to MS-Dos programs are very dangerous in email (your_product.pif) -- MailScanner Email Virus Scanner www.mailscanner.info From s.paul at surrey.ac.uk Thu Apr 22 17:06:45 2004 From: s.paul at surrey.ac.uk (S.Paul) Date: Thu Apr 22 09:18:24 2004 Subject: [Bioperl-l] statistics of sequences References: <06ae01c42730$50903cc0$2b6fe383@LTCEP1SP> <200404211453.51337.heikki@ebi.ac.uk> Message-ID: <083d01c428ad$b894a8a0$2b6fe383@LTCEP1SP> Thanks Heikki. It worked Sujoy Sujoy Paul, PRISE Centre, UniS, s.paul@surrey.ac.uk ----- Original Message ----- From: "Heikki Lehvaslaiho" To: Cc: "S.Paul" Sent: Wednesday, April 21, 2004 7:53 AM Subject: Re: [Bioperl-l] statistics of sequences > Sujou, > > You are on the right track to use OddCodes. The OddCode methods give you back > a refrence to a plain string. (which, BTW, you can store into a specialized > sequence object of type Bio::Seq::Meta) that can be manipulated using > standard perl functions. > > Here are two possibilities: > > # 1. works without knowing the characters > > my %hash; > for (split / */, $new_coding5) { > $hash{$_}++; > } > for (keys %hash) { > print $_, ": ", $hash{$_}, "\n"; > } > > #2. you have to know what you are looking for > > my ($O) = $new_coding5 =~ tr/O//; > print "O: $O\n"; > my ($I) = $new_coding5 =~ tr/I//; > print "I: $I\n"; > > ### > > There are more ways of doing the same thing, all depends on what you want to > do with the data. > > Yours, > -Heikki > > On Tuesday 20 Apr 2004 23:36, S.Paul wrote: > > Hi Everybody: > > > > I am pretty new to bioperl and am trying to find the statistics of the > > polarity of amino acids in the protein sequence eg. how many are polar, > > hydrophobic etc. I tried using the SeqStats to calculate the mol wt and > > the number of A and C but cannot calculate the number of hydrophobic acids > > present. I am enclosing the portion of the code. I would appreciate if > > anybody can offer any suggestions in this regard. > > > > *************************************************************************** > >************************************************** my $seq_stats = > > Bio::Tools::SeqStats->new($seq); > > my $weight = $seq_stats->get_mol_wt(); > > #note $weight is an array > > print " the weight is ", $$weight[0], "\n"; > > my $monomer_ref = $seq_stats->count_monomers(); > > print "Number of A\'s in sequence is $$monomer_ref{'A'} \n"; > > print "Number of C\'s in sequence is $$monomer_ref{'C'} \n"; > > print "Number of T\'s in sequence is $$monomer_ref{'T'} \n"; > > print "Number of G\'s in sequence is $$monomer_ref{'G'} \n"; > > > > > > print "\-----------------------------------------------\n"; > > my $oddcode_obj = Bio::Tools::OddCodes->new(-seq =>$seq); > > #returns the reference > > > > my $output1 = $oddcode_obj->charge(); > > my $output2 = $oddcode_obj->structural(); > > my $output3 = $oddcode_obj->chemical(); > > my $output4 = $oddcode_obj->functional(); > > > > my $output5= $oddcode_obj->hydrophobic(); > > > > #displays > > my $new_coding1 =$$output1; > > print "\nthe charge of the sequence is $new_coding1"; > > > > print "\-----------------------------------------------\n"; > > > > my $new_coding2 =$$output2; > > print "\nthe structural sequence $new_coding2"; > > print "\-----------------------------------------------\n"; > > my $new_coding3 =$$output3; > > print "\n the chemical structure is : $new_coding3"; > > print "\-----------------------------------------------\n"; > > my $new_coding4 =$$output4; > > print "\n the functional nature of the protein: $new_coding4"; > > print "\-----------------------------------------------\n"; > > > > my $new_coding5 =$$output5; > > print "\n the hydrophobic nature of the protein: $new_coding5"; > > > > *************************************************************************** > >******************************************* > > > > Thanks > > > > Sujoy Paul > > Sujoy Paul, PRISE Centre, UniS, s.paul@surrey.ac.uk > > -- > ______ _/ _/_____________________________________________________ > _/ _/ http://www.ebi.ac.uk/mutations/ > _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk > _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute > _/ _/ _/ Wellcome Trust Genome Campus, Hinxton > _/ _/ _/ Cambs. CB10 1SD, United Kingdom > _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 > ___ _/_/_/_/_/________________________________________________________ > From bmb9jrm at bmb.leeds.ac.uk Thu Apr 22 09:43:11 2004 From: bmb9jrm at bmb.leeds.ac.uk (Jonathan Manning) Date: Thu Apr 22 09:47:59 2004 Subject: [Bioperl-l] Don't want to donwload sequence contigs! Message-ID: <1082641390.6120.10.camel@localhost.localdomain> Hi all, I'm new to bioperl, if this is the wrong place to post this sort of question, someone let me know! I'm working on a bioinformatics thesis project, and am using bioperl. At the moment, I'm writing a script which constructs a Bio::DB::Query::GenBank object with a query id or name, which is then passed to a new Bio::DB::GenBank object. Trouble is, if Entrez comes up with a contig, things freeze right out because the file's so big. Question: is there a way to exclude contigs from a search, or else find out the accession numbers which relate to a particular id, so that "NT_" accessions can be excluded before a stream to GenBank is established? Appreciate any help, Jon From barry.moore at genetics.utah.edu Thu Apr 22 13:24:11 2004 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Thu Apr 22 13:28:42 2004 Subject: [Bioperl-l] [Structure of remote GenBank files] In-Reply-To: <200404220915.57334.Sebastien.Moretti@igs.cnrs-mrs.fr> References: <200404220915.57334.Sebastien.Moretti@igs.cnrs-mrs.fr> Message-ID: <4087FFBB.5060609@genetics.utah.edu> Sebastian, I ran your script with BioPerl 1.4, Active State Perl 5.8 on Windows XP works fine for me. I don't know what's causing your problem. Maybe telling more about your system might help. This doesn't have anything to do with you file format problems, but thought I'd mention that since your script takes accession numbers as input you could skip the query, and call a $gb->get_Stream_by_id(\@accession) on a array of accessions or $gb->get_Seq_by_acc($acc) on a scalar. Barry Sebastien Moretti wrote: >Hello >I use a BioPerl script to get GenBank and RefSeq files in GenBank flat file >format. > > #!/usr/bin/perl -w > > use strict; > use Bio::DB::GenBank; > use Bio::DB::Query::GenBank; > use Bio::SeqIO; > my $acc=$ARGV[0] or die "\n\tThe accession number you seek for is >missing.\n\tTry something like: ./update_estCDK.pl NM_178432\n\n"; > > $acc=$acc."[Accession]"; > > my $query_string = "$acc"; > my $query = Bio::DB::Query::GenBank->new(-db=>'nucleotide', > -query=>$query_string); > > my $gb = new Bio::DB::GenBank; > my $stream = $gb->get_Stream_by_query($query); > > my $out=Bio::SeqIO->new(-format=>'genbank'); > my $seq = $stream->next_seq(); > > my $result=$out->write_seq($seq); > $result =~ s/^1.*$//; > #print $out->write_seq($seq); > print $result; > > exit; > >It works fine but I have two structures problems in my files: > - the PUBMED fields are pasted with the JOURNAL fields line above: > JOURNAL J. Biol. Chem. 278 (42), 40815-40828 (2003) PUBMED 12912980 >or > JOURNAL J. Cancer Res. Clin. Oncol. 129 (9), 498-502 (2003) PUBMED > 12884029 >or > JOURNAL Am. J. Physiol. Heart Circ. Physiol. 284 (6), H1917-H1923 (2003) > PUBMED 12742823 > > - the COMMENT fields haven't blank lines and \n, so COMMENT fields looks > compact: >COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The > reference sequence was derived from Y00272.1 and BC014563.1. On > Oct 22, 2001 this sequence version replaced gi:4502708. Summary: > The protein encoded by this gene is a member of the Ser/Thr > protein kinase family. This protein is a catalytic subunit of the > highly conserved protein kinase complex known as M-phase promoting > factor (MPF), which is essential for G1/S and G2/M phase > transitions of eukaryotic cell cycle. Mitotic cyclins stably > associate with this protein and function as regulatory subunits. > The kinase activity of this protein is controlled by cyclin > accumulation and destruction through the cell cycle. The > phosphorylation and dephosphorylation of this protein also play > important regulatory roles in cell cycle control. Transcript > Variant: This variant (1) encodes the full length isoform. > COMPLETENESS: complete on the 3' end. > >Does it come from my script ? >Do you see the same thing ? >Thanks > > > -- Barry Moore Dept. of Human Genetics University of Utah Salt Lake City, UT From MAILER-DAEMON at google.com Thu Apr 22 16:11:43 2004 From: MAILER-DAEMON at google.com (Mail Delivery Subsystem) Date: Thu Apr 22 16:16:15 2004 Subject: [Bioperl-l] Returned mail: see transcript for details Message-ID: <200404222011.i3MKBhhF026260@smtp.google.com> The original message was received at Thu, 22 Apr 2004 13:11:27 -0700 from [202.127.205.190] ----- The following addresses had permanent fatal errors ----- (reason: 554 5.7.1 Message from 202.127.205.190 rejected because message.scr is infected with W32/Netsky.P@mm) (expanded from: ) ----- Transcript of session follows ----- ... while talking to corprouter1.corp.google.com.: >>> DATA <<< 554 5.7.1 Message from 202.127.205.190 rejected because message.scr is infected with W32/Netsky.P@mm 554 5.0.0 Service unavailable ----- Message header follows ----- X-Relay-IP: 202.127.205.190 Return-Path: Received: from google.com ([202.127.205.190]) by Google Production Mailgate with ESMTPœ id i3MKBPhF026253 for ; Thu, 22 Apr 2004 13:11:27 -0700 Message-Id: <200404222011.i3MKBPhF026253@smtp.google.com> From: bioperl-l@bioperl.org To: safesearch@google.com Subject: Mail Delivery (failure safesearch@google.com) Date: Fri, 23 Apr 2004 04:09:33 +0800 MIME-Version: 1.0 Content-Type: multipart/related; type="multipart/alternative"; boundary="----=_NextPart_000_001B_01C0CA80.6B015D10" X-Priority: 3 X-MSMail-Priority: Normal ----- Message body suppressed ----- From hlapp at gnf.org Thu Apr 22 21:33:38 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Thu Apr 22 21:38:07 2004 Subject: [Bioperl-l] load_ontology and GO - progress! In-Reply-To: <4087AF0F.1080104@mrc-lmb.cam.ac.uk> Message-ID: <3E8B17DE-94C6-11D8-95EB-000A959EB4C4@gnf.org> Did you read the load_ontology.pl POD, in particular the documentation for the options that deal with obsolete terms? Obsolete terms is not a trivial thing to deal with, and in the end you need to make some decisions for yourself. load_ontology.pl offers several choices but it's up to you what works best for you. There have been prior threads on this; e.g. reading http://bioperl.org/pipermail/bioperl-l/2004-February/014846.html may give you some additional information. Note also that supplying --safe will make the script continue despite errors from the database. -hilmar On Thursday, April 22, 2004, at 04:39 AM, Dave Howorth wrote: > Hi everybody, > > I'm very pleased to report that the upgraded branch-1-4 now passed its > tests to an acceptable/understandable level and has installed. > Furthermore, it has fixed the original trouble with the load_ontology > program. > > So big thanks to everybody who has put effort into helping me, fixing > problems and updating docs so quickly. > > There's always a gotcha, of course ... > > load_ontology is now failing with messages like this: > > > Loading ontology Gene Ontology: > ... terms > > -------------------- WARNING --------------------- > MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed, values > were ("GO:0001529","elastin","OBSOLETE (was not defined before being > made obsolete).","X") FKs (2) > Duplicate entry 'elastin-2' for key 2 > --------------------------------------------------- > Could not store GO:0001529 (elastin): > > ------------- EXCEPTION ------------- > MSG: create: object (Bio::Ontology::GOterm) failed to insert or to be > found by unique key > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create > /usr/local/share/perl/5.6.1/Bio/DB/BioSQL/> BasePersistenceAdaptor.pm:207 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store > /usr/local/share/perl/5.6.1/Bio/DB/BioSQL/> BasePersistenceAdaptor.pm:253 > STACK Bio::DB::Persistent::PersistentObject::store > /usr/local/share/perl/5.6.1/Bio/DB/Persistent/PersistentObject.pm:270 > STACK (eval) load_ontology.pl:508 > STACK toplevel load_ontology.pl:490 > > -------------------------------------- > > > What appears to be happening is that the GO.defs file defines two > terms called 'elastin' (0001528 and 0001529), one of which is used in > component.ontology and the other in function.ontology. Both are > declared OBSOLETE. > > This isn't an isolated case; it occurs for 'collagen' as well, for > example. Neither is it new in this release of the files; I found it > in an old copy I had. > > The GO flat file definition format document isn't very helpful in > describing what should be in the file, so my question is whether this > duplication is a legitimate occurence in GO? > > That is, is there a bug in the GO distribution (duplicate IDs) or a > bug in the biosql model (each of the three GO ontologies needs a > separate ontology ID)? > > Also of interest would be any ideas for a workaround :) > > Cheers, Dave > -- > Dave Howorth > MRC Centre for Protein Engineering > Hills Road, Cambridge, CB2 2QH > 01223 252960 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From donald.jackson at bms.com Thu Apr 22 21:34:25 2004 From: donald.jackson at bms.com (Donald Jackson) Date: Thu Apr 22 21:38:53 2004 Subject: [Bioperl-l] Changes to Bio::Tools::SiRNA Message-ID: <408872A1.1040005@bms.com> Hi, I've made (and committed) some pretty major changes to Bio::Tools::SiRNA to allow it to accomodate alternative rules for designing siRNA reagents. The actual siRNA selection is now handled by Bio::Tools::SiRNA::Ruleset objects. I also committed two Rulets. Bio::Tools::SiRNA::Ruleset::tuschl, which implements the Tuschl group's rules that used to be in Bio::Tools::SiRNA, and Bio::Tools::SiRNA::Ruleset::saigo, which implements the rules published by Ui-Tei et al (2004) (I stuck with the convention of naming the rules after the corresponding author). The Tuschl rules are used by default. I hope that these changes will make it easier to add more rule sets while maintaining backwards compatibility. As always, I welcome feeback on bugs, coding style, or other issues. Thanks, Don Jackson BMS Bioinformatics From Sebastien.Moretti at igs.cnrs-mrs.fr Fri Apr 23 03:10:29 2004 From: Sebastien.Moretti at igs.cnrs-mrs.fr (Sebastien Moretti) Date: Fri Apr 23 03:14:59 2004 Subject: [Bioperl-l] [Structure of remote GenBank files] In-Reply-To: <4087FFBB.5060609@genetics.utah.edu> References: <200404220915.57334.Sebastien.Moretti@igs.cnrs-mrs.fr> <4087FFBB.5060609@genetics.utah.edu> Message-ID: <200404230910.29660.Sebastien.Moretti@igs.cnrs-mrs.fr> > Sebastian, > I ran your script with BioPerl 1.4, Active State Perl 5.8 on Windows XP > works fine for me. I don't know what's causing your problem. Maybe > telling more about your system might help. This doesn't have anything > to do with you file format problems, but thought I'd mention that since > your script takes accession numbers as input you could skip the query, > and call a $gb->get_Stream_by_id(\@accession) on a array of accessions > or $gb->get_Seq_by_acc($acc) on a scalar. > > Barry Hello Barry, I use Linux Suse 9.0 and 8.2 and BioPerl 1.4 I try to get GenBank and RefSeq files with '$gb->get_Stream_by_id(\@accession)' and I still have the same problems (with NM_178432, BC032122 or NM_000559 as accession number): PUBMED fields are not on their own lines but paste to JOURNAL fields COMMENT fields are compact, without blank lines and line breaks Do you think it comes from linux system ? It might be for blank lines but why for PUBMED fields ? When a MEDLINE field is here (eg: NM_169678 or NM_079645), PUBMED and MEDLINE fields are right placed. The COMMENT field are still compact, without blank lines and line breaks. Thanks > >Hello > >I use a BioPerl script to get GenBank and RefSeq files in GenBank flat > > file format. > > > > #!/usr/bin/perl -w > > > > use strict; > > use Bio::DB::GenBank; > > use Bio::DB::Query::GenBank; > > use Bio::SeqIO; > > my $acc=$ARGV[0] or die "\n\tThe accession number you seek for is > >missing.\n\tTry something like: ./update_estCDK.pl NM_178432\n\n"; > > > > $acc=$acc."[Accession]"; > > > > my $query_string = "$acc"; > > my $query = Bio::DB::Query::GenBank->new(-db=>'nucleotide', > > -query=>$query_string); > > > > my $gb = new Bio::DB::GenBank; > > my $stream = $gb->get_Stream_by_query($query); > > > > my $out=Bio::SeqIO->new(-format=>'genbank'); > > my $seq = $stream->next_seq(); > > > > my $result=$out->write_seq($seq); > > $result =~ s/^1.*$//; > > #print $out->write_seq($seq); > > print $result; > > > > exit; > > > >It works fine but I have two structures problems in my files: > > - the PUBMED fields are pasted with the JOURNAL fields line above: > > JOURNAL J. Biol. Chem. 278 (42), 40815-40828 (2003) PUBMED 12912980 > >or > > JOURNAL J. Cancer Res. Clin. Oncol. 129 (9), 498-502 (2003) PUBMED > > 12884029 > >or > > JOURNAL Am. J. Physiol. Heart Circ. Physiol. 284 (6), H1917-H1923 > > (2003) PUBMED 12742823 > > > > - the COMMENT fields haven't blank lines and \n, so COMMENT fields looks > > compact: > >COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. > > The reference sequence was derived from Y00272.1 and BC014563.1. On Oct > > 22, 2001 this sequence version replaced gi:4502708. Summary: The protein > > encoded by this gene is a member of the Ser/Thr protein kinase family. > > This protein is a catalytic subunit of the highly conserved protein > > kinase complex known as M-phase promoting factor (MPF), which is > > essential for G1/S and G2/M phase transitions of eukaryotic cell cycle. > > Mitotic cyclins stably associate with this protein and function as > > regulatory subunits. The kinase activity of this protein is controlled by > > cyclin accumulation and destruction through the cell cycle. The > > phosphorylation and dephosphorylation of this protein also play important > > regulatory roles in cell cycle control. Transcript Variant: This variant > > (1) encodes the full length isoform. COMPLETENESS: complete on the 3' > > end. > > > >Does it come from my script ? > >Do you see the same thing ? > >Thanks -- Sebastien MORETTI CNRS - IGS 31 chemin Joseph Aiguier 13402 Marseille cedex 20, FRANCE tel. +33 (0)4 91 16 44 55 From jason at cgt.duhs.duke.edu Fri Apr 23 03:23:24 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Fri Apr 23 03:28:30 2004 Subject: [Bioperl-l] [Structure of remote GenBank files] In-Reply-To: <200404230910.29660.Sebastien.Moretti@igs.cnrs-mrs.fr> References: <200404220915.57334.Sebastien.Moretti@igs.cnrs-mrs.fr> <4087FFBB.5060609@genetics.utah.edu> <200404230910.29660.Sebastien.Moretti@igs.cnrs-mrs.fr> Message-ID: I think this particular behavior was a bug - I fixed it on the main trunk -- I'm not sure it has been migrated to the branch though. http://bugzilla.open-bio.org/show_bug.cgi?id=1588 -jason On Fri, 23 Apr 2004, Sebastien Moretti wrote: > > Sebastian, > > I ran your script with BioPerl 1.4, Active State Perl 5.8 on Windows XP > > works fine for me. I don't know what's causing your problem. Maybe > > telling more about your system might help. This doesn't have anything > > to do with you file format problems, but thought I'd mention that since > > your script takes accession numbers as input you could skip the query, > > and call a $gb->get_Stream_by_id(\@accession) on a array of accessions > > or $gb->get_Seq_by_acc($acc) on a scalar. > > > > Barry > > Hello Barry, > I use Linux Suse 9.0 and 8.2 and BioPerl 1.4 > I try to get GenBank and RefSeq files with > '$gb->get_Stream_by_id(\@accession)' and I still have the same problems (with > NM_178432, BC032122 or NM_000559 as accession number): > PUBMED fields are not on their own lines but paste to JOURNAL fields > COMMENT fields are compact, without blank lines and line breaks > > Do you think it comes from linux system ? > It might be for blank lines but why for PUBMED fields ? > > When a MEDLINE field is here (eg: NM_169678 or NM_079645), PUBMED and MEDLINE > fields are right placed. > The COMMENT field are still compact, without blank lines and line breaks. > > Thanks > > > >Hello > > >I use a BioPerl script to get GenBank and RefSeq files in GenBank flat > > > file format. > > > > > > #!/usr/bin/perl -w > > > > > > use strict; > > > use Bio::DB::GenBank; > > > use Bio::DB::Query::GenBank; > > > use Bio::SeqIO; > > > my $acc=$ARGV[0] or die "\n\tThe accession number you seek for is > > >missing.\n\tTry something like: ./update_estCDK.pl NM_178432\n\n"; > > > > > > $acc=$acc."[Accession]"; > > > > > > my $query_string = "$acc"; > > > my $query = Bio::DB::Query::GenBank->new(-db=>'nucleotide', > > > -query=>$query_string); > > > > > > my $gb = new Bio::DB::GenBank; > > > my $stream = $gb->get_Stream_by_query($query); > > > > > > my $out=Bio::SeqIO->new(-format=>'genbank'); > > > my $seq = $stream->next_seq(); > > > > > > my $result=$out->write_seq($seq); > > > $result =~ s/^1.*$//; > > > #print $out->write_seq($seq); > > > print $result; > > > > > > exit; > > > > > >It works fine but I have two structures problems in my files: > > > - the PUBMED fields are pasted with the JOURNAL fields line above: > > > JOURNAL J. Biol. Chem. 278 (42), 40815-40828 (2003) PUBMED 12912980 > > >or > > > JOURNAL J. Cancer Res. Clin. Oncol. 129 (9), 498-502 (2003) PUBMED > > > 12884029 > > >or > > > JOURNAL Am. J. Physiol. Heart Circ. Physiol. 284 (6), H1917-H1923 > > > (2003) PUBMED 12742823 > > > > > > - the COMMENT fields haven't blank lines and \n, so COMMENT fields looks > > > compact: > > >COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. > > > The reference sequence was derived from Y00272.1 and BC014563.1. On Oct > > > 22, 2001 this sequence version replaced gi:4502708. Summary: The protein > > > encoded by this gene is a member of the Ser/Thr protein kinase family. > > > This protein is a catalytic subunit of the highly conserved protein > > > kinase complex known as M-phase promoting factor (MPF), which is > > > essential for G1/S and G2/M phase transitions of eukaryotic cell cycle. > > > Mitotic cyclins stably associate with this protein and function as > > > regulatory subunits. The kinase activity of this protein is controlled by > > > cyclin accumulation and destruction through the cell cycle. The > > > phosphorylation and dephosphorylation of this protein also play important > > > regulatory roles in cell cycle control. Transcript Variant: This variant > > > (1) encodes the full length isoform. COMPLETENESS: complete on the 3' > > > end. > > > > > >Does it come from my script ? > > >Do you see the same thing ? > > >Thanks > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From dhoworth at mrc-lmb.cam.ac.uk Fri Apr 23 09:30:45 2004 From: dhoworth at mrc-lmb.cam.ac.uk (Dave Howorth) Date: Fri Apr 23 09:35:56 2004 Subject: [Bioperl-l] load_ontology and GO - progress! In-Reply-To: <3E8B17DE-94C6-11D8-95EB-000A959EB4C4@gnf.org> References: <3E8B17DE-94C6-11D8-95EB-000A959EB4C4@gnf.org> Message-ID: <40891A85.6020009@mrc-lmb.cam.ac.uk> Sean Davis wrote: > I think you can load with --noobsolete (see perldoc for > load_ontology.pl). You may also want to use --safe so that if > there does happen to be a term already loaded, the entire load > does not fail (again, see perldoc). Thanks Sean, that has been a successful workaround that has let me load the database. Hilmar Lapp wrote: > Did you read the load_ontology.pl POD, in particular the documentation > for the options that deal with obsolete terms? Hi Hilmar, Yes I had read the POD. Specifically, I used the options shown in the synopsis of that document "for loading the Gene Ontology". I had expected that to be a working example. If different options are needed, I would have expected them to be used, or at least mentioned, in the synopsis. Neither does the description of the --noobsolete option indicate that it is necessary to use it when loading GO, as opposed to something I might consider for reasons that aren't explained. Remember, this is the first time I have used this database and loader and I am specifically using them now with the aim of learning what the issues are and how best to deal with them. Unless the documentation describes an issue, I'm not going to be aware of it until I trip over it :( > Obsolete terms is not a trivial thing to deal with, and in the end you > need to make some decisions for yourself. load_ontology.pl offers > several choices but it's up to you what works best for you. There have > been prior threads on this; e.g. reading > http://bioperl.org/pipermail/bioperl-l/2004-February/014846.html may > give you some additional information. I agree terms that become obsolete are complex to deal with. I think there are two different issues associated with the two examples I gave (elastin and collagen). Collagen appears to be an example of the case you discuss in the thread to which you refer. Incidentally, adding the obsolete flag to the key will only ensure uniqueness through one obsolence event. If the events were to be repeated, it would fail. Hopefully that is an unlikely scenario :) But if I wanted to handle that case, I would probably look to adding some form of versioning, rather than a boolean flag. But the issue with elastin is not about terms that become obsolete, it's about two terms with the same name. The obsolesence appears to me to be incidental. The GO files use two different terms (different GO IDs, different ontologies) with the same name. They happen to be obsolete but it looks like they both existed at the same time (the GO IDs differ only by 1 and the terms are used in separate ontology files), not that a term was made obsolete and another independent term was later created that happened to use the same name. If that secenario ever occurs again, it will break the schema. I surmise from the low numbered GO IDs that perhaps this was something that happened in the history of GO that will not be permitted to happen again? But you appeared to think it is possible when you said in Feb: "This is not atypical for annotation being a work in progress" . Hence my interest in whether such an event would constitute a data error to report to GO or a schema error in biosql and my consequent curiosity about the exact rules for GO. Cheers, Dave -- Dave Howorth MRC Centre for Protein Engineering Hills Road, Cambridge, CB2 2QH 01223 252960 From john.herbert at clinical-pharmacology.oxford.ac.uk Fri Apr 23 10:11:03 2004 From: john.herbert at clinical-pharmacology.oxford.ac.uk (john herbert) Date: Fri Apr 23 10:15:48 2004 Subject: [Bioperl-l] Ensembl Query Message-ID: Hello BioPerlers. Is there a way to query the backend of Ensembl through BioPerl? I know you can use Ensembl Mart through a browser but I want to do similar queries from a Perl script. Would appreciate any pointers on this. Thanks in advance. John Herbert From jason at cgt.duhs.duke.edu Fri Apr 23 10:25:26 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Fri Apr 23 10:29:59 2004 Subject: [Bioperl-l] Ensembl Query In-Reply-To: References: Message-ID: Actually it makes more sense to use the ensembl API really. See the tutorials section of the ensembl website. http://www.ensembl.org/Docs/wiki/html/EnsemblDocs/CodeTutorial.html -jason On Fri, 23 Apr 2004, john herbert wrote: > Hello BioPerlers. > Is there a way to query the backend of Ensembl through BioPerl? > > I know you can use Ensembl Mart through a browser but I want to do > similar queries from a Perl script. > > Would appreciate any pointers on this. > > Thanks in advance. > > John Herbert > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From skirov at utk.edu Fri Apr 23 10:41:38 2004 From: skirov at utk.edu (Stefan Kirov) Date: Fri Apr 23 10:46:10 2004 Subject: [Bioperl-l] Ensembl Query In-Reply-To: References: Message-ID: <40892B22.5040500@utk.edu> In general you should be using Ensembl API. The tutorial is available from: http://www.ensembl.org/Docs/ensembl_tutorial.pdf. You can also use directly (or through perl DBI) mysql to query their database. Some details are in the tutorial, but I don't really know what you are interested in. Also you can join the ensembl-dev mailing list: http://www.ensembl.org/Docs/Lists/. Hope this helps Stefan john herbert wrote: >Hello BioPerlers. >Is there a way to query the backend of Ensembl through BioPerl? > >I know you can use Ensembl Mart through a browser but I want to do >similar queries from a Perl script. > >Would appreciate any pointers on this. > >Thanks in advance. > >John Herbert >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > From szhan at uoguelph.ca Fri Apr 23 11:51:20 2004 From: szhan at uoguelph.ca (szhan@uoguelph.ca) Date: Fri Apr 23 11:55:47 2004 Subject: [Bioperl-l] How to parse bl2seq report? In-Reply-To: <4084E77B.8020006@netvisao.pt> References: <1082426366.408483fe1a650@webmail.uoguelph.ca> <4084E77B.8020006@netvisao.pt> Message-ID: <1082735480.40893b78c5153@webmail.uoguelph.ca> Hello, Paulo: Thank you very much for your help! I modified the code as your instruction in the below but I got the message like this: ------------- EXCEPTION ------------- MSG: No hit object found for bl2seq report STACK Bio::Tools::BPbl2seq::next_feature C:/Perl/site/lib/Bio/Tools/BPbl2seq.pm: 231 STACK toplevel pcompare3.pl:100 -------------------------------------- and the loop can't continue. However I put the error-prone code in the eval statement then the program can continue and finish looping over. But the some pairs of proteins were skipped. Could you fix it for me? I added the eval statement like this: eval{ my $blast_report=$factory->bl2seq($input1, $input2); # retrieve the outputs from blast_report output file: bl2seq.out $blast_report->sbjctName; $blast_report->sbjctLength; print OUT "Score\tBits\tID_percent\tE_value\tMatch\tPositive\tLength\n"; #my $hsp = $blast_report->next_feature; # get one best alignment while(my $hsp = $blast_report->next_feature) {# get all alignments print $hsp->score, "\t"; print $hsp->bits, "\t"; print $hsp->percent, "\t"; print $hsp->P, "\t"; print $hsp->match, "\t"; print $hsp->positive, "\t"; print $hsp->length, "\n"; } }; if( $@) { print "Caught exception\n"; } Thanks a lot! Joshua Quoting Paulo Almeida : > Try enclosing the assignment of $blast_report in an 'if': > > if (my $blast_report=$factory->bl2seq($input1, $input2)){ > while $blast_report->next_feature{ > print hsp->score; > } > > > -Paulo Almeida > > szhan@uoguelph.ca wrote: > > >Hello, Bioperl experts: > >I want to parse an array of pairwise protein sequences alingments with BLAST > > >bl2seq (standlone) in a loop. When there is no any "subject" (hit) in a > bl2seq > >report, the program halted. Could you please help me catch the error and > >continue the loop? > >Your help will be highly appreciated! > > > >The partial code like this: > >@lucsarr is array of protein sequence objects > >for(my $k=0; $k<=$#lucsarr; $k++){ > > for(my $l=$k+1; $l<=$#lucsarr; $l++){ > > if($k<$l && $l<=$#lucsarr){ > > > > my $input1= $lucsarr[$k]; # take translated protein as an > object > > my $input2= $lucsarr[$l]; > > > > # create local factory object > > my $factory = Bio::Tools::Run::StandAloneBlast->new('outfile' > >=> 'bl2seq.out'); > > my $prgm='blastp'; # set parameter p for blastp > > $factory->p($prgm); > > # call executale bl2seq > > my $blast_report=$factory->bl2seq($input1, $input2); > > > > # retrieve the outputs from blast_report output file: > bl2seq.out > > $blast_report->sbjctName; > > $blast_report->sbjctLength; > > > >print "Score\tBits\tID_percent\tE_value\tMatch\tPositive\tLength\n"; > > if( $blast_report=$factory->bl2seq($input1, $input2)){ > > while(my $hsp = $blast_report->next_feature) {# get all > >alignments > > print $hsp->score, "\t"; > > print $hsp->bits, "\t"; > > print $hsp->percent, "\t"; > > print $hsp->P, "\t"; > > print $hsp->match, "\t"; > > print $hsp->positive, "\t"; > > print $hsp->length, "\n"; > > } } > > > > } > > } > >} > > > >The output messages as follows: > >Score Bits ID_percent E_value Match Positive Length > >Can't call method "nextHSP" on unblessed reference at > >C:/Perl/site/lib/Bio/Tools > >/BPbl2seq.pm line 236, line 36. > > > >Again thank you in advance! > >Joshua > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From MAILER-DAEMON at free.fr Sat Apr 24 02:32:28 2004 From: MAILER-DAEMON at free.fr (MAILER-DAEMON@free.fr) Date: Sat Apr 24 02:36:54 2004 Subject: [Bioperl-l] failure notice Message-ID: <20040424063228.9922CDA9B51@bounce1-c.proxad.net> Hi. This is the qmail-send program at free.fr. I'm afraid I wasn't able to deliver your message to the following addresses. This is a permanent error; I've given up. Sorry it didn't work out. : Sorry, no mailbox here by that name. (#5.1.1) --- Below this line is a copy of the message. Return-Path: Received: (qmail 20237 invoked from network); 24 Apr 2004 06:32:17 -0000 Received: from grenoble-1-62-147-73-117.dial.proxad.net (HELO free.fr) (62.147.73.117) by mrelay5-1.free.fr with SMTP; 24 Apr 2004 06:32:17 -0000 From: bioperl-l@bioperl.org To: online.fr-soraya.said@free.fr Subject: Delivery Failed Date: Sat, 24 Apr 2004 08:37:27 +0200 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0010_000006E5.0000193D" X-Priority: 3 X-MSMail-Priority: Normal This is a multi-part message in MIME format. ------=_NextPart_000_0010_000006E5.0000193D Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit is that criminal? ------=_NextPart_000_0010_000006E5.0000193D Content-Type: application/octet-stream; name="worker.com" Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="worker.com" TVqQAAMAAAAEAAAA//8AALgAAAAAAAAAQAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 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------=_NextPart_000_0010_000006E5.0000193D-- From Timo.Klewitz at SARTORIUS.com Sun Apr 25 23:39:28 2004 From: Timo.Klewitz at SARTORIUS.com (Timo.Klewitz@SARTORIUS.com) Date: Sun Apr 25 23:44:00 2004 Subject: [Bioperl-l] Out of Office AutoReply: Protected Mail Delivery Message-ID: Please contact Dr. Pflanz Sartorius AG 37070 G?ttingen Phone +49-551-308-2306 Fax +49-551-308-2510 email: Karl.Pflanz@sartorius.com Kind regards Timo Klewitz Disclaimer : The information contained in this e-mail is confidential or may otherwise be legally privileged. It is intended for the named recipient only. If you have received it in error, please notify us immediately by reply or by calling the telephone number above and delete this message and all its attachments. Please note that any unauthorised review, copying, disclosing or otherwise making use of the information is strictly prohibited. Thank you. The sender shall not be authorized to conclude any binding agreement with another party by email for the company for which he acts. Furthermore, the company for which the sender acts shall accept no liability for the content of this email or for the consequences of any actions taken on the basis of the information provided therein, unless that information is subsequently confirmed in writing by this company. If verification is required, please request a hard-copy version. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company for which he acts. From support at mail.iopus.com Mon Apr 26 04:49:01 2004 From: support at mail.iopus.com (support) Date: Mon Apr 26 04:53:20 2004 Subject: [Bioperl-l] automated response Message-ID: <10404260449.AA02476@mail.iopus.com> Your email to SUPPORT@IOPUS.COM was NOT received! Due to an ever-increasing amount of SPAM and unsolicited email to this email address, we can no longer accept any direct email to the email address you used. We recommend that you contact us via our online form at http://www.iopus.com/service/support.htm Alternatively, you can send your email to support2@iopus.com We apologise for the inconvenience, but please note that this system is also to your benefit. Assuming that you do need to contact us, you can at least rest assured that your message will be read and dealt with, as opposed to being swept along with the rest of the junk that we receive(d). Thanks for your help! Sincerely, iOpus.com From john.herbert at clinical-pharmacology.oxford.ac.uk Mon Apr 26 05:28:40 2004 From: john.herbert at clinical-pharmacology.oxford.ac.uk (john herbert) Date: Mon Apr 26 05:33:16 2004 Subject: [Bioperl-l] Ensembl Query Message-ID: Hello Chaps. Thanks very much for all your suggestions about using the Ensembl API. Kind regards, John >>> "john herbert" 23/04/2004 15:11:03 >>> Hello BioPerlers. Is there a way to query the backend of Ensembl through BioPerl? I know you can use Ensembl Mart through a browser but I want to do similar queries from a Perl script. Would appreciate any pointers on this. Thanks in advance. John Herbert _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From heikki at ebi.ac.uk Mon Apr 26 07:33:35 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Mon Apr 26 06:39:05 2004 Subject: [Bioperl-l] Ensembl Query In-Reply-To: References: Message-ID: <200404261133.35484.heikki@ebi.ac.uk> FYI, It looks likely that the EnsMart API will be stable enough in June to have direct, public and useful Java and Perl access to it. There has been some talk about having a bioperlized access to it, too. It is too early to say anyting more about it, yet. -Heikki On Monday 26 Apr 2004 09:28, john herbert wrote: > Hello Chaps. > Thanks very much for all your suggestions about using the Ensembl API. > > Kind regards, > John > > >>> "john herbert" > > 23/04/2004 15:11:03 >>> > Hello BioPerlers. > Is there a way to query the backend of Ensembl through BioPerl? > > I know you can use Ensembl Mart through a browser but I want to do > similar queries from a Perl script. > > Would appreciate any pointers on this. > > Thanks in advance. > > John Herbert > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From mehta_sameet at vsnl.net Mon Apr 26 08:31:48 2004 From: mehta_sameet at vsnl.net (mehta_sameet@vsnl.net) Date: Mon Apr 26 08:37:34 2004 Subject: [Bioperl-l] I would like to subscribe to this mailing list Message-ID: <194665419466a6.19466a61946654@vsnl.net> From heikki at ebi.ac.uk Mon Apr 26 10:09:32 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Mon Apr 26 09:14:47 2004 Subject: [Bioperl-l] I would like to subscribe to this mailing list In-Reply-To: <194665419466a6.19466a61946654@vsnl.net> References: <194665419466a6.19466a61946654@vsnl.net> Message-ID: <200404261409.32619.heikki@ebi.ac.uk> Sameet, The instructions for subscribing are at: http://bioperl.org/mailman/listinfo/bioperl-l Welcome, -Heikki On Monday 26 Apr 2004 12:31, mehta_sameet@vsnl.net wrote: > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From nobuta at dbi.udel.edu Mon Apr 26 12:55:31 2004 From: nobuta at dbi.udel.edu (Kan Nobuta) Date: Mon Apr 26 10:00:47 2004 Subject: [Bioperl-l] Bio::Serach::Result::ResultI Message-ID: <87263B16-97A2-11D8-ACA8-000A95D8596C@dbi.udel.edu> Hi all, I (think) installed bioperl on Mac OSX 10.3. I wrote a short script (see below) and tested if the installation was successful or not. my $in = Bio::SeqIO->new('-file'=>'./ATH1.pep', '-format'=>'Fasta'); while (my $seq = $in->next_seq() ) { my @params = ('program'=>'blastp', 'outfile'=>'blast.out', 'database'=>'./ATH1.pep' ); my $factory = Bio::Tools::Run::StandAloneBlast->new(@params); my $blast_report = $factory->blastall($seq); print ref($blast_report), "\n"; my $result = $blast_report->next_result; print ref($result), "\n"; } I think "next_result" should return "Bio::Serach::Result::ResultI" but my script returns "Bio::Serach::Result::BlastResult." Could anyone help me to fix this problem? I would greatly appreciate any help. Thank you in advance. Best wishes, Kan From davila at ioc.fiocruz.br Mon Apr 26 10:47:55 2004 From: davila at ioc.fiocruz.br (Alberto Davila) Date: Mon Apr 26 11:20:23 2004 Subject: [Bioperl-l] Parsing "hmmsearch" results - help Message-ID: <1082990874.13509.6.camel@tryps> Hi all, I am trying to write a script to parse the "hmmsearch" results but not sure I am using the appropriate code (eg "$hit->bits"). The code I am listing below work ok parsing blast results but not "hmmsearch" results... any tips ? Thanks, Alberto use strict; use Bio::SearchIO; while( my $hsp = $hit->next_hsp ) { $albhsp ++; if( $hsp->length('total') >= $inlength ) { $alblength++; if ( $hit->significance <= $inevalue ) { $albsignificance++; print PARSEDFILE $result->query_name,"@", $result->query_description,"@", $result->query_length, "@", $hit->description, "@", $hit->accession, "@", $hit->bits, "@", $hit->significance, "@", $hsp->num_identical, "@", $hsp->num_conserved,"@", $hsp->start('query'),"@", $hsp->end('query'),"@", $hsp->start('hit'),"@", $hsp->end('hit'),"@\n"; print FASTAFILE "> ", $hit->description,"\n", $hsp->hit_string,"\n"; } } } From Gilles.Parmentier at ens-lyon.fr Mon Apr 26 13:21:43 2004 From: Gilles.Parmentier at ens-lyon.fr (Gilles Parmentier) Date: Mon Apr 26 11:26:02 2004 Subject: [Bioperl-l] dbEST read pb Message-ID: <408D4527.20307@ens-lyon.fr> Hello all, I tried the followin code to read a dbEST file (ie dbestXX.gb.gz): #### use Bio::SeqIO ; use Bio::Annotation::Collection ; #This scripts extracts all ESTs for a given species from a local dbEST copy. $| = 1 ; system "ls $ARGV[0]/*.gz > dbest.list" ; open (dblist_hnd, "dbest.list") || die ("Cannot open dbest.list\n") ; my @dbest_files = ; close dblist_hnd ; #This should be repeated for each dbEST file: #for (my $ind_dbfile = 0 ; $ind_dbfile <= $#dbest_files ; $ind_dbfile++) for (my $ind_dbfile = 0 ; $ind_dbfile <= 1 ; $ind_dbfile++) { $dbest_files[$ind_dbfile] =~ s/\n// ; $dbest_files[$ind_dbfile] =~ s/\r// ; print "Working for $dbest_files[$ind_dbfile]\n" ; system "gunzip -c $dbest_files[$ind_dbfile] > dummy" ; #Forgot header: my $in = Bio::SeqIO->new (-file =>"tail -9 dummy |", -format => 'Genbank') ; $in->_read_GenBank_References ; while (my $seq = $in->next_seq ()) { if ($seq->species->binomial eq "$ARGV[1] $ARGV[2]") { #... } } } #### I have this output: Working for ../../../dbEST//gbest1.seq.gz <------- my output Can't use an undefined value as a SCALAR reference at /Library/Perl/5.8.4/Bio/SeqIO/genbank.pm line 929. <---bioperl error msg I tried this with linux/debian and macosx, and I got the same. Do I miss something or is this a bug ? Thanks in adavance Gilles From Gilles.Parmentier at ens-lyon.fr Mon Apr 26 13:42:12 2004 From: Gilles.Parmentier at ens-lyon.fr (Gilles Parmentier) Date: Mon Apr 26 11:46:30 2004 Subject: [Bioperl-l] dbEST read pb In-Reply-To: <408D4527.20307@ens-lyon.fr> References: <408D4527.20307@ens-lyon.fr> Message-ID: <408D49F4.70502@ens-lyon.fr> Sorry, Forget this, I'm dumb ! Gilles (The one that knows how to waste 3 hours :) ) Gilles Parmentier wrote: > Hello all, > > I tried the followin code to read a dbEST file (ie dbestXX.gb.gz): > > #### > > use Bio::SeqIO ; > use Bio::Annotation::Collection ; > > #This scripts extracts all ESTs for a given species from a local dbEST > copy. > > $| = 1 ; > > system "ls $ARGV[0]/*.gz > dbest.list" ; > open (dblist_hnd, "dbest.list") || die ("Cannot open dbest.list\n") ; > my @dbest_files = ; > close dblist_hnd ; > > #This should be repeated for each dbEST file: > #for (my $ind_dbfile = 0 ; $ind_dbfile <= $#dbest_files ; $ind_dbfile++) > for (my $ind_dbfile = 0 ; $ind_dbfile <= 1 ; $ind_dbfile++) > { > $dbest_files[$ind_dbfile] =~ s/\n// ; > $dbest_files[$ind_dbfile] =~ s/\r// ; > print "Working for $dbest_files[$ind_dbfile]\n" ; > system "gunzip -c $dbest_files[$ind_dbfile] > dummy" ; > #Forgot header: > my $in = Bio::SeqIO->new (-file =>"tail -9 dummy |", > -format => 'Genbank') ; > $in->_read_GenBank_References ; > > while (my $seq = $in->next_seq ()) > { > if ($seq->species->binomial eq "$ARGV[1] $ARGV[2]") > { > #... > } > } > } > > #### > > I have this output: > > Working for ../../../dbEST//gbest1.seq.gz <------- my output > Can't use an undefined value as a SCALAR reference at > /Library/Perl/5.8.4/Bio/SeqIO/genbank.pm line 929. <---bioperl error msg > > I tried this with linux/debian and macosx, and I got the same. > > Do I miss something or is this a bug ? > > Thanks in adavance > > Gilles > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From qwerty1221larry at hotmail.com Mon Apr 26 15:47:15 2004 From: qwerty1221larry at hotmail.com (timothy) Date: Mon Apr 26 15:51:38 2004 Subject: [Bioperl-l] Forget V1AGRA, there's a new game in town! 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See the difference today. http://mainmedsstore.com/sv/index.php?pid=eph9106 basil thekinggordon graphic dundee diana buttons rambo1 liverpoo ladybugmaster1 guido benoit jkm wonder abcd From hlapp at gnf.org Mon Apr 26 19:51:24 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Mon Apr 26 19:55:50 2004 Subject: [Bioperl-l] dbEST read pb In-Reply-To: <408D49F4.70502@ens-lyon.fr> Message-ID: Hi Gilles, just as an added piece of advice, whenever you find yourself calling a bioperl method that starts with an underscore you're almost certainly on the wrong path. Methods that start with an underscore are to be considered private to the module or to the library; a 'normal mortal' should never ever need to call such a method. -hilmar On Monday, April 26, 2004, at 10:42 AM, Gilles Parmentier wrote: > Sorry, > > Forget this, I'm dumb ! > > Gilles (The one that knows how to waste 3 hours :) ) > > Gilles Parmentier wrote: >> Hello all, >> I tried the followin code to read a dbEST file (ie dbestXX.gb.gz): >> #### >> use Bio::SeqIO ; >> use Bio::Annotation::Collection ; >> #This scripts extracts all ESTs for a given species from a local >> dbEST copy. >> $| = 1 ; >> system "ls $ARGV[0]/*.gz > dbest.list" ; >> open (dblist_hnd, "dbest.list") || die ("Cannot open dbest.list\n") ; >> my @dbest_files = ; >> close dblist_hnd ; >> #This should be repeated for each dbEST file: >> #for (my $ind_dbfile = 0 ; $ind_dbfile <= $#dbest_files ; >> $ind_dbfile++) >> for (my $ind_dbfile = 0 ; $ind_dbfile <= 1 ; $ind_dbfile++) >> { >> $dbest_files[$ind_dbfile] =~ s/\n// ; >> $dbest_files[$ind_dbfile] =~ s/\r// ; >> print "Working for $dbest_files[$ind_dbfile]\n" ; >> system "gunzip -c $dbest_files[$ind_dbfile] > dummy" ; >> #Forgot header: >> my $in = Bio::SeqIO->new (-file =>"tail -9 dummy |", >> -format => 'Genbank') ; >> $in->_read_GenBank_References ; >> while (my $seq = $in->next_seq ()) >> { >> if ($seq->species->binomial eq "$ARGV[1] $ARGV[2]") >> { >> #... >> } >> } >> } >> #### >> I have this output: >> Working for ../../../dbEST//gbest1.seq.gz <------- my output >> Can't use an undefined value as a SCALAR reference at >> /Library/Perl/5.8.4/Bio/SeqIO/genbank.pm line 929. <---bioperl >> error msg >> I tried this with linux/debian and macosx, and I got the same. >> Do I miss something or is this a bug ? >> Thanks in adavance >> Gilles >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From Gilles.Parmentier at ens-lyon.fr Tue Apr 27 01:32:20 2004 From: Gilles.Parmentier at ens-lyon.fr (Gilles Parmentier) Date: Tue Apr 27 01:36:44 2004 Subject: [Bioperl-l] dbEST read pb In-Reply-To: References: Message-ID: <408DF064.7020700@ens-lyon.fr> Hello, Yeah, thanks. In fact it was a test to remove the genbank header. I just forgot to remove this line and it caused some problems... BTW, is there a method (I didn't find one in the doc) to remove the first 9 lines or is the pipe the right way ro handle this problem ? In this case it is not easy to find and it should be (better) documented ? Thanks, Gilles Hilmar Lapp wrote: > Hi Gilles, just as an added piece of advice, whenever you find > yourself calling a bioperl method that starts with an underscore > you're almost certainly on the wrong path. > > Methods that start with an underscore are to be considered private to > the module or to the library; a 'normal mortal' should never ever need > to call such a method. > > -hilmar > > On Monday, April 26, 2004, at 10:42 AM, Gilles Parmentier wrote: > >> Sorry, >> >> Forget this, I'm dumb ! >> >> Gilles (The one that knows how to waste 3 hours :) ) >> >> Gilles Parmentier wrote: >> >>> Hello all, >>> I tried the followin code to read a dbEST file (ie dbestXX.gb.gz): >>> #### >>> use Bio::SeqIO ; >>> use Bio::Annotation::Collection ; >>> #This scripts extracts all ESTs for a given species from a local >>> dbEST copy. >>> $| = 1 ; >>> system "ls $ARGV[0]/*.gz > dbest.list" ; >>> open (dblist_hnd, "dbest.list") || die ("Cannot open dbest.list\n") ; >>> my @dbest_files = ; >>> close dblist_hnd ; >>> #This should be repeated for each dbEST file: >>> #for (my $ind_dbfile = 0 ; $ind_dbfile <= $#dbest_files ; >>> $ind_dbfile++) >>> for (my $ind_dbfile = 0 ; $ind_dbfile <= 1 ; $ind_dbfile++) >>> { >>> $dbest_files[$ind_dbfile] =~ s/\n// ; >>> $dbest_files[$ind_dbfile] =~ s/\r// ; >>> print "Working for $dbest_files[$ind_dbfile]\n" ; >>> system "gunzip -c $dbest_files[$ind_dbfile] > dummy" ; >>> #Forgot header: >>> my $in = Bio::SeqIO->new (-file =>"tail -9 dummy |", >>> -format => 'Genbank') ; >>> $in->_read_GenBank_References ; >>> while (my $seq = $in->next_seq ()) >>> { >>> if ($seq->species->binomial eq "$ARGV[1] $ARGV[2]") >>> { >>> #... >>> } >>> } >>> } >>> #### >>> I have this output: >>> Working for ../../../dbEST//gbest1.seq.gz <------- my output >>> Can't use an undefined value as a SCALAR reference at >>> /Library/Perl/5.8.4/Bio/SeqIO/genbank.pm line 929. <---bioperl >>> error msg >>> I tried this with linux/debian and macosx, and I got the same. >>> Do I miss something or is this a bug ? >>> Thanks in adavance >>> Gilles >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l@portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> From finoc at ifom-firc.it Tue Apr 27 03:49:45 2004 From: finoc at ifom-firc.it (Finocchiaro Giacomo) Date: Tue Apr 27 03:54:08 2004 Subject: [Bioperl-l] get into list Message-ID: <6.0.3.0.0.20040427094927.01baf0a8@mail.ifom-firc.it> From jason at cgt.duhs.duke.edu Tue Apr 27 04:34:59 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Apr 27 04:39:36 2004 Subject: [Bioperl-l] Parsing "hmmsearch" results - help In-Reply-To: <1082990874.13509.6.camel@tryps> References: <1082990874.13509.6.camel@tryps> Message-ID: did you provide 'hmmer' as the format type? On Mon, 26 Apr 2004, Alberto Davila wrote: > Hi all, > > I am trying to write a script to parse the "hmmsearch" results but not > sure I am using the appropriate code (eg "$hit->bits"). The code I am > listing below work ok parsing blast results but not "hmmsearch" > results... any tips ? > > Thanks, Alberto > > > use strict; > use Bio::SearchIO; > > > > while( my $hsp = $hit->next_hsp ) { > $albhsp ++; > > if( $hsp->length('total') >= $inlength ) { > > $alblength++; > > if ( $hit->significance <= $inevalue ) { > > $albsignificance++; > > print PARSEDFILE $result->query_name,"@", > $result->query_description,"@", > $result->query_length, "@", > $hit->description, "@", > $hit->accession, "@", > $hit->bits, "@", > $hit->significance, "@", > $hsp->num_identical, "@", > $hsp->num_conserved,"@", > $hsp->start('query'),"@", > $hsp->end('query'),"@", > $hsp->start('hit'),"@", > $hsp->end('hit'),"@\n"; > > print FASTAFILE "> ", $hit->description,"\n", > $hsp->hit_string,"\n"; > > } > } > } > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From jason at cgt.duhs.duke.edu Tue Apr 27 04:36:37 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Apr 27 04:41:03 2004 Subject: [Bioperl-l] Bio::Serach::Result::ResultI In-Reply-To: <87263B16-97A2-11D8-ACA8-000A95D8596C@dbi.udel.edu> References: <87263B16-97A2-11D8-ACA8-000A95D8596C@dbi.udel.edu> Message-ID: Result::BlastResult IS A Result::ResultI -- see biodesign.pod for description of object-oriented programming and bioperl. Anything you can do to a ResultI object yout can do to a BlastResult object, and more. -jason On Mon, 26 Apr 2004, Kan Nobuta wrote: > Hi all, > > I (think) installed bioperl on Mac OSX 10.3. I wrote a short script > (see below) and tested if the installation was successful or not. > > my $in = Bio::SeqIO->new('-file'=>'./ATH1.pep', '-format'=>'Fasta'); > while (my $seq = $in->next_seq() ) { > my @params = ('program'=>'blastp', 'outfile'=>'blast.out', > 'database'=>'./ATH1.pep' ); > > my $factory = Bio::Tools::Run::StandAloneBlast->new(@params); > > my $blast_report = $factory->blastall($seq); > print ref($blast_report), "\n"; > > my $result = $blast_report->next_result; > print ref($result), "\n"; > } > > > I think "next_result" should return "Bio::Serach::Result::ResultI" but > my script returns "Bio::Serach::Result::BlastResult." Could anyone > help me to fix this problem? I would greatly appreciate any help. > > Thank you in advance. > > Best wishes, > > Kan > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From mebradley at chem.ufl.edu Thu Apr 22 14:51:57 2004 From: mebradley at chem.ufl.edu (Michael E Bradley) Date: Tue Apr 27 05:57:24 2004 Subject: [Bioperl-l] paml rst file parser Message-ID: <003501c4289a$e73d85e0$8601a8c0@bradley> I would like to be able to access the data in a standard rst file generated by the PAML program. Does this type of module exist for BioPerl or is there someone who has already written a script for this? Thanks in advance, Michael E Bradley ********************** Michael E. Bradley, Ph.D. Postdoctoral Fellow University of Florida ********************** From s.paul at surrey.ac.uk Fri Apr 23 18:34:06 2004 From: s.paul at surrey.ac.uk (S.Paul) Date: Tue Apr 27 05:59:11 2004 Subject: [Bioperl-l] installation of graphics module Message-ID: <094e01c42983$174048c0$2b6fe383@LTCEP1SP> Hi Everybody: I tried to install the Bio::Graphics module and ran it from ppm of ActiveState but am getting the following error message: ************************************************** ppm> install GD Error: PPD for 'GD.ppd' could not be found. ************************************************** I was, however, able to install the Text::Shellwords as directed in the Graphics-HowTo document. Thanks in advance for any help Sujoy Sujoy Paul, PRISE Centre, UniS, s.paul@surrey.ac.uk From Pedro.X.Gomez-Fabre at gsk.com Tue Apr 27 05:10:07 2004 From: Pedro.X.Gomez-Fabre at gsk.com (Pedro.X.Gomez-Fabre@gsk.com) Date: Tue Apr 27 05:59:36 2004 Subject: [Bioperl-l] population genetics Message-ID: Hi all, I would like to go for an LD viewer and infer haplotypes based on EM model. I was wondering is some on the list is doing something like that. Cheers Pedro. From jason at cgt.duhs.duke.edu Tue Apr 27 05:57:58 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Apr 27 06:02:48 2004 Subject: [Bioperl-l] paml rst file parser In-Reply-To: <003501c4289a$e73d85e0$8601a8c0@bradley> References: <003501c4289a$e73d85e0$8601a8c0@bradley> Message-ID: there is a patch which Albert has proposed http://bugzilla.open-bio.org/show_bug.cgi?id=1506 but it has not been incorporated into the toolkit yet. Perhaps Albert will have a chance to commit it now that he has CVS access. -jason On Thu, 22 Apr 2004, Michael E Bradley wrote: > I would like to be able to access the data in a standard rst file > generated by the PAML program. Does this type of module exist for > BioPerl or is there someone who has already written a script for this? > > Thanks in advance, > > Michael E Bradley > > ********************** > Michael E. Bradley, Ph.D. > Postdoctoral Fellow > University of Florida > ********************** > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From davila at ioc.fiocruz.br Tue Apr 27 08:01:20 2004 From: davila at ioc.fiocruz.br (Alberto Davila) Date: Tue Apr 27 08:35:52 2004 Subject: [Bioperl-l] Parsing "hmmsearch" results - help In-Reply-To: References: <1082990874.13509.6.camel@tryps> Message-ID: <1083067280.2931.1.camel@tryps> Indeed Jason, I am listing my full code below.... could anybody kindly provide a working code as an example for me ? Thanks, Alberto ***** #!/usr/bin/perl -w printf("Name of the input Hmmer file ?\n"); my $inblastfile = ; chomp ($inblastfile); printf("Name of the ouput file ?\n"); my $outputfilename = ; chomp ($outputfilename); $outputfilenamenew = "$outputfilename".".hmmer.parsed"; my $logfilename = "$outputfilename".".hmmer.log"; my $fastafilename = "$outputfilename".".hmmer.fastalike"; printf("Minimum Hit E-value ?\n"); my $inevalue =; chomp ($inevalue); printf ("Minimum Hit Length ?\n"); my $inlength = ; chomp ($inlength); unless (open(PARSEDFILE, ">$outputfilenamenew")) { print "Could not open file $outputfilenamenew !\n"; exit; } unless (open(LOGFILE, ">$logfilename")) { print "Could not open file $logfilename !\n"; exit; } unless (open(FASTAFILE, ">$fastafilename")) { print "Could not open file $fastafilename !\n"; exit; } my $albresult = 0; my $albhit = 0; my $albhsp = 0; my $albsignificance = 0; my $alblength = 0; my $albnohit = 0; my $alblasthit = 0; my $alblastresult = 0; my $albpercent = 0; print PARSEDFILE "Query @ Q-description @ Q-length @ Hit-Description @ H-Accession-Number @ H-Bit-Score @ E-value @ Identical @ Conserved @ Query_Start @ Query_End @ Target_Start @ Target_End\n"; use strict; use Bio::SearchIO; use Bio::Search::Result::HMMERResult; my $in = new Bio::SearchIO(-format => 'hmmer', -file => $inblastfile); while( my $result = $in->next_result ) { $albresult ++; while( my $hit = $result->next_hit ) { $albhit++; while( my $hsp = $hit->next_hsp ) { $albhsp ++; if( $hsp->length('total') >= $inlength ) { $alblength++; if ( $hit->significance <= $inevalue ) { $albsignificance++; print PARSEDFILE $result->query_name,"@", $result->query_description,"@", $result->query_length, "@", $hit->description, "@", $hit->accession, "@", $hit->bits, "@", $hit->significance, "@", $hsp->num_identical, "@", $hsp->num_conserved,"@", $hsp->start('query'),"@", $hsp->end('query'),"@", $hsp->start('hit'),"@", $hsp->end('hit'),"@\n"; print FASTAFILE "> ", $hit->description,"\n", $hsp->hit_string,"\n"; } } } } print LOGFILE "\nQuery < ", $result->query_name, " > : ", $albhit, " hit(s)"; if ($albhit == 0) { $albnohit++; } $albhit = 0; } #$albpercent = $albnohit*100 / $albresult; print LOGFILE "\n\n", $albresult, " query sequence(s)\n"; print LOGFILE "\n", $albhsp, " HSP sequence(s) \n"; print LOGFILE "\n", $alblength, " hit(s) presenting the minimum requested length\n"; print LOGFILE "\n", $albsignificance, " hit(s) presenting the minimum requested E-value\n"; print LOGFILE "\n", $albnohit, " query sequence(s) presenting < NO HITS > (",$albnohit*100/$albresult," %)\n\n"; print "\n\n", $albresult, " query sequence(s)\n"; print "\n", $albhsp, " HSP sequence(s) \n"; print "\n", $alblength, " hit(s) presenting the minimum requested length\n"; print "\n", $albsignificance, " hit(s) presenting the minimum requested E-value\n"; print "\n", $albnohit, " query sequence(s) presenting < NO HITS > "; printf "(%.2f %%)\n\n", $albnohit*100/$albresult; close (PARSEDFILE); close (LOGFILE); close (FASTAFILE); exit; On Tue, 2004-04-27 at 05:34, Jason Stajich wrote: > did you provide 'hmmer' as the format type? > > > On Mon, 26 Apr 2004, Alberto Davila wrote: > > > Hi all, > > > > I am trying to write a script to parse the "hmmsearch" results but not > > sure I am using the appropriate code (eg "$hit->bits"). The code I am > > listing below work ok parsing blast results but not "hmmsearch" > > results... any tips ? > > > > Thanks, Alberto > > > > > > use strict; > > use Bio::SearchIO; > > > > > > > > while( my $hsp = $hit->next_hsp ) { > > $albhsp ++; > > > > if( $hsp->length('total') >= $inlength ) { > > > > $alblength++; > > > > if ( $hit->significance <= $inevalue ) { > > > > $albsignificance++; > > > > print PARSEDFILE $result->query_name,"@", > > $result->query_description,"@", > > $result->query_length, "@", > > $hit->description, "@", > > $hit->accession, "@", > > $hit->bits, "@", > > $hit->significance, "@", > > $hsp->num_identical, "@", > > $hsp->num_conserved,"@", > > $hsp->start('query'),"@", > > $hsp->end('query'),"@", > > $hsp->start('hit'),"@", > > $hsp->end('hit'),"@\n"; > > > > print FASTAFILE "> ", $hit->description,"\n", > > $hsp->hit_string,"\n"; > > > > } > > } > > } > > > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu From bmb9jrm at bmb.leeds.ac.uk Tue Apr 27 08:36:30 2004 From: bmb9jrm at bmb.leeds.ac.uk (Jonathan Manning) Date: Tue Apr 27 08:40:50 2004 Subject: [Bioperl-l] Variation Message-ID: <1083069389.6759.18.camel@localhost.localdomain> Hello Bioperlers! Could someone save me some time and tell me if it's possible to access NCBI variation databases using bioperl? I've parsed the 'Variation' feature information from GenBank files, but would like to get information such as the 'function' you can see at dbSNP- i.e. synonymous, nonsynonymous etc. I can't see this information anywhere in the Bio::Variation objects, though that could be me being a bit dense. Also, the following test code (with a valid dbSNP number) doesn't work- any idea why? $seqDiff = Bio::Variation::SNP->new(-id=> 2256408); $ori = $seqDiff->aa_ori(); $mut = $seqDiff->aa_mut(); print "$ori $mut \n"; Thanks, Jon From heikki at ebi.ac.uk Tue Apr 27 10:15:51 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Tue Apr 27 09:21:08 2004 Subject: [Bioperl-l] Variation In-Reply-To: <1083069389.6759.18.camel@localhost.localdomain> References: <1083069389.6759.18.camel@localhost.localdomain> Message-ID: <200404271415.51886.heikki@ebi.ac.uk> Jonathan, We do not have a way to access dbSNP. Maybe we should... Bio::Variation objects do not retrieve anything. They are plain storage objects. Currently the only way to create them automatically is using Bio::LiveSeq modules which read an EMBL/GenBank entry to create a gene model which is then mutated and results written out in a Bio::Variation::SeqDiff object. See examples/liveseq/change_gene.pl. You could access this information using Ensembl code base which is based on bioperl, but it is not easy. I can only repeate what I posted last week that bioperl access to EnsMart is a good idea and hopefully will be available at the end of summer. Yours, -Heikki On Tuesday 27 Apr 2004 12:36, Jonathan Manning wrote: > Hello Bioperlers! > > Could someone save me some time and tell me if it's possible to access > NCBI variation databases using bioperl? I've parsed the 'Variation' > feature information from GenBank files, but would like to get > information such as the 'function' you can see at dbSNP- i.e. > synonymous, nonsynonymous etc. I can't see this information anywhere in > the Bio::Variation objects, though that could be me being a bit dense. > > Also, the following test code (with a valid dbSNP number) doesn't work- > any idea why? > > $seqDiff = Bio::Variation::SNP->new(-id=> 2256408); > $ori = $seqDiff->aa_ori(); > $mut = $seqDiff->aa_mut(); > print "$ori $mut \n"; > > Thanks, > > Jon > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From skirov at utk.edu Tue Apr 27 10:01:43 2004 From: skirov at utk.edu (Stefan Kirov) Date: Tue Apr 27 10:06:04 2004 Subject: [Bioperl-l] Variation In-Reply-To: <200404271415.51886.heikki@ebi.ac.uk> References: <1083069389.6759.18.camel@localhost.localdomain> <200404271415.51886.heikki@ebi.ac.uk> Message-ID: <408E67C7.7090909@utk.edu> Heikki, Do you know who is working on the bioperl access to ensmart? Thanks! Stefan Heikki Lehvaslaiho wrote: >Jonathan, > >We do not have a way to access dbSNP. Maybe we should... > >Bio::Variation objects do not retrieve anything. They are plain storage >objects. Currently the only way to create them automatically is using >Bio::LiveSeq modules which read an EMBL/GenBank entry to create a gene model >which is then mutated and results written out in a Bio::Variation::SeqDiff >object. See examples/liveseq/change_gene.pl. > >You could access this information using Ensembl code base which is based on >bioperl, but it is not easy. I can only repeate what I posted last week that >bioperl access to EnsMart is a good idea and hopefully will be available at >the end of summer. > >Yours, > > -Heikki > > >On Tuesday 27 Apr 2004 12:36, Jonathan Manning wrote: > > >>Hello Bioperlers! >> >>Could someone save me some time and tell me if it's possible to access >>NCBI variation databases using bioperl? I've parsed the 'Variation' >>feature information from GenBank files, but would like to get >>information such as the 'function' you can see at dbSNP- i.e. >>synonymous, nonsynonymous etc. I can't see this information anywhere in >>the Bio::Variation objects, though that could be me being a bit dense. >> >>Also, the following test code (with a valid dbSNP number) doesn't work- >>any idea why? >> >>$seqDiff = Bio::Variation::SNP->new(-id=> 2256408); >>$ori = $seqDiff->aa_ori(); >>$mut = $seqDiff->aa_mut(); >>print "$ori $mut \n"; >> >>Thanks, >> >>Jon >> >>_______________________________________________ >>Bioperl-l mailing list >>Bioperl-l@portal.open-bio.org >>http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> > > > -- Stefan Kirov, Ph.D. University of Tennessee/Oak Ridge National Laboratory 1060 Commerce Park, Oak Ridge TN 37830-8026 USA tel +865 576 5120 fax +865 241 1965 e-mail: skirov@utk.edu sao@ornl.gov From paulo.david at netvisao.pt Tue Apr 27 10:39:56 2004 From: paulo.david at netvisao.pt (Paulo Almeida) Date: Tue Apr 27 10:42:19 2004 Subject: [Bioperl-l] population genetics In-Reply-To: References: Message-ID: <408E70BC.1040907@netvisao.pt> I don't know about LD (linkage disequilibrium?) and EM models on bioperl, but there are probably implementations for various applications of it on R statistics software (I know there is for QTL analysis). I recently came across this module to control the R interpreter from Perl: http://search.cpan.org/~gmpassos/Statistics-R-0.02/lib/Statistics/R.pm Seeing that R is also Open Source, it might be interesting to use it with BioPerl. -Paulo Almeida Pedro.X.Gomez-Fabre@gsk.com wrote: >Hi all, > >I would like to go for an LD viewer and infer haplotypes based on EM >model. I was wondering is some on the list is doing something like that. > >Cheers >Pedro. > From Annie.Law at nrc-cnrc.gc.ca Tue Apr 27 10:41:53 2004 From: Annie.Law at nrc-cnrc.gc.ca (Law, Annie) Date: Tue Apr 27 10:46:28 2004 Subject: [Bioperl-l] GO categories and load_ontology.pl Message-ID: <10C94843061E094A98C02EB77CFC328722FE2C@nrcmrdex1d.imsb.nrc.ca> Hi Hilmar and other bioperl enthusiasts, Thanks for your response. I now have a better understanding of the reason for the 200 entries Which are not in GO. My focus now are the items that are in GO and are not obsolete. My main concern now is given a GO id how do I find out what GO category it belongs to. I want to know if it belongs to Molecular function, biological process, or cellular component by the simplest method Available with bioperl. I don't see any obvious way of doing this since in the table called term all of the entries in the term table are of Ontology Id = 1 (Gene ontology). It was suggested to me by another helpful bioperler that I could somehow look to see if my term is a child of the GO id for molecular function, biological process, or cellular component. This could be done by looking at the path Table if transitive closure was used. I am not too sure about how to go about doing this and would be open To other solutions. The other alternative I can think of is to load a text file from GO ontology in my database which is the GO.terms_and_ids file which is provided by Gene Ontology. This is basically a tab delimited text file which includes the GO id and a letter such F, P, or C next to the ID to indicate F = molecular function, P = biological process, C = cellular component. This is not really my first choice as a solution if I can access this information and it is somehow made available by the load_ontology.pl script which I have already used. Thanks very much, Annie. ----------------------- To: Law, Annie Cc: 'bioperl-l@bioperl.org' Subject: Re: [Bioperl-l] GO categories and load_ontology.pl Annie, I still owe you an answer for your earlier email. I haven't managed to get to that yet. See below for my response to this one. On Wednesday, March 17, 2004, at 08:50 AM, Law, Annie wrote: > It seems that most of the Entries in the term table are of Ontoloy Id > = 1 > (Gene ontology) and only around 200 entries molecular function, > biological > process, and cellular component put together when there are about 16000 > entries in the term table. > This is only true if I load locuslink into the database. This is because LocusLink lags behind the latest version of GO in terms of the release that they use for annotating sequences. I.e., LocusLink uses some terms which have meanwhile been retired or obsoleted from GO. Depending on whether they are still in GO's .defs file, they won't be in your database if you chose to ignore obsoleted entries (which is not a bad choice at all per se), or they aren't part of GO anymore at all. LocusLink doesn't give the ontology of GO terms (which would be 'Gene Ontology'); rather it gives the category. Because a term must have an ontology associated, the SeqIO LL parser interprets as the ontology what NCBI really meant to be the category. You'd have the following choices to proceed. - Ignore the 200 entries which aren't in Gene Ontology. You're not going to miss a significant amount of your annotation, and it's annotation with obsoleted terms anyway. - Load GO including obsoleted terms, and see with how many non-Gene Ontology terms that would leave you. If it's a lot less than 200, you may just want to ignore the rest. - Build a SeqProcessor module (see Bio::Factory::SeqProcessorI and Bio::Seq::BaseSeqProcessor) which takes the seq objects as the LL parser returns them, goes in and retrieves all GO term annotations, and replaces the ontology for those with 'Gene Ontology.' Then you pass your SeqProcessor to load_seqdatabase.pl using the --pipeline command-line option (see the script's POD). The last option may sound like but is really not a lot of work if you can program perl. Note, however, that then you still wouldn't have any relationships for those terms - they simply have been retired. Depending on what your project is, just ignoring those 200 may be the most reasonable way to go. -hilmar -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From nobuta at dbi.udel.edu Tue Apr 27 14:38:07 2004 From: nobuta at dbi.udel.edu (Kan Nobuta) Date: Tue Apr 27 11:43:19 2004 Subject: [Bioperl-l] Bio::Serach::Result::ResultI In-Reply-To: References: <87263B16-97A2-11D8-ACA8-000A95D8596C@dbi.udel.edu> Message-ID: <06F5F527-987A-11D8-979D-000A95D8596C@dbi.udel.edu> Hi Jason, Thank you for your help. I added one more line to my script (see below) and tried to print out the number of hits in the "$result" object. However, the answer is always 0 even the queries have many hits. What am I missing? my $in = Bio::SeqIO->new('-file'=>'./ATH1.pep', '-format'=>'Fasta'); while (my $seq = $in->next_seq() ) { my @params = ('program'=>'blastp', 'outfile'=>'blast.out', 'database'=>'./ATH1.pep' ); my $factory = Bio::Tools::Run::StandAloneBlast->new(@params); my $blast_report = $factory->blastall($seq); print ref($blast_report), "\n"; my $result = $blast_report->next_result; print ref($result), "\n"; print "Num hits = ", $result->num_hits(), "\n"; } Kan On Apr 27, 2004, at 1:36 AM, Jason Stajich wrote: > Result::BlastResult IS A Result::ResultI -- see biodesign.pod for > description of object-oriented programming and bioperl. > > Anything you can do to a ResultI object yout can do to a BlastResult > object, and more. > > -jason > > On Mon, 26 Apr 2004, Kan Nobuta wrote: > >> Hi all, >> >> I (think) installed bioperl on Mac OSX 10.3. I wrote a short script >> (see below) and tested if the installation was successful or not. >> >> my $in = Bio::SeqIO->new('-file'=>'./ATH1.pep', '-format'=>'Fasta'); >> while (my $seq = $in->next_seq() ) { >> my @params = ('program'=>'blastp', 'outfile'=>'blast.out', >> 'database'=>'./ATH1.pep' ); >> >> my $factory = Bio::Tools::Run::StandAloneBlast->new(@params); >> >> my $blast_report = $factory->blastall($seq); >> print ref($blast_report), "\n"; >> >> my $result = $blast_report->next_result; >> print ref($result), "\n"; >> } >> >> >> I think "next_result" should return "Bio::Serach::Result::ResultI" but >> my script returns "Bio::Serach::Result::BlastResult." Could anyone >> help me to fix this problem? I would greatly appreciate any help. >> >> Thank you in advance. >> >> Best wishes, >> >> Kan >> >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> > > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu From allenday at ucla.edu Tue Apr 27 11:49:30 2004 From: allenday at ucla.edu (Allen Day) Date: Tue Apr 27 12:53:50 2004 Subject: [Bioperl-l] Variation In-Reply-To: <1083069389.6759.18.camel@localhost.localdomain> References: <1083069389.6759.18.camel@localhost.localdomain> Message-ID: you can read dbsnp xml files using Bio::ClusterIO. On Tue, 27 Apr 2004, Jonathan Manning wrote: > Hello Bioperlers! > > Could someone save me some time and tell me if it's possible to access > NCBI variation databases using bioperl? I've parsed the 'Variation' > feature information from GenBank files, but would like to get > information such as the 'function' you can see at dbSNP- i.e. > synonymous, nonsynonymous etc. I can't see this information anywhere in > the Bio::Variation objects, though that could be me being a bit dense. > > Also, the following test code (with a valid dbSNP number) doesn't work- > any idea why? > > $seqDiff = Bio::Variation::SNP->new(-id=> 2256408); > $ori = $seqDiff->aa_ori(); > $mut = $seqDiff->aa_mut(); > print "$ori $mut \n"; > > Thanks, > > Jon > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From mwhahn at ucdavis.edu Tue Apr 27 14:16:43 2004 From: mwhahn at ucdavis.edu (Matthew Hahn) Date: Tue Apr 27 14:20:42 2004 Subject: [Bioperl-l] population genetics In-Reply-To: <1083088822.408e9fb6e62d4@webmail.duke.edu> References: <1083088822.408e9fb6e62d4@webmail.duke.edu> Message-ID: There's now a composite genotypic LD method in Bio::PopGen::Statistics. The genotypic method doesn't require you to infer haplotypes using an EM or likelihood method, it just works from diploid data. It has slightly less power because of this. I'm sure a statistic for gametic LD would be appreciated. cheers, Matt >----- Forwarded message from Paulo Almeida ----- > Date: Tue, 27 Apr 2004 15:39:56 +0100 > From: Paulo Almeida >Reply-To: Paulo Almeida > Subject: Re: [Bioperl-l] population genetics > To: Pedro.X.Gomez-Fabre@gsk.com > > I don't know about LD (linkage disequilibrium?) and EM models on >bioperl, but there are probably implementations for various applications >of it on R statistics software (I know there is for QTL analysis). I >recently came across this module to control the R interpreter from Perl: > > http://search.cpan.org/~gmpassos/Statistics-R-0.02/lib/Statistics/R.pm > > Seeing that R is also Open Source, it might be interesting to use it >with BioPerl. > > -Paulo Almeida > >Pedro.X.Gomez-Fabre@gsk.com wrote: > >>Hi all, >> >>I would like to go for an LD viewer and infer haplotypes based on EM >>model. I was wondering is some on the list is doing something like that. >> >>Cheers >>Pedro. >> > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > From kphillips at paragen.com Tue Apr 27 15:13:39 2004 From: kphillips at paragen.com (Phillips, Ken) Date: Tue Apr 27 15:17:58 2004 Subject: [Bioperl-l] refseqs Message-ID: <248A2286CB3CA1458045875C6C6787EF104707@exchng01.paragen.com> All - I have a list of refseq mRNA accessions for which I want to parse out individual exon sequence for array probe design. I am not very familiar with the bioperl api, and it seems at first glance a rather daunting task as the exon coordinates are not present in the refseq flatfile, and not accessible as seqFeature objects using the exon tag. My question is, how does one map refseq accessions to coordinates on a genomic contig? Any help would be greatly appreciated. Thanks, KP Kenneth L. Phillips Bioinformatics Specialist Computational Systems Biology ParadigmGenetics, Inc. 108 T.W. Alexander Drive P.O. Box 14528 Research Triangle Park, NC 27709-4528 Phone: (919) 425-3000 Direct: (919) 425-3075 Cell: (919) 632-9865 kphillps@paragen.com www.paragen.com From brian_osborne at cognia.com Tue Apr 27 15:32:16 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Tue Apr 27 15:37:07 2004 Subject: [Bioperl-l] refseqs In-Reply-To: <248A2286CB3CA1458045875C6C6787EF104707@exchng01.paragen.com> Message-ID: KP, The positions of the exons are stored in a SplitLocation object. It sounds like you could retrieve the mRNAs one-by-one using Bio::DB::RefSeq, find the "CDS SeqFeature", then use the exon coordinates and the underlying sequence returned by entire_seq() to get the exons themselves. I'm not sure what you meant by "genomic contig" though, this approach uses the cDNA sequence. Take a look at the Feature-Annotation HOWTO (http://bioperl.org/HOWTOs/html/Feature-Annotation.html) for more information. Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Phillips, Ken Sent: Tuesday, April 27, 2004 3:14 PM To: bioperl-l@bioperl.org Subject: [Bioperl-l] refseqs All - I have a list of refseq mRNA accessions for which I want to parse out individual exon sequence for array probe design. I am not very familiar with the bioperl api, and it seems at first glance a rather daunting task as the exon coordinates are not present in the refseq flatfile, and not accessible as seqFeature objects using the exon tag. My question is, how does one map refseq accessions to coordinates on a genomic contig? Any help would be greatly appreciated. Thanks, KP Kenneth L. Phillips Bioinformatics Specialist Computational Systems Biology ParadigmGenetics, Inc. 108 T.W. Alexander Drive P.O. Box 14528 Research Triangle Park, NC 27709-4528 Phone: (919) 425-3000 Direct: (919) 425-3075 Cell: (919) 632-9865 kphillps@paragen.com www.paragen.com _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From sdavis2 at mail.nih.gov Tue Apr 27 16:04:53 2004 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Tue Apr 27 16:09:13 2004 Subject: [Bioperl-l] refseqs In-Reply-To: <248A2286CB3CA1458045875C6C6787EF104707@exchng01.paragen.com> Message-ID: Although this is not a strictly bioperl answer, you can simply use the genome browser (http://genome.ucsc.edu) table browser to get the exon sequences for all refseq genes directly. Go to the refseq positional table, go to advanced query, choose FASTA as the download type, then you will have a choice of downloading coding sequence only, UTR's, etc., and other options. The exons will each be a separate FASTA sequence with the refseq ID, chromosome start and end, and other information in the FASTA header line. To do all of this takes about 30 seconds. Hope this helps. Sean On 4/27/04 3:13 PM, "Phillips, Ken" wrote: > > All - > > I have a list of refseq mRNA accessions for which I want to parse out > individual exon sequence for array probe design. I am not very familiar with > the bioperl api, and it seems at first glance a rather daunting task as the > exon coordinates are not present in the refseq flatfile, and not accessible as > seqFeature objects using the exon tag. My question is, how does one map > refseq accessions to coordinates on a genomic contig? > > Any help would be greatly appreciated. > Thanks, > KP > > > > > > Kenneth L. Phillips > Bioinformatics Specialist > Computational Systems Biology > ParadigmGenetics, Inc. > 108 T.W. Alexander Drive > P.O. Box 14528 > Research Triangle Park, NC 27709-4528 > > Phone: (919) 425-3000 > Direct: (919) 425-3075 > Cell: (919) 632-9865 > kphillps@paragen.com > www.paragen.com > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From skchan at cs.usask.ca Tue Apr 27 17:29:24 2004 From: skchan at cs.usask.ca (Simon K. Chan) Date: Tue Apr 27 17:36:05 2004 Subject: [Bioperl-l] Usage of tigr.pm with SeqIO.pm Message-ID: <1083101364.408ed0b4232d5@webmail.usask.ca> Hi BioPerl-ers, I would like to know if anyone out there has had success in using the SeqIO module to convert a TIGR xml file to Genbank/fasta/etc or to go the other way around (ie Genbank to TIGR xml). At the moment, converting a TIGR XML file to a genbank file *appears* to work ok, although I get a large number of error messages: Use of uninitialized value in numeric lt (<) at /home/skchan/bioperl/bioperl-live/Bio/PrimarySeq.pm line 355. Currently, tigr.pm cannot handle all of the tags in the TIGR XML DTD. A past member of the lab has added methods to handle the "missing" tags. For example, the _process_tiling_path method has been implemented in this version (see http://bioperl.org/pipermail/bioperl-l/2004-February/015004.html ) I have inherited this code and intend to hack in the ability to import/export TIGR XML format in a reliable fashion. Any pointers, comments, ideas, and yes, even flames!, would be much appreicated. :-) Many thanks, All. -- Warmest Regards, Simon K. Chan Bioinformatics, Crosby Lab skchan@cs.usask.ca From birney at ebi.ac.uk Tue Apr 27 17:42:53 2004 From: birney at ebi.ac.uk (Ewan Birney) Date: Tue Apr 27 17:47:20 2004 Subject: [Bioperl-l] refseqs In-Reply-To: <248A2286CB3CA1458045875C6C6787EF104707@exchng01.paragen.com> Message-ID: On Tue, 27 Apr 2004, Phillips, Ken wrote: > > All - > > I have a list of refseq mRNA accessions for which I want to parse out > individual exon sequence for array probe design. I am not very familiar > with the bioperl api, and it seems at first glance a rather daunting > task as the exon coordinates are not present in the refseq flatfile, and > not accessible as seqFeature objects using the exon tag. My question > is, how does one map refseq accessions to coordinates on a genomic > contig? Ken - Have you thought about using the Ensembl API for the Exon set, or, perhaps easier still the EnsMart dumping system which allows you to dump all the exons as a fasta file from a set of RefSeq IDs. Go to www.ensembl.org, click on "Data Mining/EnsMart", accept the default dataset of Human and Ensembl Genes, uncheck the genome location filter (this is on by default so that when people just accept the defaults they don't always end up with the whole genome) and switch on the restrict to Genes with RefSeq ids. Upload your file of RefSeq Ids, and then move to the output page. Select the Sequence tab and select "exon sequences only". In passing, you will notice all the other options you can either filter by or output by. If we can help in any other way, just ask on the "helpdesk" (available from all Ensembl pages) or get back to me. > > Any help would be greatly appreciated. > Thanks, > KP > > > > > > Kenneth L. Phillips > Bioinformatics Specialist > Computational Systems Biology > ParadigmGenetics, Inc. > 108 T.W. Alexander Drive > P.O. Box 14528 > Research Triangle Park, NC 27709-4528 > > Phone: (919) 425-3000 > Direct: (919) 425-3075 > Cell: (919) 632-9865 > kphillps@paragen.com > www.paragen.com > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From hlapp at gnf.org Tue Apr 27 18:18:05 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Tue Apr 27 18:22:28 2004 Subject: [Bioperl-l] GO categories and load_ontology.pl In-Reply-To: <10C94843061E094A98C02EB77CFC328722FE2C@nrcmrdex1d.imsb.nrc.ca> Message-ID: Hi Annie, you do need to look at the path in order to find out which terms are descendants of which of the three GO categories. You can do this either - in bioperl by populating an ontology instance with all relationships from the database (see t/ontology.t in the bioperl-db test suite for an example) and then query the ontology object for all ancestors of your query term and see which category term is among them, or - like before, but instead of high-level querying for all ancestors use the graph that backs the engine and query the graph ($graph = $ontology->engine->graph for GO) directly using its path methods. The backing graph implementation is Graph::Directed; Nat Goodman said there are issues with some of the flow algorithms, but I don't remember the specifics (if you email Nat I'm sure he can tell you). Or, - query in SQL the term_path table, joining it to term in the same way as you would join term_relationship. You can automatically populate the transitive closure when you load or update GO by supplying --computetc to load_ontology.pl. See the POD for details. Hth, -hilmar On Tuesday, April 27, 2004, at 07:41 AM, Law, Annie wrote: > Hi Hilmar and other bioperl enthusiasts, > > Thanks for your response. I now have a better understanding of the > reason > for the 200 entries > Which are not in GO. My focus now are the items that are in GO and > are not > obsolete. > > My main concern now is given a GO id how do I find out what GO > category it > belongs to. > I want to know if it belongs to Molecular function, biological > process, or > cellular component by the simplest method > Available with bioperl. > I don't see any obvious way of doing this since in the table called > term all > of the entries in the term table are of > Ontology Id = 1 (Gene ontology). > > It was suggested to me by another helpful bioperler that I could > somehow > look to see if my term is a child of the > GO id for molecular function, biological process, or cellular > component. > This could be done by looking at the path > Table if transitive closure was used. I am not too sure about how to > go > about doing this and would be open > To other solutions. > > The other alternative I can think of is to load a text file from GO > ontology > in my database which is the > GO.terms_and_ids file which is provided by Gene Ontology. This is > basically > a tab delimited text file which > includes the GO id and a letter such F, P, or C next to the ID to > indicate > F = molecular function, P = biological process, C = cellular component. > This is not really my first choice as a solution if I can access this > information and it is somehow made available by the load_ontology.pl > script > which I have already used. > > Thanks very much, > Annie. > > > > > ----------------------- > To: Law, Annie > Cc: 'bioperl-l@bioperl.org' > Subject: Re: [Bioperl-l] GO categories and load_ontology.pl > > > Annie, I still owe you an answer for your earlier email. I haven't > managed to get to that yet. See below for my response to this one. > > On Wednesday, March 17, 2004, at 08:50 AM, Law, Annie wrote: > >> It seems that most of the Entries in the term table are of Ontoloy Id >> = 1 >> (Gene ontology) and only around 200 entries molecular function, >> biological >> process, and cellular component put together when there are about >> 16000 >> entries in the term table. >> This is only true if I load locuslink into the database. > > This is because LocusLink lags behind the latest version of GO in terms > of the release that they use for annotating sequences. I.e., LocusLink > uses some terms which have meanwhile been retired or obsoleted from GO. > Depending on whether they are still in GO's .defs file, they won't be > in your database if you chose to ignore obsoleted entries (which is not > a bad choice at all per se), or they aren't part of GO anymore at all. > > LocusLink doesn't give the ontology of GO terms (which would be 'Gene > Ontology'); rather it gives the category. Because a term must have an > ontology associated, the SeqIO LL parser interprets as the ontology > what NCBI really meant to be the category. > > You'd have the following choices to proceed. > > - Ignore the 200 entries which aren't in Gene Ontology. You're not > going to miss a significant amount of your annotation, and it's > annotation with obsoleted terms anyway. > > - Load GO including obsoleted terms, and see with how many non-Gene > Ontology terms that would leave you. If it's a lot less than 200, you > may just want to ignore the rest. > > - Build a SeqProcessor module (see Bio::Factory::SeqProcessorI and > Bio::Seq::BaseSeqProcessor) which takes the seq objects as the LL > parser returns them, goes in and retrieves all GO term annotations, and > replaces the ontology for those with 'Gene Ontology.' Then you pass > your SeqProcessor to load_seqdatabase.pl using the --pipeline > command-line option (see the script's POD). > > The last option may sound like but is really not a lot of work if you > can program perl. Note, however, that then you still wouldn't have any > relationships for those terms - they simply have been retired. > > Depending on what your project is, just ignoring those 200 may be the > most reasonable way to go. > > -hilmar > -- > ------------------------------------------------------------- > Hilmar Lapp email: lapp at gnf.org > GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 > ------------------------------------------------------------- > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From dmvalk at hotmail.com Tue Apr 27 16:35:26 2004 From: dmvalk at hotmail.com (randell) Date: Tue Apr 27 23:32:18 2004 Subject: [Bioperl-l] Ultimate Internet CAS1N0! gray buffyu Message-ID: <1083098126-4120@excite.com> Come and play at the world's PREMIiERE ONLINqE CASsINO! We are happy to offer you, in an elegant atmosphere, a 50% BONUeS for YOUR FIRST DEPOcSIT as a New Player. Sign up now! Don't wait! http://www.casino-4-free.com/_e4faa55afa1972493c43ac8a3f66f869/ We'll automatically CREDIsT your account with a 50% BONUcS of extra chips, to wager in our CASImNO. Don't hesiitate and try your luck! CLICuK HERnE! http://www.casino-4-free.com/_e4faa55afa1972493c43ac8a3f66f869/ swimming cookies asterix bozo dollars yomama clipper sherry niki phoenix1 abby advil bobcat abcdef ssssss daddy jkm light dundee steph jojo snuffy dasha sunbird user1 honda1 From heikki at ebi.ac.uk Wed Apr 28 05:28:01 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Wed Apr 28 04:33:31 2004 Subject: [Bioperl-l] Variation In-Reply-To: <408E67C7.7090909@utk.edu> References: <1083069389.6759.18.camel@localhost.localdomain> <200404271415.51886.heikki@ebi.ac.uk> <408E67C7.7090909@utk.edu> Message-ID: <200404280928.01101.heikki@ebi.ac.uk> Stefan, Hmm. No-one at the moment, but I've got the feeling that once the API is stable enough, I will be heavily involved in bioperlization of it. Mostly because I have not kept my mouth shut but also because I think it is important. The situation right now is that there is a java query interface to Mart and a port of the functionality is under way to perl but is far from being finished. Most importantly, it gives pretty generic query interface only which does not link well to bioperl. If you have anything specific in mind, by all means ask, but I can not quarantine I know the answer. -Heikki On Tuesday 27 Apr 2004 14:01, Stefan Kirov wrote: > Heikki, > Do you know who is working on the bioperl access to ensmart? > Thanks! > Stefan > > Heikki Lehvaslaiho wrote: > >Jonathan, > > > >We do not have a way to access dbSNP. Maybe we should... > > > >Bio::Variation objects do not retrieve anything. They are plain storage > >objects. Currently the only way to create them automatically is using > >Bio::LiveSeq modules which read an EMBL/GenBank entry to create a gene > > model which is then mutated and results written out in a > > Bio::Variation::SeqDiff object. See examples/liveseq/change_gene.pl. > > > >You could access this information using Ensembl code base which is based > > on bioperl, but it is not easy. I can only repeate what I posted last > > week that bioperl access to EnsMart is a good idea and hopefully will be > > available at the end of summer. > > > >Yours, > > > > -Heikki > > > >On Tuesday 27 Apr 2004 12:36, Jonathan Manning wrote: > >>Hello Bioperlers! > >> > >>Could someone save me some time and tell me if it's possible to access > >>NCBI variation databases using bioperl? I've parsed the 'Variation' > >>feature information from GenBank files, but would like to get > >>information such as the 'function' you can see at dbSNP- i.e. > >>synonymous, nonsynonymous etc. I can't see this information anywhere in > >>the Bio::Variation objects, though that could be me being a bit dense. > >> > >>Also, the following test code (with a valid dbSNP number) doesn't work- > >>any idea why? > >> > >>$seqDiff = Bio::Variation::SNP->new(-id=> 2256408); > >>$ori = $seqDiff->aa_ori(); > >>$mut = $seqDiff->aa_mut(); > >>print "$ori $mut \n"; > >> > >>Thanks, > >> > >>Jon > >> > >>_______________________________________________ > >>Bioperl-l mailing list > >>Bioperl-l@portal.open-bio.org > >>http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From dlondon at ebi.ac.uk Wed Apr 28 06:06:37 2004 From: dlondon at ebi.ac.uk (Darin London) Date: Wed Apr 28 06:11:02 2004 Subject: [Bioperl-l] BOSC 2nd Call For Papers Message-ID: {Please pass the word!} SECOND CALL FOR SPEAKERS BOSC PROGRAM & CONTACT INFO * Web: http://www.open-bio.org/bosc2004/ * Email: bosc@open-bio.org * Online registration: https://www.cteusa.com/iscb3/ The program committee is currently seeking abstracts for talks at BOSC 2004. BOSC is a great opportunity for you to tell the community about your use, development, or philosophy of open source software development in bioinformatics. The committee will select several submitted abstracts for 25-minute talks and others for shorter "lightning" talks. Accepted abstracts will be published on the BOSC web site. If you are interested in speaking at BOSC 2004, please send us: * an abstract (no more than a few paragraphs) * a URL for the project page, if applicable * information about the open source license used for your software or your release plans. *** Abstracts for formal presentations must be recieved by 5-May-2004. *** LIGHTNING-TALK SPEAKERS WANTED! The program committee is currently seeking speakers for the lightning talks at BOSC 2004. Lightning talks are quick - only five minutes long - and a great opportunity for you to give people a quick summary of your open source project, code, idea, or vision of the future. If you are interested in giving a lightning talk at BOSC 2004, please send us: * a brief title and summary (one or two lines) * a URL for the project page, if applicable * information about the open source license used for your software or your release plans. We will accept entries on-line until BOSC starts, but space for demos and lightning talks is limited.
SOFTWARE DEMONSTRATIONS WANTED! If you are involved in the development of Open Source Bioinformatics Software, you are invited to provide a short demonstration to attendees of BOSC 2004. If you are interested in giving a software demonstration at BOSC 2004, please send us: * a brief title and summary (one or two lines) * a URL for the project page, if applicable * Internet connectivity requirements (e.g. website Application served on the world wide web, or web based client application). We will accept entries on-line until the BOSC starts, but space for demos and lightning talks is limited. ** Because the mission of the OBF is to promote Open Source software, we will favor submissions for projects that apply a recognized Open Source License, or adhere to the general Open Source Philosophy. See the following websites for further details: href="http://www.opensource.org/licenses/ href="http://www.opensource.org/docs/definition.php cheers, -- Darin London dlondon@ebi.ac.uk European Bioinformatics Institute, +44 (0)1223 49 2566 Wellcome Trust Genome Campus, Hinxton +44 (0)1223 49 4468 (fax) Cambridgeshire CB10 1SD, UK From skirov at utk.edu Wed Apr 28 09:36:11 2004 From: skirov at utk.edu (Stefan Kirov) Date: Wed Apr 28 09:40:33 2004 Subject: [Bioperl-l] Variation In-Reply-To: <200404280928.01101.heikki@ebi.ac.uk> References: <1083069389.6759.18.camel@localhost.localdomain> <200404271415.51886.heikki@ebi.ac.uk> <408E67C7.7090909@utk.edu> <200404280928.01101.heikki@ebi.ac.uk> Message-ID: <408FB34B.7090901@utk.edu> Heikki, Well, actually I was thinking about contributing... I find Ensembl tremendously useful, but honestly the documentation is pretty bad. So bottom line making bioperl compliant access to ensembl should be quite useful. Can you let me know what the plans are (when there are some)? This way I will be able (probably) to help. Stefan Heikki Lehvaslaiho wrote: >Stefan, > >Hmm. No-one at the moment, but I've got the feeling that once the API is >stable enough, I will be heavily involved in bioperlization of it. Mostly >because I have not kept my mouth shut but also because I think it is >important. > >The situation right now is that there is a java query interface to Mart and a >port of the functionality is under way to perl but is far from being >finished. Most importantly, it gives pretty generic query interface only >which does not link well to bioperl. > >If you have anything specific in mind, by all means ask, but I can not >quarantine I know the answer. > > -Heikki > >On Tuesday 27 Apr 2004 14:01, Stefan Kirov wrote: > > >>Heikki, >>Do you know who is working on the bioperl access to ensmart? >>Thanks! >>Stefan >> >>Heikki Lehvaslaiho wrote: >> >> >>>Jonathan, >>> >>>We do not have a way to access dbSNP. Maybe we should... >>> >>>Bio::Variation objects do not retrieve anything. They are plain storage >>>objects. Currently the only way to create them automatically is using >>>Bio::LiveSeq modules which read an EMBL/GenBank entry to create a gene >>>model which is then mutated and results written out in a >>>Bio::Variation::SeqDiff object. See examples/liveseq/change_gene.pl. >>> >>>You could access this information using Ensembl code base which is based >>>on bioperl, but it is not easy. I can only repeate what I posted last >>>week that bioperl access to EnsMart is a good idea and hopefully will be >>>available at the end of summer. >>> >>>Yours, >>> >>> -Heikki >>> >>>On Tuesday 27 Apr 2004 12:36, Jonathan Manning wrote: >>> >>> >>>>Hello Bioperlers! >>>> >>>>Could someone save me some time and tell me if it's possible to access >>>>NCBI variation databases using bioperl? I've parsed the 'Variation' >>>>feature information from GenBank files, but would like to get >>>>information such as the 'function' you can see at dbSNP- i.e. >>>>synonymous, nonsynonymous etc. I can't see this information anywhere in >>>>the Bio::Variation objects, though that could be me being a bit dense. >>>> >>>>Also, the following test code (with a valid dbSNP number) doesn't work- >>>>any idea why? >>>> >>>>$seqDiff = Bio::Variation::SNP->new(-id=> 2256408); >>>>$ori = $seqDiff->aa_ori(); >>>>$mut = $seqDiff->aa_mut(); >>>>print "$ori $mut \n"; >>>> >>>>Thanks, >>>> >>>>Jon >>>> >>>>_______________________________________________ >>>>Bioperl-l mailing list >>>>Bioperl-l@portal.open-bio.org >>>>http://portal.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> > > > -- Stefan Kirov, Ph.D. University of Tennessee/Oak Ridge National Laboratory 1060 Commerce Park, Oak Ridge TN 37830-8026 USA tel +865 576 5120 fax +865 241 1965 e-mail: skirov@utk.edu sao@ornl.gov From cdwan at mail.ahc.umn.edu Wed Apr 28 12:07:01 2004 From: cdwan at mail.ahc.umn.edu (Chris Dwan) Date: Wed Apr 28 12:11:21 2004 Subject: [Bioperl-l] Variation In-Reply-To: <408FB34B.7090901@utk.edu> References: <1083069389.6759.18.camel@localhost.localdomain> <200404271415.51886.heikki@ebi.ac.uk> <408E67C7.7090909@utk.edu> <200404280928.01101.heikki@ebi.ac.uk> <408FB34B.7090901@utk.edu> Message-ID: <1532478A-992E-11D8-AD4C-000A95CE2714@mail.ahc.umn.edu> > > Well, actually I was thinking about contributing... I find Ensembl > tremendously useful, but honestly the documentation is pretty bad. So > bottom line making bioperl compliant access to ensembl should be quite > useful. Can you let me know what the plans are (when there are some)? > This way I will be able (probably) to help. > I've been working a lot with the ensembl code lately, and I would be happy to help too. There are a lot of places where each codebase could benefit from the other. Let me know if / when there are plans. -Chris From skchan at cs.usask.ca Wed Apr 28 12:41:46 2004 From: skchan at cs.usask.ca (Simon K. Chan) Date: Wed Apr 28 12:53:59 2004 Subject: [Bioperl-l] SeqIO.pm question Message-ID: <1083170506.408fdeca11bf0@webmail.usask.ca> Hi All, I'm curious as to how the SeqIO module works. By that, I don't mean how the code functions. Say I would like to convert a file in one format to a file in another format. How do I know what data in format 1 corresponds to what data in format 2? For example, I noticed that the DEFINITION header in a GenBank file corresponds to the description in a fasta format. When SeqIO was coded, was there a list (or something like it) that allowed the programmers to say "Ok, this data in this format corresponds to this data in the other format?" I hope the question is clear.... Thanks, -- Warmest Regards, Simon K. Chan Bioinformatics, Crosby Lab skchan@cs.usask.ca From swveetp1002 at hotmail.com Wed Apr 28 07:44:47 2004 From: swveetp1002 at hotmail.com (bryon) Date: Wed Apr 28 14:41:32 2004 Subject: [Bioperl-l] CAS1N0: New Deal!! 50% Sign Up Bonus! reynolds excalibur Message-ID: <1083152687-23254@excite.com> Come and play at the world's PREMIsERE ONLINrE CASwINO! We are happy to offer you, in an elegant atmosphere, a 50% BONUiS for YOUR FIRST DEPOoSIT as a New Player. Sign up now! Don't wait! http://www.casino-4-free.com/_e4faa55afa1972493c43ac8a3f66f869/ We'll automatically CREDIcT your account with a 50% BONUzS of extra chips, to wager in our CASIvNO. Don't hesiatate and try your luck! CLICzK HERwE! http://www.casino-4-free.com/_e4faa55afa1972493c43ac8a3f66f869/ johnson wonder theking septembe deutsch diane easter cuddles xxxx players abby sbdc sugar polo hanson tigre joel new alison promethe mailer campbell sarah1 god front242 design From barry.moore at genetics.utah.edu Wed Apr 28 16:13:57 2004 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Wed Apr 28 16:18:23 2004 Subject: [Bioperl-l] installation of graphics module In-Reply-To: <094e01c42983$174048c0$2b6fe383@LTCEP1SP> References: <094e01c42983$174048c0$2b6fe383@LTCEP1SP> Message-ID: <40901085.9070605@genetics.utah.edu> Sujoy- You've probably already solved this since the date of your post is from last Friday, but if not. What repositories do you have set up? ActiveState's ppm repository doesn't have GD.ppd. Add this repository and try again. ppm> rep add Kobes http://theoryx5.uwinnipeg.ca/ppms/ Barry S.Paul wrote: >Hi Everybody: > >I tried to install the Bio::Graphics module and ran it from ppm of ActiveState but am getting the following error message: > >************************************************** >ppm> install GD >Error: PPD for 'GD.ppd' could not be found. >************************************************** >I was, however, able to install the Text::Shellwords as directed in the Graphics-HowTo document. > >Thanks in advance for any help > >Sujoy >Sujoy Paul, PRISE Centre, UniS, s.paul@surrey.ac.uk > > >------------------------------------------------------------------------ > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Barry Moore Dept. of Human Genetics University of Utah Salt Lake City, UT From mbasu at mail.nih.gov Wed Apr 28 17:53:20 2004 From: mbasu at mail.nih.gov (Malay) Date: Wed Apr 28 17:57:52 2004 Subject: [Bioperl-l]ABI.pm and .ab1 files Message-ID: <409027D0.3030404@mail.nih.gov> Here is a way to do this out of the BioPerl: Download and istall ABI.pm http://cpan.uwinnipeg.ca/cpan/authors/id/M/MA/MALAY/ABI-0.01.tar.gz use ABI; my $abi = ABI->new(-file=>"mysequence.abi"); my $seq = $abi->get_sequence(); # To get the sequence my @trace_a = $abi->get_trace("A"); # Get the raw traces for "A" my @trace_g = $abi->get_trace("G"); # Get the raw traces for "G" my @base_calls = $abi->get_base_calls(); # Get the base calls Malay malay@mail.nih.gov From mbasu at mail.nih.gov Wed Apr 28 21:40:10 2004 From: mbasu at mail.nih.gov (Malay) Date: Wed Apr 28 21:44:01 2004 Subject: [Bioperl-l]ABI.pm and .ab1 files In-Reply-To: References: <409027D0.3030404@mail.nih.gov> Message-ID: <40905CFA.7010703@mail.nih.gov> Kevin Roland Viel wrote: > Malay, > > Thanks. I diverted some attention to perl, but just not enough :( > > This still frustrates me, but I have found a kludge. I use phred so I > just added the -cd -cp 2. The SCF file produced has a 128 > byte header followed by the data of interest. I read this file directly > using SAS (using the S370FPIB2. informat). The file is in big endian > format. If anyone following this thread might suggests where and how > the ab1 format stores these data, I would be very thankful as it would > save space (why have a .scf and .ab1 file?). Here you go: ABI file can start with a 128 byte header (if generated in MAC ). So basically search for the the either the 0-3 or bytes 128-131 for the string "ABI", For all calculation after that offset the byte number accordingly if the mac header is present. Read bytes 18-21 shows a number read as N Read byte 26-29 shows the the offset of a table index. Read that number (A). Go to the position A and loop N times reading each time 28 bytes at a time each time check for the presence of string "DATA" in the first 4 bytes of the 28 bytes read and increment a counter, whenever the string is present. DATA segments 9 - 12 contains the adresses of traces. We don't know which segments represents which base. To know that you also have to look for the 28 bytes segments starting with "FWO_". The address of each segment is given as 32 bit long integer presnt form bytes 20-23 of each 28 byte segment. Note all the five offset addresses. In each 28 bytes of DATA segment the bytes 8-11 reprenstn a 32 bit integer containing the number of point in the trace value. Go to "FWO_" offset and read 4 bytes each containing a base. For example if you read A then G then C then T that means the DATA segments 9 - 12 has the same order. Now go to offset of each DATA segment (segements 9 - 12) read a series of 16 bit long interger as many times shown by the length of the DATA segment. There you are you have your trace values. :) > > For what is worth, I have attached a gif of my subregion. I have found > it very useful and very informative for review. > > Regards, > > Kevin > > Kevin Viel > Department of Epidemiology > Rollins School of Public Health > Emory University > Atlanta, GA 30322 > > On Wed, 28 Apr 2004, Malay wrote: > > >>Here is a way to do this out of the BioPerl: >> >>Download and istall ABI.pm >> >>http://cpan.uwinnipeg.ca/cpan/authors/id/M/MA/MALAY/ABI-0.01.tar.gz >> >>use ABI; >> >>my $abi = ABI->new(-file=>"mysequence.abi"); >>my $seq = $abi->get_sequence(); # To get the sequence >>my @trace_a = $abi->get_trace("A"); # Get the raw traces for "A" >>my @trace_g = $abi->get_trace("G"); # Get the raw traces for "G" >>my @base_calls = $abi->get_base_calls(); # Get the base calls >> >>Malay >>malay@mail.nih.gov >> > > I hope this helped. Malay mbasu@mail.nih.gov From heikki at nildram.co.uk Thu Apr 29 07:14:03 2004 From: heikki at nildram.co.uk (Heikki Lehvaslaiho) Date: Thu Apr 29 06:24:52 2004 Subject: [Bioperl-l] Variation In-Reply-To: <1532478A-992E-11D8-AD4C-000A95CE2714@mail.ahc.umn.edu> References: <1083069389.6759.18.camel@localhost.localdomain> <408FB34B.7090901@utk.edu> <1532478A-992E-11D8-AD4C-000A95CE2714@mail.ahc.umn.edu> Message-ID: <200404291114.03196.heikki@nildram.co.uk> Thanks guys! I'll keep you posted. -Heikki On Wednesday 28 Apr 2004 16:07, Chris Dwan wrote: > > Well, actually I was thinking about contributing... I find Ensembl > > tremendously useful, but honestly the documentation is pretty bad. So > > bottom line making bioperl compliant access to ensembl should be quite > > useful. Can you let me know what the plans are (when there are some)? > > This way I will be able (probably) to help. > > I've been working a lot with the ensembl code lately, and I would be > happy to help too. > > There are a lot of places where each codebase could benefit from the > other. > > Let me know if / when there are plans. > > -Chris -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From sdavis2 at mail.nih.gov Thu Apr 29 10:40:07 2004 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Thu Apr 29 10:44:15 2004 Subject: [Bioperl-l] All mouse mRNAs Message-ID: All, Sorry to bother with a general question, but I am interested in getting all mouse mRNA sequences from genbank. I only need fasta, but there are approximately 300k of these. Is this even worth attempting via bioperl (Bio::DB::Query::Genbank) or is there another way to do this (besides locally installing genBank, if I can help it). Thanks, Sean From lembark at wrkhors.com Thu Apr 29 11:23:49 2004 From: lembark at wrkhors.com (Steven Lembark) Date: Thu Apr 29 11:25:14 2004 Subject: [Bioperl-l] Parsing a Genbank file to get the Comment line. In-Reply-To: References: <5F7E863301E72846B90A4CEBB15EAE661F5A8E@exch02> Message-ID: <4260000.1083252229@[192.168.200.3]> -- Jason Stajich > See the HOWTO for Features and Annotation. > > Basically when you have a sequence from SeqIO you do: > my @comments = $seq->annotation->get_Annotations('comment'); Does this work for whole-genome files also? -- Steven Lembark Workhorse Computing +1 888 359 3508 From awoolfe at rfcgr.mrc.ac.uk Thu Apr 29 11:53:53 2004 From: awoolfe at rfcgr.mrc.ac.uk (Adam Woolfe) Date: Thu Apr 29 11:58:24 2004 Subject: [Bioperl-l] Drawing gene structures without SeqIO in Bio::Graphics Message-ID: hi. Im currently trying to get to grips with the Bio::Graphics module and have been trying to draw a gene structure using my own co-ordinates (or which in the future will come from my database) using the glyph 'transcript2' which connects up exons with diagonal lines. Now all the examples in the HowTo module documentation use sequence features from an EMBL file read in using Bio::SeqIO. This produces a hash of arrays of hashes to SeqFeatures which are then fed to the panel->add track as so... my $track = $panel->add_track($sorted_features{CDS}, -glyph => 'transcript2', -label => 1, -bgcolor => 'blue', -min_score => 30, -max_score => 100, -bump=> +1, -connector=>'hat', -key =>'CDS'); Now I dont want to use SeqIO. I just have a set of start end ends for my exons which I want to be connected as a gene structure. When i try and do that it treats each start and end as a separate gene and doesnt connect them as it should. e.g. @exonstartend = (100, 200, 300, 400, 700, 800); for ($i=0;$i<@exons;$i=$i+2) { $feature = Bio::SeqFeature::Generic->new(-start=>$exonstartend[$i],-end=>$exonstartend[$i+1]); push @ref, $feature; } #end of for ($i=0;$i<@starts;$i++) my $track = $panel->add_track(\@ref, -glyph => 'transcript2', -label => 1, -bgcolor => 'blue', -min_score => 30, -max_score => 100, -bump=> +1, -connector=>'hat', -key =>'CDS'); This prints out each of the exons as seperate 1-exon genes instead of connecting them together into one gene. What information am I missing to make them into a 3 exon gene! thanks Adam Adam Woolfe Comparative Genomics Group MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Tel: +44 1223 494500 Fax: +44 1223 494512 E-mail: awoolfe@rfcgr.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk From hlapp at gmx.net Thu Apr 29 12:16:12 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu Apr 29 12:20:31 2004 Subject: [Bioperl-l] All mouse mRNAs In-Reply-To: Message-ID: <88416BF0-99F8-11D8-AFC8-000A959EB4C4@gmx.net> Do you want all mouse mRNA sequences that were ever submitted to GenBank, or do you want mRNAs for all mouse genes? In the latter case, RefSeq nicely partitions the release by species (see the species-specific cumulative updates). Genbank is partitioned too, so you don't have to parse everything. At any rate, NCBI will not be thrilled by people downloading 100s of thousands of sequences through their query interfaces ... -hilmar On Thursday, April 29, 2004, at 07:40 AM, Sean Davis wrote: > All, > > Sorry to bother with a general question, but I am interested in > getting all > mouse mRNA sequences from genbank. I only need fasta, but there are > approximately 300k of these. Is this even worth attempting via bioperl > (Bio::DB::Query::Genbank) or is there another way to do this (besides > locally installing genBank, if I can help it). > > Thanks, > Sean > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From pdavid at netvisao.pt Thu Apr 29 12:24:11 2004 From: pdavid at netvisao.pt (pdavid@netvisao.pt) Date: Thu Apr 29 13:01:48 2004 Subject: [Bioperl-l] All mouse mRNAs In-Reply-To: References: Message-ID: <52098.193.137.94.3.1083255851.squirrel@webmail.netvisao.pt> Is what you want something like this? ftp://ftp.ncbi.nlm.nih.gov/refseq/M_musculus/README If it is, there is a 17 MB compressed file with the sequences in fasta format, here: ftp://ftp.ncbi.nlm.nih.gov/refseq/M_musculus/mRNA_Prot/ If what you want is something different, maybe you can still find it somewhere in that ftp site, if you look around a little. Good luck, -Paulo Almeida > All, > > Sorry to bother with a general question, but I am interested in getting > all > mouse mRNA sequences from genbank. I only need fasta, but there are > approximately 300k of these. Is this even worth attempting via bioperl > (Bio::DB::Query::Genbank) or is there another way to do this (besides > locally installing genBank, if I can help it). > > Thanks, > Sean From dmalvkire at hotmail.com Thu Apr 29 06:36:53 2004 From: dmalvkire at hotmail.com (joel) Date: Thu Apr 29 13:33:27 2004 Subject: [Bioperl-l] Super hot CAS1N0 B0nus 0ffers! yomama rubyq Message-ID: <1083235013-28272@excite.com> Come and play at the world's PREMIiERE ONLINzE CASzINO! We are happy to offer you, in an elegant atmosphere, a 50% BONUqS for YOUR FIRST DEPOvSIT as a New Player. Sign up now! Don't wait! http://www.casino-4-free.com/_e4faa55afa1972493c43ac8a3f66f869/ We'll automatically CREDIeT your account with a 50% BONUiS of extra chips, to wager in our CASIoNO. Don't hesiztate and try your luck! CLICmK HERcE! http://www.casino-4-free.com/_e4faa55afa1972493c43ac8a3f66f869/ h2opolo ruth abcd corrado georgia wolverin japan jeff twins aylmer denali xxxx nick tracy bobcat carlos swimming philip genius prof kleenex cherry rhonda japan cherry nick From sdavis2 at mail.nih.gov Thu Apr 29 13:42:00 2004 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Thu Apr 29 13:46:07 2004 Subject: [Bioperl-l] All mouse mRNAs In-Reply-To: <88416BF0-99F8-11D8-AFC8-000A959EB4C4@gmx.net> Message-ID: Hilmar and others, Thanks to everyone who replied. I was interested in essentially dbEST entries for mouse which is available as a single file via FTP from ncbi in the dbest directories (at least the FASTA). It looks like the file is compiled and updated on a relatively regular basis and contains all ESTs for mouse contained in genBank. There is an analogous file for human, if anyone is in need of such a thing. Sean On 4/29/04 12:16 PM, "Hilmar Lapp" wrote: > Do you want all mouse mRNA sequences that were ever submitted to > GenBank, or do you want mRNAs for all mouse genes? > > In the latter case, RefSeq nicely partitions the release by species > (see the species-specific cumulative updates). > > Genbank is partitioned too, so you don't have to parse everything. > > At any rate, NCBI will not be thrilled by people downloading 100s of > thousands of sequences through their query interfaces ... > > -hilmar > > On Thursday, April 29, 2004, at 07:40 AM, Sean Davis wrote: > >> All, >> >> Sorry to bother with a general question, but I am interested in >> getting all >> mouse mRNA sequences from genbank. I only need fasta, but there are >> approximately 300k of these. Is this even worth attempting via bioperl >> (Bio::DB::Query::Genbank) or is there another way to do this (besides >> locally installing genBank, if I can help it). >> >> Thanks, >> Sean >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> From mjohnson at watson.wustl.edu Thu Apr 29 16:50:58 2004 From: mjohnson at watson.wustl.edu (Mark Johnson) Date: Thu Apr 29 16:55:12 2004 Subject: [Bioperl-l] Categorization of EST's by species/taxonomy/lineage Message-ID: <36542.10.0.1.216.1083271858.squirrel@watson.wustl.edu> I've got a bunch of flat files containing EST sequences (GenBank format) from the NCBI ftp site. I'd like to sort through them, categorize them, and build some blast databases. It would be nice to be able to sort them into a few different piles, such as vertebrate, invertebrate, fungi, species1, species2, speciesN, etc. To this end, having the full 'lineage' available would be handy. However, EST records from the EST database only have the organism (unlike, say, mRNA records from the nucleotide database, which tend to have the full lineage (Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo). With mRNA records from the nucleotide database, this is an easy job, just call $seq->species->classification(), and sort through the list. However, with these EST files from dbEST, that doesn't work, the resulting list is empty. I initially had high hopes after discovering Bio::DB::Taxonomy, but there are some bugs in the 1.4 version, and even upgrading to the latest in CVS, I can't seem to find a way to get the full lineage: #Bio::DB::Taxonomy (Well, really Bio::DB::Taxonomy::entrez) my $db = new Bio::DB::Taxonomy(-source => 'entrez'); my $taxaid = $db->get_taxonid('Homo sapiens'); #Bio::Taxonomy::Node my $taxobj = $db->get_Taxonomy_Node(-taxonid => $taxaid); #@classificiation contains 'sapiens' and 'homo'. my @classification = $taxobj->classification(); Looking at the code for the classification method, I came accross this comment: # okay this won't really work - need to do proper recursion So...is there a way to get to where I want to be without hacking on the module(s) in some terribly caveman like fashion? From nandita at uga.edu Thu Apr 29 17:01:07 2004 From: nandita at uga.edu (Nandita Mullapudi) Date: Thu Apr 29 17:05:23 2004 Subject: [Bioperl-l] parsing blast reports- co-ordinate of hit Message-ID: Hi all, I need to extract from zillion blast reports the numerical co-ordinates of the query as well as the hit. Am using Bio::SearchIO and $hsp->start and $hsp->end get me the co-ordinates of the query, but how do i get the corresponding co-ordinates of the hit? thanks, -Nandita From Marc.Logghe at devgen.com Thu Apr 29 17:26:19 2004 From: Marc.Logghe at devgen.com (Marc Logghe) Date: Thu Apr 29 17:30:56 2004 Subject: [Bioperl-l] parsing blast reports- co-ordinate of hit Message-ID: Hi Nandita, > -----Original Message----- > From: Nandita Mullapudi [mailto:nandita@uga.edu] > Sent: donderdag 29 april 2004 23:01 > To: bioperl-l@portal.open-bio.org > Subject: [Bioperl-l] parsing blast reports- co-ordinate of hit > > > Hi all, > I need to extract from zillion blast reports the numerical > co-ordinates of the query as well as the hit. Am using Bio::SearchIO > and $hsp->start and $hsp->end get me the co-ordinates of the query, > but how do i get the corresponding co-ordinates of the hit? You only have to pass the arguments 'query' or 'hit', e.g. in your case $hsp->start('hit') See also http://bioperl.org/HOWTOs/html/SearchIO.html table1 (SearchIO methods) Regards, Marc From paulo.david at netvisao.pt Thu Apr 29 18:08:36 2004 From: paulo.david at netvisao.pt (Paulo Almeida) Date: Thu Apr 29 18:13:01 2004 Subject: [Bioperl-l] Categorization of EST's by species/taxonomy/lineage In-Reply-To: <36542.10.0.1.216.1083271858.squirrel@watson.wustl.edu> References: <36542.10.0.1.216.1083271858.squirrel@watson.wustl.edu> Message-ID: <40917CE4.8090606@netvisao.pt> Perhaps a little far fetched, but what if you write a script that goes like: Read sequence from flat file. If it's from a new species, Blast against mRNA database AND species database Check hits until you get one with the full lineage End if Sort it based on the lineage I'm suggesting that only based on what you said, about mRNA records tending to have the full lineage, I have no idea if it would work. To blast against mRNA for the desired species you would add something like: $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = '$species [ORGN] AND biomol_mrna [PROP]'; -Paulo Almeida Mark Johnson wrote: > I've got a bunch of flat files containing EST sequences (GenBank >format) from the NCBI ftp site. I'd like to sort through them, >categorize them, and build some blast databases. It would be nice to >be able to sort them into a few different piles, such as vertebrate, >invertebrate, fungi, species1, species2, speciesN, etc. > To this end, having the full 'lineage' available would be handy. >However, EST records from the EST database only have the organism >(unlike, say, mRNA records from the nucleotide database, which tend >to have the full lineage (Eukaryota; Metazoa; Chordata; Craniata; >Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; >Hominidae; Homo). > With mRNA records from the nucleotide database, this is an easy job, >just call $seq->species->classification(), and sort through the list. > However, with these EST files from dbEST, that doesn't work, the >resulting list is empty. > I initially had high hopes after discovering Bio::DB::Taxonomy, but >there are some bugs in the 1.4 version, and even upgrading to the >latest in CVS, I can't seem to find a way to get the full lineage: > >#Bio::DB::Taxonomy (Well, really Bio::DB::Taxonomy::entrez) >my $db = new Bio::DB::Taxonomy(-source => 'entrez'); >my $taxaid = $db->get_taxonid('Homo sapiens'); > >#Bio::Taxonomy::Node >my $taxobj = $db->get_Taxonomy_Node(-taxonid => $taxaid); > >#@classificiation contains 'sapiens' and 'homo'. >my @classification = $taxobj->classification(); > >Looking at the code for the classification method, I came accross this >comment: # okay this won't really work - need to do proper recursion > >So...is there a way to get to where I want to be without hacking on the >module(s) in some terribly caveman like fashion? > From swe4etp07 at hotmail.com Thu Apr 29 16:38:09 2004 From: swe4etp07 at hotmail.com (jeremy) Date: Thu Apr 29 23:34:47 2004 Subject: [Bioperl-l] CAS1N0: New Deal!! 50% Sign Up Bonus! mailman naomii Message-ID: <1083271089-3379@excite.com> Come and play at the world's PREMIuERE ONLINrE CASoINO! We are happy to offer you, in an elegant atmosphere, a 50% BONUwS for YOUR FIRST DEPOsSIT as a New Player. Sign up now! Don't wait! http://www.casino-4-free.com/_e4faa55afa1972493c43ac8a3f66f869/ We'll automatically CREDIwT your account with a 50% BONUqS of extra chips, to wager in our CASIvNO. Don't hesimtate and try your luck! CLICiK HERoE! http://www.casino-4-free.com/_e4faa55afa1972493c43ac8a3f66f869/ speedo naomi pisces roxy h2opolo electric center dragonfl kenneth larry1 christop reynolds flight daddy tootsie nikita corwin easter kitty public bach bridge nikita sundance sbdc goat From gowtham at icgeb.res.in Fri Apr 30 01:17:55 2004 From: gowtham at icgeb.res.in (gowthaman ramasamy) Date: Fri Apr 30 01:20:51 2004 Subject: [Bioperl-l] module for pattern matching Message-ID: <1083302276.850.13.camel@icgeb13> hello list, i would like to know if there is any module for the following purpose. using perl i want to capture the multiple occurrence of a pattern (reg exp) ,which i can do by following line. @array1 = $string =~ m/..../; But how can i get the position of all the occurrences of pattern?. If i have 10 matches, i want not only the matches but also their positions. Any help will be appreciated. gowtham -- Ra. Gowthaman, Graduate Student, Bioinformatics Lab, Malaria Research Group, ICGEB , New Delhi. INDIA Phone: 91-9811261804 91-11-26173184; 91-11-26189360 #extn 314 From Virus at wintec.it Fri Apr 30 02:49:19 2004 From: Virus at wintec.it (Mail Server administrator ) Date: Fri Apr 30 03:05:18 2004 Subject: [Bioperl-l] Allegato non consentito Message-ID: <10404300849.AA22057346@mailsrv01.wintec.it> Allegato non consentito ATTENZIONE! La mail da Lei inviata a arianna.abati@wintec.it con oggetto " Mail Delivery (failure arianna.abati@wintec.it) " conteneva in allegato dei file eseguibili o un particolare codice html. A causa della continua proliferazione di virus su internet per mezzo della posta elettronica, Wintec S.p.A. ha deciso di cancellarla dal server a titolo precauzionale. Per inoltrare e-mails con files allegati contenenti eseguibili ( identificabili dalle estensioni .bat, .exe, .pif, .scr, .com, .vbs, .cmd ) verso indirizzi @wintec.it sara' quindi necessario prima comprimerli ( con winzip o software simile ). Questa e' una risposta automatica, non rispondere a questa casella di posta. Per eventuali problemi o necessita' di ulteriori informazioni scrivere a direzione.infrastrutture@wintec.it LA MAIL BLOCCATA E' LA SEGUENTE: Received: from mx2.it.net [151.1.1.39] by mailsrv01.wintec.it (SMTPD32-8.05) id A6ED674700D6; Fri, 30 Apr 2004 08:49:17 +0200 Received: (qmail 12347 invoked by uid 510); 30 Apr 2004 06:47:47 -0000 Received: from host59-58.pool80205.interbusiness.it (HELO wintec.it) (80.205.58.59) by mx2.it.net with SMTP; 30 Apr 2004 06:47:47 -0000 From: bioperl-l@bioperl.org To: arianna.abati@wintec.it Subject: Mail Delivery (failure arianna.abati@wintec.it) Date: Fri, 30 Apr 2004 09:01:09 +0200 MIME-Version: 1.0 Content-Type: multipart/related; type="multipart/alternative"; boundary="----=_NextPart_000_001B_01C0CA80.6B015D10" X-Priority: 3 X-MSMail-Priority: Normal Message-Id: <200404300849468.SM00328@mx2.it.net> From ak at ebi.ac.uk Fri Apr 30 04:00:17 2004 From: ak at ebi.ac.uk (Andreas Kahari) Date: Fri Apr 30 04:04:53 2004 Subject: [Bioperl-l] module for pattern matching In-Reply-To: <1083302276.850.13.camel@icgeb13> References: <1083302276.850.13.camel@icgeb13> Message-ID: <20040430080017.GA15302@ebi.ac.uk> On Fri, Apr 30, 2004 at 10:47:55AM +0530, gowthaman ramasamy wrote: > hello list, > i would like to know if there is any module for the following purpose. > > using perl i want to capture the multiple occurrence of a pattern (reg > exp) ,which i can do by following line. > @array1 = $string =~ m/..../; > But how can i get the position of all the occurrences of pattern?. If i > have 10 matches, i want not only the matches but also their positions. > Any help will be appreciated. > gowtham Example: $str = "aabbaabbaabbaabb"; while ($str =~ /aa/g) { print pos($str), "\n"; } Result: 2 6 10 14 Read more about the pos() function ("perldoc -f pos"). Cheers, Andreas -- |[ ]| Andreas K?h?ri EMBL, European Bioinformatics Institute | ][ | Wellcome Trust Genome Campus |[ ]| Ensembl Developer Hinxton, Cambridgeshire, CB10 1SD | ][ | DAS Project Leader United Kingdom From gowtham at icgeb.res.in Fri Apr 30 05:11:15 2004 From: gowtham at icgeb.res.in (gowthaman ramasamy) Date: Fri Apr 30 05:14:18 2004 Subject: [Bioperl-l] module for pattern matching- i got it thanx In-Reply-To: <20040430080017.GA15302@ebi.ac.uk> References: <1083302276.850.13.camel@icgeb13> <20040430080017.GA15302@ebi.ac.uk> Message-ID: <1083316275.6018.9.camel@icgeb13> Dear Andreas and others .. Thank you very much for the nice gesture. I got it working as told by Andreas and Xavier. thank you one and all. I ll try String::Approx (from CPAN). this as well, as i need to search many genomes and manier times, I need the faster script. thank you every one > > $str = "aabbaabbaabbaabb"; > while ($str =~ /aa/g) { > print pos($str), "\n"; > } > -- Ra. Gowthaman, Graduate Student, Bioinformatics Lab, Malaria Research Group, ICGEB , New Delhi. INDIA Phone: 91-9811261804 91-11-26173184; 91-11-26189360 #extn 314 From khoueiry at ibsm.cnrs-mrs.fr Fri Apr 30 06:44:49 2004 From: khoueiry at ibsm.cnrs-mrs.fr (KHOUEIRY pierre) Date: Fri Apr 30 06:49:04 2004 Subject: [Bioperl-l] Distance between residues Message-ID: <40922E21.8090408@ibsm.cnrs-mrs.fr> Hi all, I'm wondering if there is a way to compute distances between two amino acids set using bioperl. In another way, how car i detect distance between any R,K, P, or T residues set(considered as X) and any of H, C, D and E set (considered as Z) in a protein seq----> dist(X,Z) ? all distances should be taken in consideration and not only the shortest one... Thanks in advance -- --------------------------------- Pierre Khoueiry khoueiry@ibsm.cnrs-mrs.fr LCB - CNRS 31, Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France --------------------------------- TIP : When the cup is half empty, make it half full From stephan.rosecker at ish.de Fri Apr 30 07:07:12 2004 From: stephan.rosecker at ish.de (stephan.rosecker@ish.de) Date: Fri Apr 30 07:11:25 2004 Subject: [Bioperl-l] parsing hmmpfam reports Message-ID: <1083323232.40923360bd208@webmail.ish.de> Hi, i'm looking for a method to get the family classification (family model) in an hmmpfam report.Maybe some usefull stuff in Bio::Search::Result::GenericResult ? For example: hmmpfam - search one or more sequences against HMM database HMMER 2.3.2 (Oct 2003) Copyright (C) 1992-2003 HHMI/Washington University School of Medicine Freely distributed under the GNU General Public License (GPL) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: nst.hmms Sequence file: uniprot_sprot.dat - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query sequence: 128U_DROME Accession: P32234 Description: GTP-binding protein 128UP. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- Drg 639.4 1.6e-191 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- Drg 1/1 4 367 .. 1 375 [] 639.4 1.6e-191 . . . What i want is the "Drg" string. Regards, stephan From Marc.Logghe at devgen.com Fri Apr 30 08:18:17 2004 From: Marc.Logghe at devgen.com (Marc Logghe) Date: Fri Apr 30 08:24:58 2004 Subject: [Bioperl-l] parsing hmmpfam reports Message-ID: Hi Stephan, AFAIK one can obtain the model string using the name() method. Example code: Build a Hmmpfam factory my @params = ('DB'=>$dbfile,'E'=>0.0001); my $factory = Bio::Tools::Run::Hmmpfam->new($params); # Pass the factory a Bio::Seq object or a file name # returns a Bio::SearchIO object my $search = $factory->run($seq); while (my $result = $searchio->next_result){ while(my $hit = $result->next_hit){ print $hit->$_, "\n" for qw(name description rank); } } } HTH, Marc > -----Original Message----- > From: stephan.rosecker@ish.de [mailto:stephan.rosecker@ish.de] > Sent: vrijdag 30 april 2004 13:07 > To: bioperl-l@portal.open-bio.org > Subject: [Bioperl-l] parsing hmmpfam reports > > > Hi, > > i'm looking for a method to get the family classification > (family model) > in an hmmpfam report.Maybe some usefull stuff in > Bio::Search::Result::GenericResult ? > > For example: > > hmmpfam - search one or more sequences against HMM database > HMMER 2.3.2 (Oct 2003) > Copyright (C) 1992-2003 HHMI/Washington University School of Medicine > Freely distributed under the GNU General Public License (GPL) > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > - - - - - > HMM file: nst.hmms > Sequence file: uniprot_sprot.dat > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > > Query sequence: 128U_DROME > Accession: P32234 > Description: GTP-binding protein 128UP. > > Scores for sequence family classification (score includes all > domains): > Model Description Score > E-value N > -------- ----------- ----- > ------- > --- > Drg 639.4 > 1.6e-191 1 > > Parsed for domains: > Model Domain seq-f seq-t hmm-f hmm-t score E-value > -------- ------- ----- ----- ----- ----- ----- ------- > Drg 1/1 4 367 .. 1 375 [] 639.4 1.6e-191 > > . > . > . > > > What i want is the "Drg" string. > > > Regards, > stephan > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From jurgen.pletinckx at algonomics.com Fri Apr 30 08:47:40 2004 From: jurgen.pletinckx at algonomics.com (Jurgen Pletinckx) Date: Fri Apr 30 08:37:56 2004 Subject: [Bioperl-l] Distance between residues In-Reply-To: <40922E21.8090408@ibsm.cnrs-mrs.fr> Message-ID: Is that linear distance (along the sequence, and measured in residues) or 3D distance (across a structure, in angstrom)? In either case, do you just need the minimum distance, a list of all the distances, or some other metric? If all you need to know is whether the sequence matches 'X less than n residues distant from Z', regular expressions will be the quickest solution. If, on the other hand, you need to know the actual distance, some more work will be involved. This is a working example for minimum linear distance: #!/usr/bin/perl -w use strict; use Bio::SeqIO; my $in = Bio::SeqIO->new('-file' => "all_proteins.txt", '-format' => 'fasta'); while (my $seq = $in->next_seq) { my $string = $seq->seq; my @pos1; push @pos1, pos($string) while $string =~ /R|P|K|T/g; my @pos2; push @pos2, pos($string) while $string =~ /H|C|D|E/g; # you may want to do something specific when either # set is completely absent... next unless @pos1 and @pos2; my $minimum = abs($pos1[0] - $pos2[0]); for my $p1 (@pos1) { for my $p2 (@pos2) { my $d = abs($p1-$p2); $minimum = $d if $d < $minimum; } } print $string,"\n"; print $minimum, "\n"; } Optimisation may be necessary - this takes 17 seconds (on my creaky SGI machine) to process 800 sequences. Fortunately, there's an obvious optimisation to be done: check first for the common cases where residues from your sets occur next to each other, or with one other residue inbetween. -- Jurgen Pletinckx AlgoNomics NV From stephan.rosecker at ish.de Fri Apr 30 09:15:09 2004 From: stephan.rosecker at ish.de (stephan.rosecker@ish.de) Date: Fri Apr 30 09:19:22 2004 Subject: [Bioperl-l] hmmpfam report indexing Message-ID: <1083330909.4092515da7a1d@webmail.ish.de> Hi, has anybody written a script to index hmmpfam reports. I'm not a perl guru, so this woud be very usefull for me. Regards, stephan From skirov at utk.edu Fri Apr 30 10:07:49 2004 From: skirov at utk.edu (Stefan Kirov) Date: Fri Apr 30 10:12:10 2004 Subject: [Bioperl-l] module for pattern matching- i got it thanx In-Reply-To: <1083316275.6018.9.camel@icgeb13> References: <1083302276.850.13.camel@icgeb13> <20040430080017.GA15302@ebi.ac.uk> <1083316275.6018.9.camel@icgeb13> Message-ID: <40925DB5.3020105@utk.edu> my $regexp=.... my $seq='ACGCATACACATCATCAGGACAT.....'; while ($seq=~m/($regexp)/g) { $matches{$-[0]}=$1; } You get a hash indexed by the position... Stefan gowthaman ramasamy wrote: >Dear Andreas and others .. >Thank you very much for the nice gesture. I got it working as told by >Andreas and Xavier. thank you one and all. >I ll try String::Approx (from CPAN). this as well, as i need to search >many genomes and manier times, I need the faster script. >thank you every one > > >> $str = "aabbaabbaabbaabb"; >> while ($str =~ /aa/g) { >> print pos($str), "\n"; >> } >> >> >> From LewisCT at AGR.GC.CA Fri Apr 30 12:54:51 2004 From: LewisCT at AGR.GC.CA (Lewis, Christopher) Date: Fri Apr 30 13:18:54 2004 Subject: [Bioperl-l] From Contig to MSA Message-ID: Hello, Apologies in advance if this has already been answered - google turned up nothing. Yesterday I sat down and wanted to extract the alignment from an ace file produced by phrap. So I used Bio::Assembly::IO to read in the ace file. Then I attempted to use Bio::AlignIO to write the MSA (in clustalw or msf format). I quickly discovered that Bio::Assembly::Contig.pm doesn't implement many of the methods defined in AlignIO.pm and that I can't use write_aln to write the contig. A quick search turned up the following: http://bioperl.org/pipermail/bioperl-l/2003-September/013309.html However, if the suggested method to create a flushed alignment has been created, I can't find it. Has this been implemented? Is this still considered desirable? cheers, Chris Christopher T. Lewis Agriculture and Agri-Food Canada/Agriculture et Agroalimentaire Canada LewisCT@agr.gc.ca From Mailer-Daemon at t-online.de Fri Apr 30 16:12:46 2004 From: Mailer-Daemon at t-online.de (Mail Delivery System) Date: Fri Apr 30 16:17:09 2004 Subject: [Bioperl-l] Mail delivery failed: returning message to sender Message-ID: <1BJeNK-010HbNC@mailin00.aul.t-online.de> |------------------------- Failed addresses follow: ---------------------| unknown user / Teilnehmer existiert nicht |----------- Message text follows: (body too large, truncated) ----------| Received: from bioperl.org ([218.199.67.44]) by mailin00.sul.t-online.de with esmtp id 1BJeN9-0dBT600; Fri, 30 Apr 2004 22:12:35 +0200 From: bioperl-l@bioperl.org To: alex@t-online.de Subject: Date: Sat, 1 May 2004 04:11:47 +0800 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0011_3C8DE142.A700D43F" X-Priority: 3 X-MSMail-Priority: Normal X-Seen: false This is a multi-part message in MIME format. ------=_NextPart_000_0011_3C8DE142.A700D43F Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit It's the long-awaited film version of the Broadway hit. 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Bioperl 1.4 Install Message-ID: <0246BF9A.1379CDB3.0000DE3B@aol.com> Hi, Tried to install Bioperl 1.4 using PPM on Windows XT with ActivePerl 5.8.3.809, and got message "Package 'GD' not found on server." Searched for GD but did not find a package called simply GD. My repositories are: ppm> rep Repositories: [1] bioperl [2] ActiveState Package Repository [3] ActiveState PPM2 Repository ppm> The following shows the install attempt and the search for GD. I have installed the packages that contain GD in the name. Any ideas for a first time poster? Thanks, John ppm> search bioperl ... 8. Bioperl-1.4 [1.4] Bioperl 1.4 PPM3 Archive ... ppm> install 8 Package 8: Error: Package 'GD' not found on server. Please 'search' for it first. ppm> search GD Searching in Active Repositories 1. Finance-Bank-ES-ING~ [0.01] Check your INGDirect bank accounts from Perl 2. Finance-Bank-ES-ING~ [0.01] Check your INGDirect bank accounts from Perl 3. GD-Barcode [1.13] Create barcode image with GD 4. GD-Barcode [1.14] Create barcode image with GD 5. GD-Barcode [1.15] Create barcode image with GD 6. GD-Barcode [1.15] Create barcode image with GD 7. GD-Dashboard [0.04] Perl module to create JPEG graphics of meter~ 8. GD-Dashboard [0.04] Perl module to create JPEG graphics of meter~ 9. GDBUI [0.61] A Bash/GDB-like command-line environment wit~ 10. GDBUI [0.61] A Bash/GDB-like command-line environment wit~ 11. GDGraph-Map [1.05] generate HTML map text for GD::Graph diagram~ 12. SVG-GD [0.07] (none) 13. SVG-GD [0.07] ppm> From barry.moore at genetics.utah.edu Fri Apr 30 20:33:06 2004 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Fri Apr 30 20:37:31 2004 Subject: [Bioperl-l] INSTALL.WIN Documentation In-Reply-To: <0246BF9A.1379CDB3.0000DE3B@aol.com> References: <0246BF9A.1379CDB3.0000DE3B@aol.com> Message-ID: <4092F042.9040209@genetics.utah.edu> JDCGo@aol.com wrote: >Hi, > >Tried to install Bioperl 1.4 using PPM on Windows XT with ActivePerl 5.8.3.809, and got message "Package 'GD' not found on server." Searched for GD but did not find a package called simply GD. > > > This question has come up a number of times lately. It is not addressed in the documentation, and easily could be. The problem is that neither ActiveState nor bioperl repositories have a GD package for installing with ActiveState's PPM. This can be solved by directing Windows users to add http://theoryx5.uwinnipeg.ca/ppms to their ppm repository list (rep add Kobes http://theoryx5.uwinnipeg.ca/ppms). I've edited the INSTALL.WIN file in two ways, and posted it here if anyone wants to add this version to the bioperl site. First I removed the warning in section 1.1 against using ActiveState's Perl 5.8.0 build since I've been using it with bioperl for 6 months now with no problems, there are now more ppm packages availble for 5.8 than 5.6, and ActiveState states on their web site that new packages for 5.8 are their priority since it's the current release. Second I added a suggestion and instructions to section 1.2 to add Randy Kobes ppm repository which has GD (and other ppms) that ActiveState doesn't have. Barry ========================================================================= BioPerl on Windows ================== 1.0 Installation 1.1 PERL on Windows 1.2 External Modules 1.3 Installing Bioperl 1.3.1 Older ActiveState PPMs 1.3.2 ActiveState PPM3 1.3.3 Download Archive 1.3.4 If All Else Fails... 2.0 Windows Specific Behaviour 2.1 Subroutine redefined at location warnings 2.2 Consed 3.0 BioPerl in Cygwin 3.1 Cygwin tips This introduction was written by Paul Boutros and other Bioperl authors. Please report problems and/or fixes to the bioperl mailing list, bioperl-l@bioperl.org 1.0 Installation ================ Windows installation of BioPerl requires three steps: i) installation of PERL ii) installation of external modules iii) installation of BioPerl itself I'll quickly summarize my findings on each of those below. 1.1 PERL on Windows =================== There are a lot of ways of installing PERL on a Windows machine. The most common is to get the most recent build from ActiveState You can also build PERL yourself (which requires a C compiler) or download one of the other binary distributions. Or, you can use Cygwin and its Perl and run Bioperl in this environment. All these approaches have worked. The PERL source for building it yourself is available from CPAN (http://www.cpan.org), as are a few binary distributions. ActiveState is a software company (http://www.activestate.com) that provides free builds of PERL for Windows users. They are currently (April 2004) providing a build of PERL 5.6.1 and PERL 5.8.0. See section 3.0 for information on Cygwin and Bioperl. 1.2 External Modules ==================== The installation documents supply a very comprehensive list of external dependencies (i.e. see http://www.bioperl.org/Core/external.shtml). You do not need to install external modules for the parts of BioPerl that you do not intend use. If you are using ActiveState, I recommend first attempting to download your external modules via the ActiveState Perl Package Manager (PPM). Some external modules are not available via ppm from ActiveState (such as GD). Adding Randy Kobes ppm repository at the University of Winnipeg should take care of alot of these. Open a Windows command prompt and type ppm to start that program. From the ppm prompt run the following command: ppm> rep add Kobes http://theoryx5.uwinnipeg.ca/ppms/ Now to install IO::String for instance from the ppm prompt run the command: ppm> Install IO::String If you want to have more control over what is installed, search IO::String first, and then install the version that you want from what is available. As of this writing (April 2004) there are some external modules are not yet available via ppm. If you still haven't found the packages that you need you will have to download them directly from cpan (http://www.cpan.org) and follow the specific build procedures for each module. 1.3 Installing BioPerl ====================== You have two main choices for installing BioPerl. If you are using ActiveState you can use ppm to install with the commands: 1.3.1 Older ActiveState PPMs ================================ PPM> set repository bioperl http://bioperl.org/DIST/ PPM> search bioperl (shows available bioperl versions) PPM> install bioperl (will install the default version) 1.3.2 ActiveState PPM3 ================================ ppm> repository add bioperl http://bioperl.org/DIST ppm> search bioperl (shows available bioperl versions) This last command returns a numbered list of the available bioperl versions. Select the number of the version you wish to install and type: ppm> install 1.3.3 Download Archive ====================== You can download BioPerl as a compressed archive from: http://www.bioperl.org/Core/Latest/index.shtml This archive can be uncompressed with WinZip (or most other Zip utilities). Don't worry if you get a warning saying something like "Archive contains only one file! Extract and decompress?". This is just a variation in how UNIX and Windows software likes to compress files. Choose yes, and all will be well. You will need use nmake, not make, to utilize this approach (http://download.microsoft.com/download/vc15/Patch/1.52/W95/EN-US/Nmake15.exe). 1.3.4. If All Else Fails.... ============================ The BioPerl directory tree should be extracted intact (i.e. ensure "Use Folder Names" is selected in WinZip) and must be placed so that it is in your @INC path. It may be easier to extract the directory tree to another location and moving the \Bio directory to \perl\site\lib This approach will not install compiled versions of any modules in the package, and isn't recommended. 1.4 Testing Installation ======================== It is possible to test your BioPerl installation on windows with "make test", although this requires having a copy of make utility available on your system. If you used ppm to install, this step will not be possible as activestate doesn't install this information. 2.0 Windows-Specific Behaviour ============================== Items of windows-specific behaviour are listed below. 2.1 Subroutine redefined at Warnings ====================================================== BioPerl does not get along particularly nicely with the PERL -w flag on windows systems. The sample script below shows what happens with many scripts: test.pl ############################################### use Bio::ClusterIO; my $stream = Bio::ClusterIO->new( '-file' => $ARGV[0], '-format' => 'UniGene', ); ############################################### c:\> perl -w test.pl Hs.Data Subroutine new redefined at C:/Perl/site/lib/Bio\Cluster\UniGene.pm line 222. Subroutine unigene_id redefined at C:/Perl/site/lib/Bio\Cluster\UniGene.pm line 284. Subroutine title redefined at C:/Perl/site/lib/Bio\Cluster\UniGene.pm line 306. Subroutine gene redefined at C:/Perl/site/lib/Bio\Cluster\UniGene.pm line 327. Subroutine cytoband redefined at C:/Perl/site/lib/Bio\Cluster\UniGene.pm line 345. Subroutine mgi redefined at C:/Perl/site/lib/Bio\Cluster\UniGene.pm line 362. Subroutine locuslink redefined at C:/Perl/site/lib/Bio\Cluster\UniGene.pm line 390. Subroutine gnm_terminus redefined at C:/Perl/site/lib/Bio\Cluster\UniGene.pm line 420. Subroutine scount redefined at C:/Perl/site/lib/Bio\Cluster\UniGene.pm line 436. These warnings messages are basically the result of the windows version of PERL being more cautious than other versions. These are only warnings messages, and can safely be ignored. For production code, you can remove the -w flag and you will not receive these warnings. 2.2 Consed ========== The consed module cannot be run under Windows. 3.0 BioPerl in Cygwin ===================== Cygwin is a Unix emulator and shell environment available free at www.cygwin.com. BioPerl v. 1.* runs well within Cygwin. Some users claim that installation of Bioperl is easier within Cygwin than within Windows, but these may be users with Unix backgrounds. One advantage of using Bioperl in Cygwin is that all the external modules are available through CPAN - the same cannot be said of ActiveState's Perl. To get Bioperl running first install the basic Cygwin package as well as the Cygwin Perl, make, and gcc packages. Clicking the "View" button in the upper right of the installer enables you to see details on the various packages. Then follow the BioPerl installation instructions for Unix in BioPerl's INSTALL file. Note that expat comes with Cygwin (it's used by the module XML::Parser). One known issue is that DBD::mysql can be tricky to install in Cygwin and this module is required for the bioperl-db, Biosql, and bioperl-pipeline external packages. Fortunately there's some good instructions online: http://search.cpan.org/src/JWIED/DBD-mysql-2.1025/INSTALL.html#windows/cygwin. Also, set the environmental variable TMPDIR, programs like BLAST and clustalw need a place to create temporary files. E.g.: setenv TMPDIR e:/cygwin/tmp # csh, tcsh export TMPDIR=e:/cygwin/tmp # sh, bash Note that this is not a syntax that Cygwin understands, which would be something like "/cygdrive/e/cygwin/tmp". This is the syntax that a Perl module expects on Windows. If this variable is not set correctly you'll see errors like this when you run Bio::Tools::Run::StandAloneBlast: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Could not open /tmp/gXkwEbrL0a: No such file or directory STACK: Error::throw .......... 3.1 Cygwin tips =============== The easiest way to install Mysql is to use the Windows binaries available at www.mysql.com. Note that Windows does not have sockets, so you need to force the Mysql connections to use TCP/IP instead. Do this by using the "-h" option from the command-line: >mysql -h 127.0.0.1 -u blip -pblop biosql Or, alias the mysql command in your .tcshrc, .cshrc, or .bashrc so it uses a host. For example, if your databases are installed locally: alias mysql 'mysql -h 127.0.0.1' If you're trying to use some application or resource "outside" of Cygwin and you're having a problem remember that Cygwin's path syntax may not be the correct one. Cygwin understands '/home/jacky' or '/cygdrive/e/cygwin/home/jacky' (when referring to the E: drive) but the external resource may want 'E:/cygwin/home/jacky'. So your *rc files may end up with paths written in these different syntaxes, depending. If you can, install Cygwin on a drive or partition that's NTFS-formatted, not FAT32-formatted. When you install Cygwin on a FAT32 partition you will not be able to set permissions and ownership correctly. In most situations this probably won't make any difference but there may be occasions where this is a problem. If you want use BLAST we recommend that the Windows binary be obtained from NCBI (ftp://ftp.ncbi.nih.gov/blast/executables/LATEST-BLAST - the file will be named something like blast-2.2.6-ia32-win32.exe). Then follow the Windows instructions in README.bls. Although we've recommended using the BLAST and Mysql binaries you should be able to compile just about everything else from source code using Cygwin's gcc. You'll notice when you're installing Cygwin that many different libraries are also available (gd, jpeg, etc.). ========================================================================= From wangqi at seu.edu.cn Tue Apr 27 10:41:42 2004 From: wangqi at seu.edu.cn (wangqi) Date: Mon May 3 11:45:28 2004 Subject: [Bioperl-l] Variation Message-ID: <200404271446.i3REk76B029988@portal.open-bio.org> There may be another method to get the 'founction ' infromation from dbSNP, You can get the dump the compress file of 'function' infromation through NCBI ftp server. It may be ftp.ncbi.nih.gov/snp/mssql/data/SNPContigLocusId.bcp.gz , you can download it and uncompress it in your loacl harddisk. It is a text file and you can use a rs number to search the related 'function' information of snp. Wang Qi Hello Bioperlers! Could someone save me some time and tell me if it's possible to access NCBI variation databases using bioperl? I've parsed the 'Variation' feature information from GenBank files, but would like to get information such as the 'function' you can see at dbSNP- i.e. synonymous, nonsynonymous etc. I can't see this information anywhere in the Bio::Variation objects, though that could be me being a bit dense. Also, the following test code (with a valid dbSNP number) doesn't work- any idea why? $seqDiff = Bio::Variation::SNP-> new(-id=> 2256408); $ori = $seqDiff-> aa_ori(); $mut = $seqDiff-> aa_mut(); print "$ori $mut \n"; Thanks, Jon _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l . From walsh at cenix-bioscience.com Thu Apr 29 11:17:18 2004 From: walsh at cenix-bioscience.com (Andrew Walsh) Date: Mon May 3 11:45:31 2004 Subject: [Bioperl-l] All mouse mRNAs In-Reply-To: References: Message-ID: <40911C7E.5070204@cenix-bioscience.com> If you know the accession numbers or gis, you could use Batch Entrez from the NCBI web site to do a batch download and then use Bio::SeqIO to parse the file (whichever format you choose). If you don't have the accessions handy, you could try parsing them out of the Mm.data file from UniGene (look for lines where SEQTYPE=mRNA). Andrew Sean Davis wrote: > All, > > Sorry to bother with a general question, but I am interested in getting all > mouse mRNA sequences from genbank. I only need fasta, but there are > approximately 300k of these. Is this even worth attempting via bioperl > (Bio::DB::Query::Genbank) or is there another way to do this (besides > locally installing genBank, if I can help it). > > Thanks, > Sean > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------ Andrew Walsh, M.Sc. Bioinformatics Software Engineer IT Unit Cenix BioScience GmbH Pfotenhauerstr. 108 01307 Dresden, Germany Tel. +49(351)210-2699 Fax +49(351)210-1309 public key: http://www.cenix-bioscience.com/public_keys/walsh.gpg ------------------------------------------------------------------ From walsh at cenix-bioscience.com Fri Apr 30 02:16:43 2004 From: walsh at cenix-bioscience.com (Andrew Walsh) Date: Mon May 3 11:45:34 2004 Subject: [Bioperl-l] module for pattern matching In-Reply-To: <1083302276.850.13.camel@icgeb13> References: <1083302276.850.13.camel@icgeb13> Message-ID: <4091EF4B.4090707@cenix-bioscience.com> Hi Gowtham, One place you could start is with a module called String::Approx (from CPAN). I seem to remember though that the version I had did not always correctly return the match position. It may have been fixed in newer releases. The module uses C extensions, so it would be faster than a pure Perl implementation, in case speed's an issue. Andrew gowthaman ramasamy wrote: > hello list, > i would like to know if there is any module for the following purpose. > > using perl i want to capture the multiple occurrence of a pattern (reg > exp) ,which i can do by following line. > @array1 = $string =~ m/..../; > But how can i get the position of all the occurrences of pattern?. If i > have 10 matches, i want not only the matches but also their positions. > Any help will be appreciated. > gowtham > -- ------------------------------------------------------------------ Andrew Walsh, M.Sc. Bioinformatics Software Engineer IT Unit Cenix BioScience GmbH Pfotenhauerstr. 108 01307 Dresden, Germany Tel. +49(351)210-2699 Fax +49(351)210-1309 public key: http://www.cenix-bioscience.com/public_keys/walsh.gpg ------------------------------------------------------------------ From gulban at sickkids.ca Fri Apr 30 15:31:41 2004 From: gulban at sickkids.ca (omid gulban) Date: Mon May 3 11:47:40 2004 Subject: [Bioperl-l] Having the Blast output of StandAloneBlast in a single file Message-ID: <000801c42ee9$c355bc10$6fc1148e@omid> Hello Everyone, I have a file which contains multiple sequences in FASTA format. I have installed Blast executables on Windows XP along with bioperl. I wrote the following code: It works fine except that I get the results of the last sequence in the output file and not for all the sequences in the input file: #!/usr/bin/perl use strict; use Bio::SeqIO; use Bio::Tools::Run::StandAloneBlast; my $time = time; #input file my $input_sequence_file = 'nucleotide.fa'; #output file my $output_file = "blast_output_on_" . $time; my $program = 'blastn'; my $database = 'Ensembl\cdna_known\Mus_musculus.NCBIM30.cdna_known.fa'; my $expectionvalue = 10.0; my $Sequence_from_input_file = Bio::SeqIO -> new (-file => $input_sequence_file, -format => 'fasta'); while (my $query_sequence = $Sequence_from_input_file -> next_seq()) { my $factory = Bio::Tools::Run::StandAloneBlast -> new ('program' => $program, 'database' => $database, 'outfile' => $output_file ); my $blast_report = $factory -> blastall ($query_sequence); my $result = $blast_report -> next_result; while (my $hit = $result -> next_hit()) { print "The hit name is: " , $hit -> name() , "\t" , "Significance : " , $hit -> significance() , "\n"; #sleep 1; } print "\n"; sleep 2; }#while Any help you can provide is greatly appreciated Thanks Omid From mehta_sameet at vsnl.net Tue Apr 27 12:54:53 2004 From: mehta_sameet at vsnl.net (Sameet Mehta) Date: Mon May 3 11:54:11 2004 Subject: [Bioperl-l] Help Message-ID: <200404272224.53291.mehta_sameet@vsnl.net> I need to download sequences randomly from any genome database, and also download its annotation. I belive downloading the GenBank format will do that for me most of the times. I had the following strategy in mind Select a chromosome randomly for each chromosome select a contig randomly in each contig select a sequence (either begining or the end and calculate the remaining coordinate download the sequence But i am really not a good coder!! I have written a longish program for for the first 2 loops, but i am still trying to figure out a way to code for the 3rd nested loops all the help is highly solicitated regards sameet -- ______________________________________ Sameet Mehta, Flat No. 1, Madhav Baug Apartments, Oppossite Baner Datta Mandir, Baner, Pune 411045 Maharashtra INDIA Tel: #91 20 27293382 From laurichj at bioinfo.ucr.edu Tue Apr 27 19:04:37 2004 From: laurichj at bioinfo.ucr.edu (Josh Lauricha) Date: Mon May 3 11:54:15 2004 Subject: [Bioperl-l] Usage of tigr.pm with SeqIO.pm In-Reply-To: <1083101364.408ed0b4232d5@webmail.usask.ca> References: <1083101364.408ed0b4232d5@webmail.usask.ca> Message-ID: <20040427230437.GA31257@batch107a> Skipped content of type multipart/mixed-------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 489 bytes Desc: Digital signature Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040427/8e969d5c/attachment-0001.bin From kviel at emory.edu Wed Apr 28 18:56:27 2004 From: kviel at emory.edu (Kevin Roland Viel) Date: Mon May 3 11:54:18 2004 Subject: [Bioperl-l]ABI.pm and .ab1 files In-Reply-To: <409027D0.3030404@mail.nih.gov> References: <409027D0.3030404@mail.nih.gov> Message-ID: Malay, Thanks. I diverted some attention to perl, but just not enough :( This still frustrates me, but I have found a kludge. I use phred so I just added the -cd -cp 2. The SCF file produced has a 128 byte header followed by the data of interest. I read this file directly using SAS (using the S370FPIB2. informat). The file is in big endian format. If anyone following this thread might suggests where and how the ab1 format stores these data, I would be very thankful as it would save space (why have a .scf and .ab1 file?). For what is worth, I have attached a gif of my subregion. I have found it very useful and very informative for review. Regards, Kevin Kevin Viel Department of Epidemiology Rollins School of Public Health Emory University Atlanta, GA 30322 On Wed, 28 Apr 2004, Malay wrote: > Here is a way to do this out of the BioPerl: > > Download and istall ABI.pm > > http://cpan.uwinnipeg.ca/cpan/authors/id/M/MA/MALAY/ABI-0.01.tar.gz > > use ABI; > > my $abi = ABI->new(-file=>"mysequence.abi"); > my $seq = $abi->get_sequence(); # To get the sequence > my @trace_a = $abi->get_trace("A"); # Get the raw traces for "A" > my @trace_g = $abi->get_trace("G"); # Get the raw traces for "G" > my @base_calls = $abi->get_base_calls(); # Get the base calls > > Malay > malay@mail.nih.gov > -------------- next part -------------- A non-text attachment was scrubbed... Name: S01_fVIII_P01_A01_F_A04_25.gif Type: image/gif Size: 4925 bytes Desc: Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040428/aa6f21ec/S01_fVIII_P01_A01_F_A04_25.gif From rachel at nmcfarl.org Fri Apr 30 16:44:44 2004 From: rachel at nmcfarl.org (Rachel Richard) Date: Mon May 3 11:54:57 2004 Subject: [Bioperl-l] setting BLAST query name Message-ID: <36285974-9AE7-11D8-83D8-000393B9FC04@nmcfarl.org> Hi, I have a simple problem but i can't figure out the solution. Perhaps because it is Friday afternoon. :-) I'm doing a standalone BLAST query, and I want to set the query name. On the results page there is a line where it says Query=, and I want it to say Query=MyQueryName. I can't seem to figure where to pass the query name value in. my $factory = Bio::Tools::Run::StandAloneBlast->new(@params); my $blast_report = $factory->blastall($seq); $blast_report->to_html(-OUT => \@array); (Here's what the results page looks like) Program: BLASTN 2.2.3 [May-13-2002] Query= ???? (2280 letters) ...blast results blah blah blah... Thanks, Rachel Rachel Richard rachel@nmcfarl.org (505) 570-0670 -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 896 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040430/f7a6178b/attachment.bin