From gabrielle_doan at gmx.net Tue Jul 1 04:29:37 2008 From: gabrielle_doan at gmx.net (Gabrielle Doan) Date: Tue, 01 Jul 2008 10:29:37 +0200 Subject: [Bioperl-l] Problems when trying to persist a sequence in my BioSQL database using BioPerl Message-ID: <4869EAF1.7010807@gmx.net> Hi Hilmar and Sendu, thanks a lot for your help! After installing the latest version of Scalar::Util I didn't get the error anymore. Unfortunately, I'm facing an other problem. I tried to insert the Genbank file of the human Chromosome 1 - downloaded from the NCBI (ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_01/hs_ref_chr1.gbk.gz) - into my BioSQL database with a perl script (load_seqdatabase.pl from the BioPerl db package), but after about one hour I received the message 'Out of memory'. After the abort I have only 13 entries in my database. I can't image that four GB RAM are not sufficient. Does anybody have the same problem? I am greateful for any hint! Cheers, Gabrielle From captainrave at hotmail.com Tue Jul 1 04:19:41 2008 From: captainrave at hotmail.com (Captainrave) Date: Tue, 1 Jul 2008 01:19:41 -0700 (PDT) Subject: [Bioperl-l] re ading in cds, outputting products Message-ID: <18211537.post@talk.nabble.com> How would I use bioperl to read in CDS positions (maybe in csv format in a list), find the releated products and/or genes for each and output these into a new csv file or similar file? -- View this message in context: http://www.nabble.com/reading-in-cds%2C-outputting-products-tp18211537p18211537.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From pallavi.sarmah at igib.res.in Wed Jul 2 03:36:24 2008 From: pallavi.sarmah at igib.res.in (Pallavi Sarmah) Date: Wed, 2 Jul 2008 13:06:24 +0530 Subject: [Bioperl-l] not being able to install Bio-ext-1.4 Message-ID: <4C33FA201D55F743B5DE794497FCA8971F0C9C@n1ex> Hi I am having problem installing Bio::Ext-1.4. I have forced installed BioPerl1.4 and now trying to install Bio::Ext but getting the following errors in Ubuntu. This is not the full list of errors but I am not being able to get all. Can anyone please help me with this. I have been trying the mailing list for quite sometime now. Align.c:5835: error: array subscript is not an integer Align.c:5835: error: array subscript is not an integer Align.c:5835: error: array subscript is not an integer Align.c:5836: error: array subscript is not an integer Align.c:5836: error: array subscript is not an integer Align.c:5836: error: array subscript is not an integer Align.c:5836: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:5838: error: ?OP? has no member named ?op_private? Align.c:5838: error: ?OP? has no member named ?op_targ? Align.c:5842: error: invalid operands to binary + Align.c:5842: error: ?IV? undeclared (first use in this function) Align.c:5842: error: expected ?)? before ?RETVAL? Align.c:5842: error: too many arguments to function ?Perl_sv_setiv? Align.c:5842: error: ?SV? has no member named ?sv_flags? Align.c:5844: error: expected ?;? before ?tmpXSoff? Align.c:5844: error: invalid operands to binary + Align.c:5844: error: ?tmpXSoff? undeclared (first use in this function) Align.c: In function ?XS_Bio__Ext__Align__FileSource_filename?: Align.c:5851: error: function ?ax? is initialized like a variable Align.c:5851: error: invalid lvalue in increment Align.c:5851: error: function ?items? is initialized like a variable Align.c:5852: warning: comparison between pointer and integer Align.c:5855: error: array subscript is not an integer Align.c:5855: error: array subscript is not an integer Align.c:5855: error: array subscript is not an integer Align.c:5855: error: array subscript is not an integer Align.c:5857: error: ?OP? has no member named ?op_private? Align.c:5857: error: ?OP? has no member named ?op_targ? Align.c:5865: error: invalid operands to binary + Align.c:5865: error: ?SV? has no member named ?sv_flags? Align.c:5867: error: ?IV? undeclared (first use in this function) Align.c:5867: error: expected ?;? before ?tmpXSoff? Align.c:5867: error: invalid operands to binary + Align.c:5867: error: ?tmpXSoff? undeclared (first use in this function) Align.c: In function ?XS_Bio__Ext__Align__FileSource_set_input?: Align.c:5874: error: function ?ax? is initialized like a variable Align.c:5874: error: invalid lvalue in increment Align.c:5874: error: function ?items? is initialized like a variable Align.c:5875: warning: comparison between pointer and integer Align.c:5878: error: array subscript is not an integer Align.c:5878: error: array subscript is not an integer Align.c:5878: error: array subscript is not an integer Align.c:5878: error: array subscript is not an integer Align.c:5879: error: array subscript is not an integer Align.c:5879: error: ?XPVIO? has no member named ?xio_ifp? Align.c:5881: error: ?OP? has no member named ?op_private? Align.c:5881: error: ?OP? has no member named ?op_targ? Align.c:5885: error: invalid operands to binary + Align.c:5885: error: ?IV? undeclared (first use in this function) Align.c:5885: error: expected ?)? before ?RETVAL? Align.c:5885: error: too many arguments to function ?Perl_sv_setiv? Align.c:5885: error: ?SV? has no member named ?sv_flags? Align.c:5887: error: expected ?;? before ?tmpXSoff? Align.c:5887: error: invalid operands to binary + Align.c:5887: error: ?tmpXSoff? undeclared (first use in this function) Align.c: In function ?XS_Bio__Ext__Align__FileSource_input?: Align.c:5894: error: function ?ax? is initialized like a variable Align.c:5894: error: invalid lvalue in increment Align.c:5894: error: function ?items? is initialized like a variable Align.c:5895: warning: comparison between pointer and integer Align.c:5898: error: array subscript is not an integer Align.c:5898: error: array subscript is not an integer Align.c:5898: error: array subscript is not an integer Align.c:5898: error: array subscript is not an integer Align.c:5903: error: array subscript is not an integer Align.c:5907: warning: passing argument 3 of ?Perl_do_open? makes pointer from integer without a cast Align.c:5908: error: array subscript is not an integer Align.c:5908: warning: passing argument 2 of ?Perl_gv_stashpv? makes pointer from integer without a cast Align.c:5908: warning: passing argument 3 of ?Perl_sv_setsv_flags? makes pointer from integer without a cast Align.c:5910: error: array subscript is not an integer Align.c:5913: error: ?IV? undeclared (first use in this function) Align.c:5913: error: expected ?;? before ?tmpXSoff? Align.c:5913: error: invalid operands to binary + Align.c:5913: error: ?tmpXSoff? undeclared (first use in this function) Align.c: In function ?XS_Bio__Ext__Align__FileSource_set_format?: Align.c:5920: error: function ?ax? is initialized like a variable Align.c:5920: error: invalid lvalue in increment Align.c:5920: error: function ?items? is initialized like a variable Align.c:5921: warning: comparison between pointer and integer Align.c:5924: error: array subscript is not an integer Align.c:5924: error: array subscript is not an integer Align.c:5924: error: array subscript is not an integer Align.c:5924: error: array subscript is not an integer Align.c:5925: error: array subscript is not an integer Align.c:5925: error: array subscript is not an integer Align.c:5925: error: array subscript is not an integer Align.c:5927: error: ?OP? has no member named ?op_private? Align.c:5927: error: ?OP? has no member named ?op_targ? Align.c:5931: error: invalid operands to binary + Align.c:5931: error: ?IV? undeclared (first use in this function) Align.c:5931: error: expected ?)? before ?RETVAL? Align.c:5931: error: too many arguments to function ?Perl_sv_setiv? Align.c:5931: error: ?SV? has no member named ?sv_flags? Align.c:5933: error: expected ?;? before ?tmpXSoff? Align.c:5933: error: invalid operands to binary + Align.c:5933: error: ?tmpXSoff? undeclared (first use in this function) Align.c: In function ?XS_Bio__Ext__Align__FileSource_format?: Align.c:5940: error: function ?ax? is initialized like a variable Align.c:5940: error: invalid lvalue in increment Align.c:5940: error: function ?items? is initialized like a variable Align.c:5941: warning: comparison between pointer and integer Align.c:5944: error: array subscript is not an integer Align.c:5944: error: array subscript is not an integer Align.c:5944: error: array subscript is not an integer Align.c:5944: error: array subscript is not an integer Align.c:5946: error: ?OP? has no member named ?op_private? Align.c:5946: error: ?OP? has no member named ?op_targ? Align.c:5950: error: invalid operands to binary + Align.c:5950: error: ?IV? undeclared (first use in this function) Align.c:5950: error: expected ?)? before ?RETVAL? Align.c:5950: error: too many arguments to function ?Perl_sv_setiv? Align.c:5950: error: ?SV? has no member named ?sv_flags? Align.c:5952: error: expected ?;? before ?tmpXSoff? Align.c:5952: error: invalid operands to binary + Align.c:5952: error: ?tmpXSoff? undeclared (first use in this function) Align.c: In function ?XS_Bio__Ext__Align__FileSource_set_type?: Align.c:5959: error: function ?ax? is initialized like a variable Align.c:5959: error: invalid lvalue in increment Align.c:5959: error: function ?items? is initialized like a variable Align.c:5960: warning: comparison between pointer and integer Align.c:5963: error: array subscript is not an integer Align.c:5963: error: array subscript is not an integer Align.c:5963: error: array subscript is not an integer Align.c:5963: error: array subscript is not an integer Align.c:5964: error: array subscript is not an integer Align.c:5964: error: array subscript is not an integer Align.c:5964: error: array subscript is not an integer Align.c:5966: error: ?OP? has no member named ?op_private? Align.c:5966: error: ?OP? has no member named ?op_targ? Align.c:5970: error: invalid operands to binary + Align.c:5970: error: ?IV? undeclared (first use in this function) Align.c:5970: error: expected ?)? before ?RETVAL? Align.c:5970: error: too many arguments to function ?Perl_sv_setiv? Align.c:5970: error: ?SV? has no member named ?sv_flags? Align.c:5972: error: expected ?;? before ?tmpXSoff? Align.c:5972: error: invalid operands to binary + Align.c:5972: error: ?tmpXSoff? undeclared (first use in this function) Align.c: In function ?XS_Bio__Ext__Align__FileSource_type?: Align.c:5979: error: function ?ax? is initialized like a variable Align.c:5979: error: invalid lvalue in increment Align.c:5979: error: function ?items? is initialized like a variable Align.c:5980: warning: comparison between pointer and integer Align.c:5983: error: array subscript is not an integer Align.c:5983: error: array subscript is not an integer Align.c:5983: error: array subscript is not an integer Align.c:5983: error: array subscript is not an integer Align.c:5985: error: ?OP? has no member named ?op_private? Align.c:5985: error: ?OP? has no member named ?op_targ? Align.c:5989: error: invalid operands to binary + Align.c:5989: error: ?IV? undeclared (first use in this function) Align.c:5989: error: expected ?)? before ?RETVAL? Align.c:5989: error: too many arguments to function ?Perl_sv_setiv? Align.c:5989: error: ?SV? has no member named ?sv_flags? Align.c:5991: error: expected ?;? before ?tmpXSoff? Align.c:5991: error: invalid operands to binary + Align.c:5991: error: ?tmpXSoff? undeclared (first use in this function) Align.c: In function ?XS_Bio__Ext__Align__FileSource_new?: Align.c:5998: error: function ?ax? is initialized like a variable Align.c:5998: error: invalid lvalue in increment Align.c:5998: error: function ?items? is initialized like a variable Align.c:5999: warning: comparison between pointer and integer Align.c:6001: error: invalid operands to binary - Align.c:6003: error: array subscript is not an integer Align.c:6003: error: array subscript is not an integer Align.c:6003: error: array subscript is not an integer Align.c:6003: error: too many arguments to function ?Perl_sv_2pv_flags? Align.xs:3253: error: array subscript is not an integer Align.xs:3254: error: array subscript is not an integer Align.xs:3255: error: ?IV? undeclared (first use in this function) Align.xs:3255: error: expected ?;? before ?tmpXSoff? Align.xs:3255: error: invalid operands to binary + Align.xs:3255: error: ?tmpXSoff? undeclared (first use in this function) Align.c: In function ?XS_Bio__Ext__Align__FileSource_DESTROY?: Align.c:6021: error: function ?ax? is initialized like a variable Align.c:6021: error: invalid lvalue in increment Align.c:6021: error: function ?items? is initialized like a variable Align.c:6022: warning: comparison between pointer and integer Align.c:6025: error: array subscript is not an integer Align.c:6025: error: array subscript is not an integer Align.c:6025: error: array subscript is not an integer Align.c:6025: error: array subscript is not an integer Align.c:6030: error: ?IV? undeclared (first use in this function) Align.c:6030: error: expected ?;? before ?tmpXSoff? Align.c:6030: error: invalid operands to binary + Align.c:6030: error: ?tmpXSoff? undeclared (first use in this function) Align.c: In function ?XS_Bio__Ext__Align_Align_strings_ProteinSmithWaterman?: Align.c:6037: error: function ?ax? is initialized like a variable Align.c:6037: error: invalid lvalue in increment Align.c:6037: error: function ?items? is initialized like a variable Align.c:6038: warning: comparison between pointer and integer Align.c:6041: error: array subscript is not an integer Align.c:6041: error: array subscript is not an integer Align.c:6041: error: array subscript is not an integer Align.c:6041: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6042: error: array subscript is not an integer Align.c:6042: error: array subscript is not an integer Align.c:6042: error: array subscript is not an integer Align.c:6042: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6043: error: array subscript is not an integer Align.c:6043: error: array subscript is not an integer Align.c:6043: error: array subscript is not an integer Align.c:6043: error: array subscript is not an integer Align.c:6044: error: array subscript is not an integer Align.c:6044: error: array subscript is not an integer Align.c:6044: error: array subscript is not an integer Align.c:6045: error: array subscript is not an integer Align.c:6045: error: array subscript is not an integer Align.c:6045: error: array subscript is not an integer Align.c:6050: error: array subscript is not an integer Align.c:6051: error: array subscript is not an integer Align.c:6054: error: ?IV? undeclared (first use in this function) Align.c:6054: error: expected ?;? before ?tmpXSoff? Align.c:6054: error: invalid operands to binary + Align.c:6054: error: ?tmpXSoff? undeclared (first use in this function) Align.c: In function ?XS_Bio__Ext__Align_Align_Sequences_ProteinSmithWaterman?: Align.c:6061: error: function ?ax? is initialized like a variable Align.c:6061: error: invalid lvalue in increment Align.c:6061: error: function ?items? is initialized like a variable Align.c:6062: warning: comparison between pointer and integer Align.c:6065: error: array subscript is not an integer Align.c:6065: error: array subscript is not an integer Align.c:6065: error: array subscript is not an integer Align.c:6065: error: array subscript is not an integer Align.c:6066: error: array subscript is not an integer Align.c:6066: error: array subscript is not an integer Align.c:6066: error: array subscript is not an integer Align.c:6066: error: array subscript is not an integer Align.c:6067: error: array subscript is not an integer Align.c:6067: error: array subscript is not an integer Align.c:6067: error: array subscript is not an integer Align.c:6067: error: array subscript is not an integer Align.c:6068: error: array subscript is not an integer Align.c:6068: error: array subscript is not an integer Align.c:6068: error: array subscript is not an integer Align.c:6069: error: array subscript is not an integer Align.c:6069: error: array subscript is not an integer Align.c:6069: error: array subscript is not an integer Align.c:6074: error: array subscript is not an integer Align.c:6075: error: array subscript is not an integer Align.c:6078: error: ?IV? undeclared (first use in this function) Align.c:6078: error: expected ?;? before ?tmpXSoff? Align.c:6078: error: invalid operands to binary + Align.c:6078: error: ?tmpXSoff? undeclared (first use in this function) Align.c: In function ?XS_Bio__Ext__Align_Align_Proteins_SmithWaterman?: Align.c:6085: error: function ?ax? is initialized like a variable Align.c:6085: error: invalid lvalue in increment Align.c:6085: error: function ?items? is initialized like a variable Align.c:6086: warning: comparison between pointer and integer Align.c:6089: error: array subscript is not an integer Align.c:6089: error: array subscript is not an integer Align.c:6089: error: array subscript is not an integer Align.c:6089: error: array subscript is not an integer Align.c:6090: error: array subscript is not an integer Align.c:6090: error: array subscript is not an integer Align.c:6090: error: array subscript is not an integer Align.c:6090: error: array subscript is not an integer Align.c:6091: error: array subscript is not an integer Align.c:6091: error: array subscript is not an integer Align.c:6091: error: array subscript is not an integer Align.c:6091: error: array subscript is not an integer Align.c:6092: error: array subscript is not an integer Align.c:6092: error: array subscript is not an integer Align.c:6092: error: array subscript is not an integer Align.c:6093: error: array subscript is not an integer Align.c:6093: error: array subscript is not an integer Align.c:6093: error: array subscript is not an integer Align.c:6098: error: array subscript is not an integer Align.c:6099: error: array subscript is not an integer Align.c:6102: error: ?IV? undeclared (first use in this function) Align.c:6102: error: expected ?;? before ?tmpXSoff? Align.c:6102: error: invalid operands to binary + Align.c:6102: error: ?tmpXSoff? undeclared (first use in this function) Align.c: In function ?XS_Bio__Ext__Align_Align_DNA_Sequences?: Align.c:6109: error: function ?ax? is initialized like a variable Align.c:6109: error: invalid lvalue in increment Align.c:6109: error: function ?items? is initialized like a variable Align.c:6110: warning: comparison between pointer and integer Align.c:6113: error: array subscript is not an integer Align.c:6113: error: array subscript is not an integer Align.c:6113: error: array subscript is not an integer Align.c:6113: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6114: error: array subscript is not an integer Align.c:6114: error: array subscript is not an integer Align.c:6114: error: array subscript is not an integer Align.c:6114: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6115: error: array subscript is not an integer Align.c:6115: error: array subscript is not an integer Align.c:6115: error: array subscript is not an integer Align.c:6116: error: array subscript is not an integer Align.c:6116: error: array subscript is not an integer Align.c:6116: error: array subscript is not an integer Align.c:6117: error: array subscript is not an integer Align.c:6117: error: array subscript is not an integer Align.c:6117: error: array subscript is not an integer Align.c:6118: error: array subscript is not an integer Align.c:6118: error: array subscript is not an integer Align.c:6118: error: array subscript is not an integer Align.c:6119: error: array subscript is not an integer Align.c:6119: error: array subscript is not an integer Align.c:6119: error: array subscript is not an integer Align.c:6131: error: array subscript is not an integer Align.c:6132: error: array subscript is not an integer Align.c:6135: error: ?IV? undeclared (first use in this function) Align.c:6135: error: expected ?;? before ?tmpXSoff? Align.c:6135: error: invalid operands to binary + Align.c:6135: error: ?tmpXSoff? undeclared (first use in this function) Align.c: In function ?XS_Bio__Ext__Align_Align_Protein_Sequences?: Align.c:6142: error: function ?ax? is initialized like a variable Align.c:6142: error: invalid lvalue in increment Align.c:6142: error: function ?items? is initialized like a variable Align.c:6143: warning: comparison between pointer and integer Align.c:6146: error: array subscript is not an integer Align.c:6146: error: array subscript is not an integer Align.c:6146: error: array subscript is not an integer Align.c:6146: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6147: error: array subscript is not an integer Align.c:6147: error: array subscript is not an integer Align.c:6147: error: array subscript is not an integer Align.c:6147: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6148: error: array subscript is not an integer Align.c:6148: error: array subscript is not an integer Align.c:6148: error: array subscript is not an integer Align.c:6148: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6153: error: array subscript is not an integer Align.c:6154: error: array subscript is not an integer Align.c:6157: error: ?IV? undeclared (first use in this function) Align.c:6157: error: expected ?;? before ?tmpXSoff? Align.c:6157: error: invalid operands to binary + Align.c:6157: error: ?tmpXSoff? undeclared (first use in this function) Align.c: In function ?XS_Bio__Ext__Align__AlignOutput_aln1?: Align.c:6164: error: function ?ax? is initialized like a variable Align.c:6164: error: invalid lvalue in increment Align.c:6164: error: function ?items? is initialized like a variable Align.c:6165: warning: comparison between pointer and integer Align.c:6168: error: array subscript is not an integer Align.c:6168: error: array subscript is not an integer Align.c:6168: error: array subscript is not an integer Align.c:6168: error: array subscript is not an integer Align.c:6170: error: ?OP? has no member named ?op_private? Align.c:6170: error: ?OP? has no member named ?op_targ? Align.c:6174: error: invalid operands to binary + Align.c:6174: error: ?SV? has no member named ?sv_flags? Align.c:6176: error: ?IV? undeclared (first use in this function) Align.c:6176: error: expected ?;? before ?tmpXSoff? Align.c:6176: error: invalid operands to binary + Align.c:6176: error: ?tmpXSoff? undeclared (first use in this function) Align.c: In function ?XS_Bio__Ext__Align__AlignOutput_aln2?: Align.c:6183: error: function ?ax? is initialized like a variable Align.c:6183: error: invalid lvalue in increment Align.c:6183: error: function ?items? is initialized like a variable Align.c:6184: warning: comparison between pointer and integer Align.c:6187: error: array subscript is not an integer Align.c:6187: error: array subscript is not an integer Align.c:6187: error: array subscript is not an integer Align.c:6187: error: array subscript is not an integer Align.c:6189: error: ?OP? has no member named ?op_private? Align.c:6189: error: ?OP? has no member named ?op_targ? Align.c:6193: error: invalid operands to binary + Align.c:6193: error: ?SV? has no member named ?sv_flags? Align.c:6195: error: ?IV? undeclared (first use in this function) Align.c:6195: error: expected ?;? before ?tmpXSoff? Align.c:6195: error: invalid operands to binary + Align.c:6195: error: ?tmpXSoff? undeclared (first use in this function) Align.c: In function ?XS_Bio__Ext__Align__AlignOutput_start1?: Align.c:6202: error: function ?ax? is initialized like a variable Align.c:6202: error: invalid lvalue in increment Align.c:6202: error: function ?items? is initialized like a variable Align.c:6203: warning: comparison between pointer and integer Align.c:6206: error: array subscript is not an integer Align.c:6206: error: array subscript is not an integer Align.c:6206: error: array subscript is not an integer Align.c:6206: error: array subscript is not an integer Align.c:6208: error: ?OP? has no member named ?op_private? Align.c:6208: error: ?OP? has no member named ?op_targ? Align.c:6212: error: invalid operands to binary + Align.c:6212: error: ?IV? undeclared (first use in this function) Align.c:6212: error: expected ?)? before ?RETVAL? Align.c:6212: error: too many arguments to function ?Perl_sv_setiv? Align.c:6212: error: ?SV? has no member named ?sv_flags? Align.c:6214: error: expected ?;? before ?tmpXSoff? Align.c:6214: error: invalid operands to binary + Align.c:6214: error: ?tmpXSoff? undeclared (first use in this function) Align.c: In function ?XS_Bio__Ext__Align__AlignOutput_end1?: Align.c:6221: error: function ?ax? is initialized like a variable Align.c:6221: error: invalid lvalue in increment Align.c:6221: error: function ?items? is initialized like a variable Align.c:6222: warning: comparison between pointer and integer Align.c:6225: error: array subscript is not an integer Align.c:6225: error: array subscript is not an integer Align.c:6225: error: array subscript is not an integer Align.c:6225: error: array subscript is not an integer Align.c:6227: error: ?OP? has no member named ?op_private? Align.c:6227: error: ?OP? has no member named ?op_targ? Align.c:6231: error: invalid operands to binary + Align.c:6231: error: ?IV? undeclared (first use in this function) Align.c:6231: error: expected ?)? before ?RETVAL? Align.c:6231: error: too many arguments to function ?Perl_sv_setiv? Align.c:6231: error: ?SV? has no member named ?sv_flags? Align.c:6233: error: expected ?;? before ?tmpXSoff? Align.c:6233: error: invalid operands to binary + Align.c:6233: error: ?tmpXSoff? undeclared (first use in this function) Align.c: In function ?XS_Bio__Ext__Align__AlignOutput_start2?: Align.c:6240: error: function ?ax? is initialized like a variable Align.c:6240: error: invalid lvalue in increment Align.c:6240: error: function ?items? is initialized like a variable Align.c:6241: warning: comparison between pointer and integer Align.c:6244: error: array subscript is not an integer Align.c:6244: error: array subscript is not an integer Align.c:6244: error: array subscript is not an integer Align.c:6244: error: array subscript is not an integer Align.c:6246: error: ?OP? has no member named ?op_private? Align.c:6246: error: ?OP? has no member named ?op_targ? Align.c:6250: error: invalid operands to binary + Align.c:6250: error: ?IV? undeclared (first use in this function) Align.c:6250: error: expected ?)? before ?RETVAL? Align.c:6250: error: too many arguments to function ?Perl_sv_setiv? Align.c:6250: error: ?SV? has no member named ?sv_flags? Align.c:6252: error: expected ?;? before ?tmpXSoff? Align.c:6252: error: invalid operands to binary + Align.c:6252: error: ?tmpXSoff? undeclared (first use in this function) Align.c: In function ?XS_Bio__Ext__Align__AlignOutput_end2?: Align.c:6259: error: function ?ax? is initialized like a variable Align.c:6259: error: invalid lvalue in increment Align.c:6259: error: function ?items? is initialized like a variable Align.c:6260: warning: comparison between pointer and integer Align.c:6263: error: array subscript is not an integer Align.c:6263: error: array subscript is not an integer Align.c:6263: error: array subscript is not an integer Align.c:6263: error: array subscript is not an integer Align.c:6265: error: ?OP? has no member named ?op_private? Align.c:6265: error: ?OP? has no member named ?op_targ? Align.c:6269: error: invalid operands to binary + Align.c:6269: error: ?IV? undeclared (first use in this function) Align.c:6269: error: expected ?)? before ?RETVAL? Align.c:6269: error: too many arguments to function ?Perl_sv_setiv? Align.c:6269: error: ?SV? has no member named ?sv_flags? Align.c:6271: error: expected ?;? before ?tmpXSoff? Align.c:6271: error: invalid operands to binary + Align.c:6271: error: ?tmpXSoff? undeclared (first use in this function) Align.c: In function ?boot_Bio__Ext__Align?: Align.c:6280: error: function ?ax? is initialized like a variable Align.c:6280: error: invalid lvalue in increment Align.c:6280: error: function ?items? is initialized like a variable Align.c:6283: error: array subscript is not an integer Align.c:6283: error: array subscript is not an integer Align.c:6283: error: array subscript is not an integer Align.c:6283: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6283: warning: comparison between pointer and integer Align.c:6283: error: array subscript is not an integer Align.c:6283: error: ?SV? has no member named ?sv_flags? Align.c:6283: error: ?SV? has no member named ?sv_flags? Align.c:6283: error: ?SV? has no member named ?sv_flags? Align.c:6283: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6283: error: ?SV? has no member named ?sv_flags? Align.c:6283: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6283: error: ?SV? has no member named ?sv_flags? Align.c:6283: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6283: error: ?SV? has no member named ?sv_flags? Align.c:6283: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6283: error: ?SV? has no member named ?sv_flags? Align.c:6283: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6283: error: ?SV? has no member named ?sv_flags? Align.c:6283: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6283: error: ?SV? has no member named ?sv_flags? Align.c:6283: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6283: error: ?SV? has no member named ?sv_flags? Align.c:6283: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6283: error: ?SV? has no member named ?sv_flags? Align.c:6283: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6283: error: ?SV? has no member named ?sv_flags? Align.c:6283: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6283: error: ?SV? has no member named ?sv_flags? Align.c:6283: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6283: error: ?SV? has no member named ?sv_flags? Align.c:6283: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6283: error: ?SV? has no member named ?sv_flags? Align.c:6283: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6283: error: ?SV? has no member named ?sv_flags? Align.c:6283: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6283: error: ?SV? has no member named ?sv_flags? Align.c:6283: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6283: error: ?SV? has no member named ?sv_flags? Align.c:6283: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6283: error: ?SV? has no member named ?sv_flags? Align.c:6283: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6283: error: ?SV? has no member named ?sv_flags? Align.c:6283: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6283: error: ?SV? has no member named ?sv_flags? Align.c:6283: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6283: error: ?SV? has no member named ?sv_flags? Align.c:6283: error: too many arguments to function ?Perl_sv_2pv_flags? Align.c:6595: error: array subscript is not an integer Align.c:6595: error: ?IV? undeclared (first use in this function) Align.c:6595: error: expected ?;? before ?tmpXSoff? Align.c:6595: error: invalid operands to binary + Align.c:6595: error: ?tmpXSoff? undeclared (first use in this function) make[1]: *** [Align.o] Error 1 make[1]: Leaving directory `/home/pallavi/Pallavi/downloads/bioperl-ext-1.4/Bio/Ext/Align' make: *** [subdirs] Error 2 thanks Pallavi From nsh9351 at rit.edu Wed Jul 2 10:34:51 2008 From: nsh9351 at rit.edu (Nathan Haseley (RIT Student)) Date: Wed, 2 Jul 2008 10:34:51 -0400 Subject: [Bioperl-l] Clustalw module Message-ID: <7D75703BC8E1C149BF78A1E79AAAB169035BC544@svits28.main.ad.rit.edu> Hello, I am working with the Bioperl module Bio::Tools::Run::Alignment::Clustalw. I try to include the package in my script as follows: #!/usr/bin/perl use Bio::Seq; use Bio::SearchIO; use Bio::Tools::Run::StandAloneBlast; use Bio::DB::GenBank; use Bio::Tools::Run::Alignment::Clustalw; use Bio::Root::Exception; use Error qw(:try); but I keep getting the following error message: Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.8.8 /usr/local/share/perl/5.8.8 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.8 /usr/share/perl/5.8 /usr/local/lib/site_perl .) at ./BlastTwoCompare.pl line 6. BEGIN failed--compilation aborted at ./BlastTwoCompare.pl line 6. The Clustalw program is configured correctly to work in my directory. Am I missing something obvious or is there something wrong with my BioPerl configuration? Any advice on how to fix this? Thank you for your time. Nathan From jason at bioperl.org Wed Jul 2 11:02:24 2008 From: jason at bioperl.org (Jason Stajich) Date: Wed, 2 Jul 2008 11:02:24 -0400 Subject: [Bioperl-l] Clustalw module In-Reply-To: <7D75703BC8E1C149BF78A1E79AAAB169035BC544@svits28.main.ad.rit.edu> References: <7D75703BC8E1C149BF78A1E79AAAB169035BC544@svits28.main.ad.rit.edu> Message-ID: did you install bioperl-run package as well as bioperl core? -jason On Jul 2, 2008, at 10:34 AM, Nathan Haseley (RIT Student) wrote: > Hello, > I am working with the Bioperl module > Bio::Tools::Run::Alignment::Clustalw. I try to include the package > in my script as follows: > > #!/usr/bin/perl > use Bio::Seq; > use Bio::SearchIO; > use Bio::Tools::Run::StandAloneBlast; > use Bio::DB::GenBank; > use Bio::Tools::Run::Alignment::Clustalw; > use Bio::Root::Exception; > use Error qw(:try); > > but I keep getting the following error message: > Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC > contains: /etc/perl /usr/local/lib/perl/5.8.8 /usr/local/share/perl/ > 5.8.8 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.8 /usr/share/ > perl/5.8 /usr/local/lib/site_perl .) at ./BlastTwoCompare.pl line 6. > BEGIN failed--compilation aborted at ./BlastTwoCompare.pl line 6. > > The Clustalw program is configured correctly to work in my > directory. Am I missing something obvious or is there something > wrong with my BioPerl configuration? Any advice on how to fix > this? Thank you for your time. > > Nathan > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From Kevin.M.Brown at asu.edu Wed Jul 2 11:10:43 2008 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Wed, 2 Jul 2008 08:10:43 -0700 Subject: [Bioperl-l] not being able to install Bio-ext-1.4 In-Reply-To: <4C33FA201D55F743B5DE794497FCA8971F0C9C@n1ex> References: <4C33FA201D55F743B5DE794497FCA8971F0C9C@n1ex> Message-ID: <1A4207F8295607498283FE9E93B775B405072F29@EX02.asurite.ad.asu.edu> Bioperl 1.4 is more than 5 years old. Try following the install instructions on the bioperl website for a more up2date version (v1.5.2): http://www.bioperl.org/wiki/Installing_BioPerl_on_Ubuntu_Server Or http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Pallavi Sarmah > Sent: Wednesday, July 02, 2008 12:36 AM > To: ymc at paxil.stanford.edu; birney at sanger.ac.uk; bioperl-l at bioperl.org > Subject: [Bioperl-l] not being able to install Bio-ext-1.4 > > > Hi > > I am having problem installing Bio::Ext-1.4. I have forced > installed BioPerl1.4 and now trying to install Bio::Ext but > getting the following errors in Ubuntu. This is not the full > list of errors but I am not being able to get all. Can anyone > please help me with this. I have been trying the mailing list > for quite sometime now. > > Align.c:5835: error: array subscript is not an integer > Align.c:5835: error: array subscript is not an integer > Align.c:5835: error: array subscript is not an integer > Align.c:5836: error: array subscript is not an integer > Align.c:5836: error: array subscript is not an integer > Align.c:5836: error: array subscript is not an integer > Align.c:5836: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:5838: error: 'OP' has no member named 'op_private' > Align.c:5838: error: 'OP' has no member named 'op_targ' > Align.c:5842: error: invalid operands to binary + > Align.c:5842: error: 'IV' undeclared (first use in this function) > Align.c:5842: error: expected ')' before 'RETVAL' > Align.c:5842: error: too many arguments to function 'Perl_sv_setiv' > Align.c:5842: error: 'SV' has no member named 'sv_flags' > Align.c:5844: error: expected ';' before 'tmpXSoff' > Align.c:5844: error: invalid operands to binary + > Align.c:5844: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__FileSource_filename': > Align.c:5851: error: function 'ax' is initialized like a variable > Align.c:5851: error: invalid lvalue in increment > Align.c:5851: error: function 'items' is initialized like a variable > Align.c:5852: warning: comparison between pointer and integer > Align.c:5855: error: array subscript is not an integer > Align.c:5855: error: array subscript is not an integer > Align.c:5855: error: array subscript is not an integer > Align.c:5855: error: array subscript is not an integer > Align.c:5857: error: 'OP' has no member named 'op_private' > Align.c:5857: error: 'OP' has no member named 'op_targ' > Align.c:5865: error: invalid operands to binary + > Align.c:5865: error: 'SV' has no member named 'sv_flags' > Align.c:5867: error: 'IV' undeclared (first use in this function) > Align.c:5867: error: expected ';' before 'tmpXSoff' > Align.c:5867: error: invalid operands to binary + > Align.c:5867: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__FileSource_set_input': > Align.c:5874: error: function 'ax' is initialized like a variable > Align.c:5874: error: invalid lvalue in increment > Align.c:5874: error: function 'items' is initialized like a variable > Align.c:5875: warning: comparison between pointer and integer > Align.c:5878: error: array subscript is not an integer > Align.c:5878: error: array subscript is not an integer > Align.c:5878: error: array subscript is not an integer > Align.c:5878: error: array subscript is not an integer > Align.c:5879: error: array subscript is not an integer > Align.c:5879: error: 'XPVIO' has no member named 'xio_ifp' > Align.c:5881: error: 'OP' has no member named 'op_private' > Align.c:5881: error: 'OP' has no member named 'op_targ' > Align.c:5885: error: invalid operands to binary + > Align.c:5885: error: 'IV' undeclared (first use in this function) > Align.c:5885: error: expected ')' before 'RETVAL' > Align.c:5885: error: too many arguments to function 'Perl_sv_setiv' > Align.c:5885: error: 'SV' has no member named 'sv_flags' > Align.c:5887: error: expected ';' before 'tmpXSoff' > Align.c:5887: error: invalid operands to binary + > Align.c:5887: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__FileSource_input': > Align.c:5894: error: function 'ax' is initialized like a variable > Align.c:5894: error: invalid lvalue in increment > Align.c:5894: error: function 'items' is initialized like a variable > Align.c:5895: warning: comparison between pointer and integer > Align.c:5898: error: array subscript is not an integer > Align.c:5898: error: array subscript is not an integer > Align.c:5898: error: array subscript is not an integer > Align.c:5898: error: array subscript is not an integer > Align.c:5903: error: array subscript is not an integer > Align.c:5907: warning: passing argument 3 of 'Perl_do_open' > makes pointer from integer without a cast > Align.c:5908: error: array subscript is not an integer > Align.c:5908: warning: passing argument 2 of > 'Perl_gv_stashpv' makes pointer from integer without a cast > Align.c:5908: warning: passing argument 3 of > 'Perl_sv_setsv_flags' makes pointer from integer without a cast > Align.c:5910: error: array subscript is not an integer > Align.c:5913: error: 'IV' undeclared (first use in this function) > Align.c:5913: error: expected ';' before 'tmpXSoff' > Align.c:5913: error: invalid operands to binary + > Align.c:5913: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__FileSource_set_format': > Align.c:5920: error: function 'ax' is initialized like a variable > Align.c:5920: error: invalid lvalue in increment > Align.c:5920: error: function 'items' is initialized like a variable > Align.c:5921: warning: comparison between pointer and integer > Align.c:5924: error: array subscript is not an integer > Align.c:5924: error: array subscript is not an integer > Align.c:5924: error: array subscript is not an integer > Align.c:5924: error: array subscript is not an integer > Align.c:5925: error: array subscript is not an integer > Align.c:5925: error: array subscript is not an integer > Align.c:5925: error: array subscript is not an integer > Align.c:5927: error: 'OP' has no member named 'op_private' > Align.c:5927: error: 'OP' has no member named 'op_targ' > Align.c:5931: error: invalid operands to binary + > Align.c:5931: error: 'IV' undeclared (first use in this function) > Align.c:5931: error: expected ')' before 'RETVAL' > Align.c:5931: error: too many arguments to function 'Perl_sv_setiv' > Align.c:5931: error: 'SV' has no member named 'sv_flags' > Align.c:5933: error: expected ';' before 'tmpXSoff' > Align.c:5933: error: invalid operands to binary + > Align.c:5933: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__FileSource_format': > Align.c:5940: error: function 'ax' is initialized like a variable > Align.c:5940: error: invalid lvalue in increment > Align.c:5940: error: function 'items' is initialized like a variable > Align.c:5941: warning: comparison between pointer and integer > Align.c:5944: error: array subscript is not an integer > Align.c:5944: error: array subscript is not an integer > Align.c:5944: error: array subscript is not an integer > Align.c:5944: error: array subscript is not an integer > Align.c:5946: error: 'OP' has no member named 'op_private' > Align.c:5946: error: 'OP' has no member named 'op_targ' > Align.c:5950: error: invalid operands to binary + > Align.c:5950: error: 'IV' undeclared (first use in this function) > Align.c:5950: error: expected ')' before 'RETVAL' > Align.c:5950: error: too many arguments to function 'Perl_sv_setiv' > Align.c:5950: error: 'SV' has no member named 'sv_flags' > Align.c:5952: error: expected ';' before 'tmpXSoff' > Align.c:5952: error: invalid operands to binary + > Align.c:5952: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__FileSource_set_type': > Align.c:5959: error: function 'ax' is initialized like a variable > Align.c:5959: error: invalid lvalue in increment > Align.c:5959: error: function 'items' is initialized like a variable > Align.c:5960: warning: comparison between pointer and integer > Align.c:5963: error: array subscript is not an integer > Align.c:5963: error: array subscript is not an integer > Align.c:5963: error: array subscript is not an integer > Align.c:5963: error: array subscript is not an integer > Align.c:5964: error: array subscript is not an integer > Align.c:5964: error: array subscript is not an integer > Align.c:5964: error: array subscript is not an integer > Align.c:5966: error: 'OP' has no member named 'op_private' > Align.c:5966: error: 'OP' has no member named 'op_targ' > Align.c:5970: error: invalid operands to binary + > Align.c:5970: error: 'IV' undeclared (first use in this function) > Align.c:5970: error: expected ')' before 'RETVAL' > Align.c:5970: error: too many arguments to function 'Perl_sv_setiv' > Align.c:5970: error: 'SV' has no member named 'sv_flags' > Align.c:5972: error: expected ';' before 'tmpXSoff' > Align.c:5972: error: invalid operands to binary + > Align.c:5972: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__FileSource_type': > Align.c:5979: error: function 'ax' is initialized like a variable > Align.c:5979: error: invalid lvalue in increment > Align.c:5979: error: function 'items' is initialized like a variable > Align.c:5980: warning: comparison between pointer and integer > Align.c:5983: error: array subscript is not an integer > Align.c:5983: error: array subscript is not an integer > Align.c:5983: error: array subscript is not an integer > Align.c:5983: error: array subscript is not an integer > Align.c:5985: error: 'OP' has no member named 'op_private' > Align.c:5985: error: 'OP' has no member named 'op_targ' > Align.c:5989: error: invalid operands to binary + > Align.c:5989: error: 'IV' undeclared (first use in this function) > Align.c:5989: error: expected ')' before 'RETVAL' > Align.c:5989: error: too many arguments to function 'Perl_sv_setiv' > Align.c:5989: error: 'SV' has no member named 'sv_flags' > Align.c:5991: error: expected ';' before 'tmpXSoff' > Align.c:5991: error: invalid operands to binary + > Align.c:5991: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__FileSource_new': > Align.c:5998: error: function 'ax' is initialized like a variable > Align.c:5998: error: invalid lvalue in increment > Align.c:5998: error: function 'items' is initialized like a variable > Align.c:5999: warning: comparison between pointer and integer > Align.c:6001: error: invalid operands to binary - > Align.c:6003: error: array subscript is not an integer > Align.c:6003: error: array subscript is not an integer > Align.c:6003: error: array subscript is not an integer > Align.c:6003: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.xs:3253: error: array subscript is not an integer > Align.xs:3254: error: array subscript is not an integer > Align.xs:3255: error: 'IV' undeclared (first use in this function) > Align.xs:3255: error: expected ';' before 'tmpXSoff' > Align.xs:3255: error: invalid operands to binary + > Align.xs:3255: error: 'tmpXSoff' undeclared (first use in > this function) > Align.c: In function 'XS_Bio__Ext__Align__FileSource_DESTROY': > Align.c:6021: error: function 'ax' is initialized like a variable > Align.c:6021: error: invalid lvalue in increment > Align.c:6021: error: function 'items' is initialized like a variable > Align.c:6022: warning: comparison between pointer and integer > Align.c:6025: error: array subscript is not an integer > Align.c:6025: error: array subscript is not an integer > Align.c:6025: error: array subscript is not an integer > Align.c:6025: error: array subscript is not an integer > Align.c:6030: error: 'IV' undeclared (first use in this function) > Align.c:6030: error: expected ';' before 'tmpXSoff' > Align.c:6030: error: invalid operands to binary + > Align.c:6030: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function > 'XS_Bio__Ext__Align_Align_strings_ProteinSmithWaterman': > Align.c:6037: error: function 'ax' is initialized like a variable > Align.c:6037: error: invalid lvalue in increment > Align.c:6037: error: function 'items' is initialized like a variable > Align.c:6038: warning: comparison between pointer and integer > Align.c:6041: error: array subscript is not an integer > Align.c:6041: error: array subscript is not an integer > Align.c:6041: error: array subscript is not an integer > Align.c:6041: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6042: error: array subscript is not an integer > Align.c:6042: error: array subscript is not an integer > Align.c:6042: error: array subscript is not an integer > Align.c:6042: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6043: error: array subscript is not an integer > Align.c:6043: error: array subscript is not an integer > Align.c:6043: error: array subscript is not an integer > Align.c:6043: error: array subscript is not an integer > Align.c:6044: error: array subscript is not an integer > Align.c:6044: error: array subscript is not an integer > Align.c:6044: error: array subscript is not an integer > Align.c:6045: error: array subscript is not an integer > Align.c:6045: error: array subscript is not an integer > Align.c:6045: error: array subscript is not an integer > Align.c:6050: error: array subscript is not an integer > Align.c:6051: error: array subscript is not an integer > Align.c:6054: error: 'IV' undeclared (first use in this function) > Align.c:6054: error: expected ';' before 'tmpXSoff' > Align.c:6054: error: invalid operands to binary + > Align.c:6054: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function > 'XS_Bio__Ext__Align_Align_Sequences_ProteinSmithWaterman': > Align.c:6061: error: function 'ax' is initialized like a variable > Align.c:6061: error: invalid lvalue in increment > Align.c:6061: error: function 'items' is initialized like a variable > Align.c:6062: warning: comparison between pointer and integer > Align.c:6065: error: array subscript is not an integer > Align.c:6065: error: array subscript is not an integer > Align.c:6065: error: array subscript is not an integer > Align.c:6065: error: array subscript is not an integer > Align.c:6066: error: array subscript is not an integer > Align.c:6066: error: array subscript is not an integer > Align.c:6066: error: array subscript is not an integer > Align.c:6066: error: array subscript is not an integer > Align.c:6067: error: array subscript is not an integer > Align.c:6067: error: array subscript is not an integer > Align.c:6067: error: array subscript is not an integer > Align.c:6067: error: array subscript is not an integer > Align.c:6068: error: array subscript is not an integer > Align.c:6068: error: array subscript is not an integer > Align.c:6068: error: array subscript is not an integer > Align.c:6069: error: array subscript is not an integer > Align.c:6069: error: array subscript is not an integer > Align.c:6069: error: array subscript is not an integer > Align.c:6074: error: array subscript is not an integer > Align.c:6075: error: array subscript is not an integer > Align.c:6078: error: 'IV' undeclared (first use in this function) > Align.c:6078: error: expected ';' before 'tmpXSoff' > Align.c:6078: error: invalid operands to binary + > Align.c:6078: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function > 'XS_Bio__Ext__Align_Align_Proteins_SmithWaterman': > Align.c:6085: error: function 'ax' is initialized like a variable > Align.c:6085: error: invalid lvalue in increment > Align.c:6085: error: function 'items' is initialized like a variable > Align.c:6086: warning: comparison between pointer and integer > Align.c:6089: error: array subscript is not an integer > Align.c:6089: error: array subscript is not an integer > Align.c:6089: error: array subscript is not an integer > Align.c:6089: error: array subscript is not an integer > Align.c:6090: error: array subscript is not an integer > Align.c:6090: error: array subscript is not an integer > Align.c:6090: error: array subscript is not an integer > Align.c:6090: error: array subscript is not an integer > Align.c:6091: error: array subscript is not an integer > Align.c:6091: error: array subscript is not an integer > Align.c:6091: error: array subscript is not an integer > Align.c:6091: error: array subscript is not an integer > Align.c:6092: error: array subscript is not an integer > Align.c:6092: error: array subscript is not an integer > Align.c:6092: error: array subscript is not an integer > Align.c:6093: error: array subscript is not an integer > Align.c:6093: error: array subscript is not an integer > Align.c:6093: error: array subscript is not an integer > Align.c:6098: error: array subscript is not an integer > Align.c:6099: error: array subscript is not an integer > Align.c:6102: error: 'IV' undeclared (first use in this function) > Align.c:6102: error: expected ';' before 'tmpXSoff' > Align.c:6102: error: invalid operands to binary + > Align.c:6102: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align_Align_DNA_Sequences': > Align.c:6109: error: function 'ax' is initialized like a variable > Align.c:6109: error: invalid lvalue in increment > Align.c:6109: error: function 'items' is initialized like a variable > Align.c:6110: warning: comparison between pointer and integer > Align.c:6113: error: array subscript is not an integer > Align.c:6113: error: array subscript is not an integer > Align.c:6113: error: array subscript is not an integer > Align.c:6113: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6114: error: array subscript is not an integer > Align.c:6114: error: array subscript is not an integer > Align.c:6114: error: array subscript is not an integer > Align.c:6114: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6115: error: array subscript is not an integer > Align.c:6115: error: array subscript is not an integer > Align.c:6115: error: array subscript is not an integer > Align.c:6116: error: array subscript is not an integer > Align.c:6116: error: array subscript is not an integer > Align.c:6116: error: array subscript is not an integer > Align.c:6117: error: array subscript is not an integer > Align.c:6117: error: array subscript is not an integer > Align.c:6117: error: array subscript is not an integer > Align.c:6118: error: array subscript is not an integer > Align.c:6118: error: array subscript is not an integer > Align.c:6118: error: array subscript is not an integer > Align.c:6119: error: array subscript is not an integer > Align.c:6119: error: array subscript is not an integer > Align.c:6119: error: array subscript is not an integer > Align.c:6131: error: array subscript is not an integer > Align.c:6132: error: array subscript is not an integer > Align.c:6135: error: 'IV' undeclared (first use in this function) > Align.c:6135: error: expected ';' before 'tmpXSoff' > Align.c:6135: error: invalid operands to binary + > Align.c:6135: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align_Align_Protein_Sequences': > Align.c:6142: error: function 'ax' is initialized like a variable > Align.c:6142: error: invalid lvalue in increment > Align.c:6142: error: function 'items' is initialized like a variable > Align.c:6143: warning: comparison between pointer and integer > Align.c:6146: error: array subscript is not an integer > Align.c:6146: error: array subscript is not an integer > Align.c:6146: error: array subscript is not an integer > Align.c:6146: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6147: error: array subscript is not an integer > Align.c:6147: error: array subscript is not an integer > Align.c:6147: error: array subscript is not an integer > Align.c:6147: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6148: error: array subscript is not an integer > Align.c:6148: error: array subscript is not an integer > Align.c:6148: error: array subscript is not an integer > Align.c:6148: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6153: error: array subscript is not an integer > Align.c:6154: error: array subscript is not an integer > Align.c:6157: error: 'IV' undeclared (first use in this function) > Align.c:6157: error: expected ';' before 'tmpXSoff' > Align.c:6157: error: invalid operands to binary + > Align.c:6157: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__AlignOutput_aln1': > Align.c:6164: error: function 'ax' is initialized like a variable > Align.c:6164: error: invalid lvalue in increment > Align.c:6164: error: function 'items' is initialized like a variable > Align.c:6165: warning: comparison between pointer and integer > Align.c:6168: error: array subscript is not an integer > Align.c:6168: error: array subscript is not an integer > Align.c:6168: error: array subscript is not an integer > Align.c:6168: error: array subscript is not an integer > Align.c:6170: error: 'OP' has no member named 'op_private' > Align.c:6170: error: 'OP' has no member named 'op_targ' > Align.c:6174: error: invalid operands to binary + > Align.c:6174: error: 'SV' has no member named 'sv_flags' > Align.c:6176: error: 'IV' undeclared (first use in this function) > Align.c:6176: error: expected ';' before 'tmpXSoff' > Align.c:6176: error: invalid operands to binary + > Align.c:6176: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__AlignOutput_aln2': > Align.c:6183: error: function 'ax' is initialized like a variable > Align.c:6183: error: invalid lvalue in increment > Align.c:6183: error: function 'items' is initialized like a variable > Align.c:6184: warning: comparison between pointer and integer > Align.c:6187: error: array subscript is not an integer > Align.c:6187: error: array subscript is not an integer > Align.c:6187: error: array subscript is not an integer > Align.c:6187: error: array subscript is not an integer > Align.c:6189: error: 'OP' has no member named 'op_private' > Align.c:6189: error: 'OP' has no member named 'op_targ' > Align.c:6193: error: invalid operands to binary + > Align.c:6193: error: 'SV' has no member named 'sv_flags' > Align.c:6195: error: 'IV' undeclared (first use in this function) > Align.c:6195: error: expected ';' before 'tmpXSoff' > Align.c:6195: error: invalid operands to binary + > Align.c:6195: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__AlignOutput_start1': > Align.c:6202: error: function 'ax' is initialized like a variable > Align.c:6202: error: invalid lvalue in increment > Align.c:6202: error: function 'items' is initialized like a variable > Align.c:6203: warning: comparison between pointer and integer > Align.c:6206: error: array subscript is not an integer > Align.c:6206: error: array subscript is not an integer > Align.c:6206: error: array subscript is not an integer > Align.c:6206: error: array subscript is not an integer > Align.c:6208: error: 'OP' has no member named 'op_private' > Align.c:6208: error: 'OP' has no member named 'op_targ' > Align.c:6212: error: invalid operands to binary + > Align.c:6212: error: 'IV' undeclared (first use in this function) > Align.c:6212: error: expected ')' before 'RETVAL' > Align.c:6212: error: too many arguments to function 'Perl_sv_setiv' > Align.c:6212: error: 'SV' has no member named 'sv_flags' > Align.c:6214: error: expected ';' before 'tmpXSoff' > Align.c:6214: error: invalid operands to binary + > Align.c:6214: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__AlignOutput_end1': > Align.c:6221: error: function 'ax' is initialized like a variable > Align.c:6221: error: invalid lvalue in increment > Align.c:6221: error: function 'items' is initialized like a variable > Align.c:6222: warning: comparison between pointer and integer > Align.c:6225: error: array subscript is not an integer > Align.c:6225: error: array subscript is not an integer > Align.c:6225: error: array subscript is not an integer > Align.c:6225: error: array subscript is not an integer > Align.c:6227: error: 'OP' has no member named 'op_private' > Align.c:6227: error: 'OP' has no member named 'op_targ' > Align.c:6231: error: invalid operands to binary + > Align.c:6231: error: 'IV' undeclared (first use in this function) > Align.c:6231: error: expected ')' before 'RETVAL' > Align.c:6231: error: too many arguments to function 'Perl_sv_setiv' > Align.c:6231: error: 'SV' has no member named 'sv_flags' > Align.c:6233: error: expected ';' before 'tmpXSoff' > Align.c:6233: error: invalid operands to binary + > Align.c:6233: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__AlignOutput_start2': > Align.c:6240: error: function 'ax' is initialized like a variable > Align.c:6240: error: invalid lvalue in increment > Align.c:6240: error: function 'items' is initialized like a variable > Align.c:6241: warning: comparison between pointer and integer > Align.c:6244: error: array subscript is not an integer > Align.c:6244: error: array subscript is not an integer > Align.c:6244: error: array subscript is not an integer > Align.c:6244: error: array subscript is not an integer > Align.c:6246: error: 'OP' has no member named 'op_private' > Align.c:6246: error: 'OP' has no member named 'op_targ' > Align.c:6250: error: invalid operands to binary + > Align.c:6250: error: 'IV' undeclared (first use in this function) > Align.c:6250: error: expected ')' before 'RETVAL' > Align.c:6250: error: too many arguments to function 'Perl_sv_setiv' > Align.c:6250: error: 'SV' has no member named 'sv_flags' > Align.c:6252: error: expected ';' before 'tmpXSoff' > Align.c:6252: error: invalid operands to binary + > Align.c:6252: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__AlignOutput_end2': > Align.c:6259: error: function 'ax' is initialized like a variable > Align.c:6259: error: invalid lvalue in increment > Align.c:6259: error: function 'items' is initialized like a variable > Align.c:6260: warning: comparison between pointer and integer > Align.c:6263: error: array subscript is not an integer > Align.c:6263: error: array subscript is not an integer > Align.c:6263: error: array subscript is not an integer > Align.c:6263: error: array subscript is not an integer > Align.c:6265: error: 'OP' has no member named 'op_private' > Align.c:6265: error: 'OP' has no member named 'op_targ' > Align.c:6269: error: invalid operands to binary + > Align.c:6269: error: 'IV' undeclared (first use in this function) > Align.c:6269: error: expected ')' before 'RETVAL' > Align.c:6269: error: too many arguments to function 'Perl_sv_setiv' > Align.c:6269: error: 'SV' has no member named 'sv_flags' > Align.c:6271: error: expected ';' before 'tmpXSoff' > Align.c:6271: error: invalid operands to binary + > Align.c:6271: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'boot_Bio__Ext__Align': > Align.c:6280: error: function 'ax' is initialized like a variable > Align.c:6280: error: invalid lvalue in increment > Align.c:6280: error: function 'items' is initialized like a variable > Align.c:6283: error: array subscript is not an integer > Align.c:6283: error: array subscript is not an integer > Align.c:6283: error: array subscript is not an integer > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: warning: comparison between pointer and integer > Align.c:6283: error: array subscript is not an integer > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6595: error: array subscript is not an integer > Align.c:6595: error: 'IV' undeclared (first use in this function) > Align.c:6595: error: expected ';' before 'tmpXSoff' > Align.c:6595: error: invalid operands to binary + > Align.c:6595: error: 'tmpXSoff' undeclared (first use in this > function) > make[1]: *** [Align.o] Error 1 > make[1]: Leaving directory > `/home/pallavi/Pallavi/downloads/bioperl-ext-1.4/Bio/Ext/Align' > make: *** [subdirs] Error 2 > > > thanks > Pallavi > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From jason at bioperl.org Wed Jul 2 11:25:09 2008 From: jason at bioperl.org (Jason Stajich) Date: Wed, 2 Jul 2008 11:25:09 -0400 Subject: [Bioperl-l] Clustalw module In-Reply-To: <7D75703BC8E1C149BF78A1E79AAAB169035BC545@svits28.main.ad.rit.edu> References: <7D75703BC8E1C149BF78A1E79AAAB169035BC544@svits28.main.ad.rit.edu> <7D75703BC8E1C149BF78A1E79AAAB169035BC545@svits28.main.ad.rit.edu> Message-ID: <47229074-D5EA-44C7-B820-6447BA8F19AA@bioperl.org> re: StandAloneBlast and RemoteBlast - due to their perceived widespread use was not moved from the core package to run so they come in with the basic Core modules install package. Given the error message I would again say that the bioperl-run was not installed. If you do perldoc ModuleName it will tell you if the module can be found. locate Clustalw.pm can also help you locate if it is installed but just not in PERL5LIB path. -jason On Jul 2, 2008, at 11:04 AM, Nathan Haseley (RIT Student) wrote: > I am running my script on a remote server, so I didn't do the > installation. I would assume so, however, since StandAloneBlast > works fine. > Nathan > > > -----Original Message----- > From: Jason Stajich on behalf of Jason Stajich > Sent: Wed 7/2/2008 11:02 AM > To: Nathan Haseley (RIT Student) > Cc: bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] Clustalw module > > did you install bioperl-run package as well as bioperl core? > -jason > On Jul 2, 2008, at 10:34 AM, Nathan Haseley (RIT Student) wrote: > >> Hello, >> I am working with the Bioperl module >> Bio::Tools::Run::Alignment::Clustalw. I try to include the package >> in my script as follows: >> >> #!/usr/bin/perl >> use Bio::Seq; >> use Bio::SearchIO; >> use Bio::Tools::Run::StandAloneBlast; >> use Bio::DB::GenBank; >> use Bio::Tools::Run::Alignment::Clustalw; >> use Bio::Root::Exception; >> use Error qw(:try); >> >> but I keep getting the following error message: >> Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC >> contains: /etc/perl /usr/local/lib/perl/5.8.8 /usr/local/share/perl/ >> 5.8.8 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.8 /usr/share/ >> perl/5.8 /usr/local/lib/site_perl .) at ./BlastTwoCompare.pl line 6. >> BEGIN failed--compilation aborted at ./BlastTwoCompare.pl line 6. >> >> The Clustalw program is configured correctly to work in my >> directory. Am I missing something obvious or is there something >> wrong with my BioPerl configuration? Any advice on how to fix >> this? Thank you for your time. >> >> Nathan >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From greener at u.washington.edu Wed Jul 2 14:10:20 2008 From: greener at u.washington.edu (RICHARD GREEN) Date: Wed, 2 Jul 2008 11:10:20 -0700 (PDT) Subject: [Bioperl-l] finding sequence 2000 bp upstream in bioperl? Message-ID: Howdy Bioperlers, Quick question, I have scripts that pull out a sequence from genbank, but I am looking for a command that would extract 2000 base pairs upstream of the sequence. Is there a way to extract just the Gene promoter region from genbank? Any advice that folks can give me a is muchly appreciated. Thanks again -Rich Green From Kevin.M.Brown at asu.edu Wed Jul 2 15:36:43 2008 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Wed, 2 Jul 2008 12:36:43 -0700 Subject: [Bioperl-l] finding sequence 2000 bp upstream in bioperl? In-Reply-To: References: Message-ID: <1A4207F8295607498283FE9E93B775B405073020@EX02.asurite.ad.asu.edu> Get the start point for a Sequence Feature and request a subseq of the main object that starts 2000 above that. my $gb = new Bio::DB::GenBank; $entry = $gb->get_Seq_by_id($id); foreach my $f ($entry->all_SeqFeatures()) { if ($f->primary_tag eq 'CDS') { my $seq = $entry->subseq($f->start - 2000,$f->start - 1); $out->write_seq($seq); } } > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > RICHARD GREEN > Sent: Wednesday, July 02, 2008 11:10 AM > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] finding sequence 2000 bp upstream in bioperl? > > Howdy Bioperlers, > > Quick question, I have scripts that pull out a sequence from > genbank, but I am looking for a command that would extract > 2000 base pairs upstream of the sequence. Is there a way to > extract just the Gene promoter region from genbank? Any > advice that folks can give me a is muchly appreciated. > > Thanks again > > -Rich Green > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From snoze.pa at gmail.com Wed Jul 2 15:56:18 2008 From: snoze.pa at gmail.com (snoze pa) Date: Wed, 2 Jul 2008 14:56:18 -0500 Subject: [Bioperl-l] Install help errors Message-ID: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> Dear Users, I am trying to install bioperl in fedora machine. I am using precompiled rpm from fedora repo. it is installed. Next I download the biosql and put in a dir /usr/local/biosql create a database bioseqdb and load the scema. However the bioperl-db is not working.. it is giving lots of error. I used CPAN and also the perl Build.PL. following are the results Please help me. thank you. Test Summary Report ------------------- t/04swiss (Wstat: 65280 Tests: 5 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 52 tests but ran 5. t/05seqfeature (Wstat: 65280 Tests: 3 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 48 tests but ran 3. t/06comment (Wstat: 65280 Tests: 2 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 11 tests but ran 2. t/07dblink (Wstat: 65280 Tests: 2 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 18 tests but ran 2. t/08genbank (Wstat: 65280 Tests: 2 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 18 tests but ran 2. t/09fuzzy2 (Wstat: 65280 Tests: 2 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 21 tests but ran 2. t/10ensembl (Wstat: 65280 Tests: 2 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 15 tests but ran 2. t/11locuslink (Wstat: 65280 Tests: 4 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 110 tests but ran 4. t/12ontology (Wstat: 65280 Tests: 4 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 738 tests but ran 4. t/13remove (Wstat: 0 Tests: 4 Failed: 1) Failed test: 4 Parse errors: Bad plan. You planned 59 tests but ran 4. t/15cluster (Wstat: 65280 Tests: 5 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 160 tests but ran 5. t/16obda (Wstat: 65280 Tests: 2 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 12 tests but ran 2. Files=16, Tests=198, 26 wallclock secs ( 0.21 usr 0.07 sys + 22.81 cusr 1.25 csys = 24.34 CPU) Result: FAIL Failed 12/16 test programs. 1/198 subtests failed. From jason at bioperl.org Wed Jul 2 15:57:15 2008 From: jason at bioperl.org (Jason Stajich) Date: Wed, 2 Jul 2008 15:57:15 -0400 Subject: [Bioperl-l] finding sequence 2000 bp upstream in bioperl? In-Reply-To: <1A4207F8295607498283FE9E93B775B405073020@EX02.asurite.ad.asu.edu> References: <1A4207F8295607498283FE9E93B775B405073020@EX02.asurite.ad.asu.edu> Message-ID: <3B11F357-E8FD-4027-B2D9-DB83634753E7@bioperl.org> Right on Kevin - except that you have to call trunc() not subseq() if you want to get back a sequence object that can be written out with Bio::SeqIO and you'll have to do it slightly differently if the gene is on the opposite strand operating on the $f->end, $f->end + 2000 and then doing a revcom. I *think* this will get you what you want: my $promotor; if( $f->strand < 0 ) { $promotor = $entry->trunc($f->end+1, $f->end + 2000)->revcom; } else { $promotor = $entry->trunc($f->start - 2000, $f->start -1); } -jason On Jul 2, 2008, at 3:36 PM, Kevin Brown wrote: > Get the start point for a Sequence Feature and request a subseq of the > main object that starts 2000 above that. > > my $gb = new Bio::DB::GenBank; > $entry = $gb->get_Seq_by_id($id); > foreach my $f ($entry->all_SeqFeatures()) > { > if ($f->primary_tag eq 'CDS') > { > my $seq = $entry->subseq($f->start - 2000,$f->start - > 1); > $out->write_seq($seq); > } > } > >> -----Original Message----- >> From: bioperl-l-bounces at lists.open-bio.org >> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of >> RICHARD GREEN >> Sent: Wednesday, July 02, 2008 11:10 AM >> To: bioperl-l at lists.open-bio.org >> Subject: [Bioperl-l] finding sequence 2000 bp upstream in bioperl? >> >> Howdy Bioperlers, >> >> Quick question, I have scripts that pull out a sequence from >> genbank, but I am looking for a command that would extract >> 2000 base pairs upstream of the sequence. Is there a way to >> extract just the Gene promoter region from genbank? Any >> advice that folks can give me a is muchly appreciated. >> >> Thanks again >> >> -Rich Green >> >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From apapanicolaou at ice.mpg.de Wed Jul 2 16:11:31 2008 From: apapanicolaou at ice.mpg.de (Alexie Papanicolaou) Date: Wed, 02 Jul 2008 22:11:31 +0200 Subject: [Bioperl-l] IUPAC support for DNA alignment In-Reply-To: References: Message-ID: <486BE0F3.4060702@ice.mpg.de> Hello I agree if it is not too much trouble for you. I think X (if users put them in DNA sequences) they will be masking characters (I 'm foolish enough to do it) so perhaps X =0? Does anyone else use Xs? I dunno about Ns too. They could be unknown characters (in which case full score version could be 0 as well) or really mean all four nucleotides are equally likely. Is it too much trouble to allow users to set X and N manually (since it is the same whether they align with an A,T,C,G)? ta a Yee Man Chan wrote: > Hi guys > > What about providing two switches; one for full score and one for > probabilistic score? > > Assume match is +3 and mismatch -1 > > Full score version: > 1) T - U = +3 (I assume U is the same as T for alignment purpose, right?) > 2) A - W = +3 > 3) A - D = +3 > 4) A - N = +3 > 5) A - X = -1 (not so sure about this one) > > Probabilistic score version: > 1) T - U = +3 > 2) A - W = +3/2-1/2 = +1 > 3) A - D = +3/3-1*2/3 = +1/3 > 4) A - N = +3/4-1*3/4 = 0 > 5) A - X = -1 > > What do you think? > > Yee Man > > On Fri, 27 Jun 2008 aaron.j.mackey at gsk.com wrote: > > >> You could replicate what they do here with EST_GENOME (re-engineered to >> accept ambiguity codes): >> >> http://www.genome.org/cgi/content/short/17/2/212 >> >> But I think the answer is user-dependent -- some might want the "full >> score" (as in the above case), others might want the "(probabilistically) >> averaged score", etc. So, let the scoring matrix be subclass-able (or >> mix-able), so that users can specify the exact desired behavior via a >> handful of predefined (and useful) behaviors. >> >> -Aaron >> >> > > -- "You can't find a hermit to teach you herming, because of course that rather spoils the whole thing." -- (Terry Pratchett, Small Gods) Alexie Papanicolaou Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, D-07745 Jena, Germany. From cain.cshl at gmail.com Wed Jul 2 16:13:24 2008 From: cain.cshl at gmail.com (Scott Cain) Date: Wed, 2 Jul 2008 16:13:24 -0400 Subject: [Bioperl-l] Install help errors In-Reply-To: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> Message-ID: <536f21b00807021313l6cec00devfd452db661ec1449@mail.gmail.com> Hello, When you say you installed the BioPerl RPM, do you mean the one at biopackages.net? It is very old and the likely problem you are running into is that it is too old to work with the version of BioSQL you have. Scott On Wed, Jul 2, 2008 at 3:56 PM, snoze pa wrote: > Dear Users, > I am trying to install bioperl in fedora machine. I am using > precompiled rpm from fedora repo. it is installed. Next I download the > biosql and put in a dir /usr/local/biosql > create a database bioseqdb and load the scema. > > However the bioperl-db is not working.. it is giving lots of error. I > used CPAN and also the perl Build.PL. following are the results > > Please help me. > thank you. > > > Test Summary Report > ------------------- > t/04swiss (Wstat: 65280 Tests: 5 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 52 tests but ran 5. > t/05seqfeature (Wstat: 65280 Tests: 3 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 48 tests but ran 3. > t/06comment (Wstat: 65280 Tests: 2 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 11 tests but ran 2. > t/07dblink (Wstat: 65280 Tests: 2 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 18 tests but ran 2. > t/08genbank (Wstat: 65280 Tests: 2 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 18 tests but ran 2. > t/09fuzzy2 (Wstat: 65280 Tests: 2 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 21 tests but ran 2. > t/10ensembl (Wstat: 65280 Tests: 2 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 15 tests but ran 2. > t/11locuslink (Wstat: 65280 Tests: 4 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 110 tests but ran 4. > t/12ontology (Wstat: 65280 Tests: 4 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 738 tests but ran 4. > t/13remove (Wstat: 0 Tests: 4 Failed: 1) > Failed test: 4 > Parse errors: Bad plan. You planned 59 tests but ran 4. > t/15cluster (Wstat: 65280 Tests: 5 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 160 tests but ran 5. > t/16obda (Wstat: 65280 Tests: 2 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 12 tests but ran 2. > Files=16, Tests=198, 26 wallclock secs ( 0.21 usr 0.07 sys + 22.81 > cusr 1.25 csys = 24.34 CPU) > Result: FAIL > Failed 12/16 test programs. 1/198 subtests failed. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain.cshl at gmail.com GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory From apapanicolaou at ice.mpg.de Wed Jul 2 16:20:51 2008 From: apapanicolaou at ice.mpg.de (Alexie Papanicolaou) Date: Wed, 02 Jul 2008 22:20:51 +0200 Subject: [Bioperl-l] IUPAC support for DNA alignment In-Reply-To: <134AD76F-E008-4288-91BB-CBFA6042F54A@gmx.net> References: <134AD76F-E008-4288-91BB-CBFA6042F54A@gmx.net> Message-ID: <486BE323.60109@ice.mpg.de> >> Full score version: >> 1) T - U = +3 (I assume U is the same as T for alignment purpose, >> right?) > Right. yea... unless you are aligning RNAs and thus have wobble pairing UG :-) let's start simple though... > Note that there are also M, R, V, and H, and their complements (which > by definition would not match your example of 'A'). oh, I assumed Yee Man was just giving us a trimmed down example. Hilmar is very right. > Note also that the above implicitly assumes 50% GC content or equal > likelihood of the code-constituent bases, which in reality for most > coding sequences is not true.Also, if you have a known polymorphism at > the site, for 3-letter ambiguities not all 3 may be equally likely. > For example, if you have letter D for a [A/G] SNP, one may not want to > give 1/3 of weight to possibility T. > I would at least allow for the possibility to assign expected base > frequencies and weight the ambiguous possibilities by those. > -hilmar Ehm, wouldn't we now be walking in the twilight of modeling it? That might be a bit harder work for Yee Man, which I was trying to avoid. Perhaps for starters Yee Man can just document how the user can provide their own substitution matrix? ((s)he may have done already, sorry dunno if Yee is a boy or girl; like alexie too :-)) right a -- "You can't find a hermit to teach you herming, because of course that rather spoils the whole thing." -- (Terry Pratchett, Small Gods) Alexie Papanicolaou Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, D-07745 Jena, Germany. From apapanicolaou at ice.mpg.de Wed Jul 2 16:21:05 2008 From: apapanicolaou at ice.mpg.de (Alexie Papanicolaou) Date: Wed, 02 Jul 2008 22:21:05 +0200 Subject: [Bioperl-l] IUPAC support for DNA alignment In-Reply-To: <134AD76F-E008-4288-91BB-CBFA6042F54A@gmx.net> References: <134AD76F-E008-4288-91BB-CBFA6042F54A@gmx.net> Message-ID: <486BE331.7000605@ice.mpg.de> >> >> Full score version: >> 1) T - U = +3 (I assume U is the same as T for alignment purpose, >> right?) > > Right. > yea... unless you have wobble pairing UG :-) let's keep it simple though... >> >> 2) A - W = +3 >> 3) A - D = +3 >> 4) A - N = +3 >> 5) A - X = -1 (not so sure about this one) >> >> Probabilistic score version: >> 1) T - U = +3 >> 2) A - W = +3/2-1/2 = +1 >> 3) A - D = +3/3-1*2/3 = +1/3 >> 4) A - N = +3/4-1*3/4 = 0 >> 5) A - X = -1 > > Note that there are also M, R, V, and H, and their complements (which > by definition would not match your example of 'A'). > oh, I assumed Yee Man was just giving us a trimmed down example. Hilmar is very right. > Note also that the above implicitly assumes 50% GC content or equal > likelihood of the code-constituent bases, which in reality for most > coding sequences is not true.Also, if you have a known polymorphism at > the site, for 3-letter ambiguities not all 3 may be equally likely. > For example, if you have letter D for a [A/G] SNP, one may not want to > give 1/3 of weight to possibility T. > I would at least allow for the possibility to assign expected base > frequencies and weight the ambiguous possibilities by those. > -hilmar Ehm, wouldn't we now be walking in the twilight of modeling it? That might be a bit harder work for Yee Man, perhaps Yee Man can document how the user can provide their own substitution matrix? -- "You can't find a hermit to teach you herming, because of course that rather spoils the whole thing." -- (Terry Pratchett, Small Gods) Alexie Papanicolaou Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, D-07745 Jena, Germany. From apapanicolaou at ice.mpg.de Wed Jul 2 16:24:50 2008 From: apapanicolaou at ice.mpg.de (Alexie Papanicolaou) Date: Wed, 02 Jul 2008 22:24:50 +0200 Subject: [Bioperl-l] IUPAC support for DNA alignment In-Reply-To: <486BE0F3.4060702@ice.mpg.de> References: <486BE0F3.4060702@ice.mpg.de> Message-ID: <486BE412.4020807@ice.mpg.de> clarifying (also sorry for the double post before). "equally likely" => "found in sample in which case it is match" right it's dark outside, time to go home. a > > > I dunno about Ns too. They could be unknown characters (in which case > full score version could be 0 as well) or really mean all four > nucleotides are equally likely. From snoze.pa at gmail.com Wed Jul 2 16:49:39 2008 From: snoze.pa at gmail.com (snoze pa) Date: Wed, 2 Jul 2008 15:49:39 -0500 Subject: [Bioperl-l] Install help errors In-Reply-To: <536f21b00807021313l6cec00devfd452db661ec1449@mail.gmail.com> References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <536f21b00807021313l6cec00devfd452db661ec1449@mail.gmail.com> Message-ID: <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> I used the latest rpm shipped with fedora 9. Next I removed the bioperl from fedora 9 and try to installed it from the CPAN.. it worked fine but thr bioperl-db again give me following messages using cpan. Seems nothing working properly! thanks a lot for your help. Test Summary Report ------------------- t/01dbadaptor (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 19 tests but ran 0. t/02species (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 65 tests but ran 0. t/03simpleseq (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 59 tests but ran 0. t/04swiss (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 52 tests but ran 0. t/05seqfeature (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 48 tests but ran 0. t/06comment (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 11 tests but ran 0. t/07dblink (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 18 tests but ran 0. t/08genbank (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 18 tests but ran 0. t/09fuzzy2 (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 21 tests but ran 0. t/10ensembl (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 15 tests but ran 0. t/11locuslink (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 110 tests but ran 0. t/12ontology (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 738 tests but ran 0. t/13remove (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 59 tests but ran 0. t/14query (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 18 tests but ran 0. t/15cluster (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 160 tests but ran 0. t/16obda (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 12 tests but ran 0. Files=16, Tests=0, 2 wallclock secs ( 0.09 usr 0.06 sys + 1.19 cusr 0.20 csys = 1.54 CPU) Result: FAIL Failed 16/16 test programs. 0/0 subtests failed. SENDU/bioperl-db-1.5.2_100.tar.gz ./Build test -- NOT OK //hint// to see the cpan-testers results for installing this module, try: reports SENDU/bioperl-db-1.5.2_100.tar.gz Warning (usually harmless): 'YAML' not installed, will not store persistent state Running Build install make test had returned bad status, won't install without force Failed during this command: BIRNEY/bioperl-1.4.tar.gz : make_test NO SENDU/bioperl-db-1.5.2_100.tar.gz : make_test NO On Wed, Jul 2, 2008 at 3:13 PM, Scott Cain wrote: > Hello, > > When you say you installed the BioPerl RPM, do you mean the one at > biopackages.net? It is very old and the likely problem you are > running into is that it is too old to work with the version of BioSQL > you have. > > Scott > > > On Wed, Jul 2, 2008 at 3:56 PM, snoze pa wrote: >> Dear Users, >> I am trying to install bioperl in fedora machine. I am using >> precompiled rpm from fedora repo. it is installed. Next I download the >> biosql and put in a dir /usr/local/biosql >> create a database bioseqdb and load the scema. >> >> However the bioperl-db is not working.. it is giving lots of error. I >> used CPAN and also the perl Build.PL. following are the results >> >> Please help me. >> thank you. >> >> >> Test Summary Report >> ------------------- >> t/04swiss (Wstat: 65280 Tests: 5 Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 52 tests but ran 5. >> t/05seqfeature (Wstat: 65280 Tests: 3 Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 48 tests but ran 3. >> t/06comment (Wstat: 65280 Tests: 2 Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 11 tests but ran 2. >> t/07dblink (Wstat: 65280 Tests: 2 Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 18 tests but ran 2. >> t/08genbank (Wstat: 65280 Tests: 2 Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 18 tests but ran 2. >> t/09fuzzy2 (Wstat: 65280 Tests: 2 Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 21 tests but ran 2. >> t/10ensembl (Wstat: 65280 Tests: 2 Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 15 tests but ran 2. >> t/11locuslink (Wstat: 65280 Tests: 4 Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 110 tests but ran 4. >> t/12ontology (Wstat: 65280 Tests: 4 Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 738 tests but ran 4. >> t/13remove (Wstat: 0 Tests: 4 Failed: 1) >> Failed test: 4 >> Parse errors: Bad plan. You planned 59 tests but ran 4. >> t/15cluster (Wstat: 65280 Tests: 5 Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 160 tests but ran 5. >> t/16obda (Wstat: 65280 Tests: 2 Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 12 tests but ran 2. >> Files=16, Tests=198, 26 wallclock secs ( 0.21 usr 0.07 sys + 22.81 >> cusr 1.25 csys = 24.34 CPU) >> Result: FAIL >> Failed 12/16 test programs. 1/198 subtests failed. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. cain.cshl at gmail.com > GMOD Coordinator (http://www.gmod.org/) 216-392-3087 > Cold Spring Harbor Laboratory > From bosborne11 at verizon.net Wed Jul 2 15:56:03 2008 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 02 Jul 2008 15:56:03 -0400 Subject: [Bioperl-l] finding sequence 2000 bp upstream in bioperl? In-Reply-To: References: Message-ID: <59E17CD3-C61E-4C4C-BAD7-D535D1F1134F@verizon.net> Richard, Some approaches are discussed here: http://www.bioperl.org/wiki/HOWTO:Getting_Genomic_Sequences Brian O. On Jul 2, 2008, at 2:10 PM, RICHARD GREEN wrote: > Howdy Bioperlers, > > Quick question, I have scripts that pull out a sequence from > genbank, but I am looking for a command that would extract 2000 base > pairs upstream of the sequence. Is there a way to extract just the > Gene promoter region from genbank? Any advice that folks can give me > a is muchly appreciated. > > Thanks again > > -Rich Green > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From captainrave at hotmail.com Wed Jul 2 17:00:09 2008 From: captainrave at hotmail.com (Captainrave) Date: Wed, 2 Jul 2008 14:00:09 -0700 (PDT) Subject: [Bioperl-l] re ading in cds, outputting products In-Reply-To: <18211537.post@talk.nabble.com> References: <18211537.post@talk.nabble.com> Message-ID: <18246685.post@talk.nabble.com> Captainrave wrote: > > How would I use bioperl to read in CDS positions (maybe in csv format in a > list), find the releated products and/or genes for each and output these > into a new csv file or similar file? > Any ideas? I obviously have rough ideas, but nothing substantial! Any help would REALLY be appreciated!!! This place has been good to me before :) -- View this message in context: http://www.nabble.com/reading-in-cds%2C-outputting-products-tp18211537p18246685.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From bix at sendu.me.uk Wed Jul 2 17:54:54 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 02 Jul 2008 22:54:54 +0100 Subject: [Bioperl-l] re ading in cds, outputting products In-Reply-To: <18246685.post@talk.nabble.com> References: <18211537.post@talk.nabble.com> <18246685.post@talk.nabble.com> Message-ID: <486BF92E.2070308@sendu.me.uk> Captainrave wrote: > > Captainrave wrote: >> How would I use bioperl to read in CDS positions (maybe in csv format in a >> list), find the releated products and/or genes for each and output these >> into a new csv file or similar file? > > Any ideas? I obviously have rough ideas, but nothing substantial! Any help > would REALLY be appreciated!!! This place has been good to me before :) Your question might be too broad. Narrow your problem down, give some specifics (what data are you working with?), tell us what you've tried. Have you checked the obvious HOW-TOs on the wiki? From ymc at shgc.stanford.edu Wed Jul 2 19:48:07 2008 From: ymc at shgc.stanford.edu (Yee Man Chan) Date: Wed, 2 Jul 2008 16:48:07 -0700 (PDT) Subject: [Bioperl-l] IUPAC support for DNA alignment In-Reply-To: <486BE412.4020807@ice.mpg.de> References: <486BE0F3.4060702@ice.mpg.de> <486BE412.4020807@ice.mpg.de> Message-ID: How about I implement the full score version first? I am going to do it as specified in my previous email. I can also add comments to ask people to specify their own matrix. Yee Man On Wed, 2 Jul 2008, Alexie Papanicolaou wrote: > clarifying (also sorry for the double post before). > > "equally likely" => "found in sample in which case it is match" > > right it's dark outside, time to go home. > a > > > > > > > I dunno about Ns too. They could be unknown characters (in which case > > full score version could be 0 as well) or really mean all four > > nucleotides are equally likely. > From David.Messina at sbc.su.se Thu Jul 3 05:08:19 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Thu, 3 Jul 2008 11:08:19 +0200 Subject: [Bioperl-l] Install help errors In-Reply-To: <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <536f21b00807021313l6cec00devfd452db661ec1449@mail.gmail.com> <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> Message-ID: <628aabb70807030208y183e7ca7rb3f37f491b5fb6e3@mail.gmail.com> Here's your problem -- bioperl 1.4 is waaaay out of date. Don't use that. > BIRNEY/bioperl-1.4.tar.gz : make_test NO > Instead, use the 1.5.2_100 version of bioperl-core that matches this: > SENDU/bioperl-db-1.5.2_100.tar.gz : make_test NO > Or even better, you might want to get the latest versions of each from the bioperl website. Look here: http://www.bioperl.org/wiki/Getting_BioPerl and here: http://www.bioperl.org/wiki/Installing_BioPerl Dave From andreas.draeger at uni-tuebingen.de Thu Jul 3 07:48:55 2008 From: andreas.draeger at uni-tuebingen.de (=?ISO-8859-1?Q?Andreas_Dr=E4ger?=) Date: Thu, 03 Jul 2008 13:48:55 +0200 Subject: [Bioperl-l] Memory not sufficient when storing human chromosom 1 in BioSQL Message-ID: <486CBCA7.8080201@uni-tuebingen.de> Hi all, Recently I have successfully installed the latest version of BioPerl and BioSQL on my computer, which has 2 GB RAM. Both works fine, but when trying to insert the genbank file of the human chromosome 1, which I have downloaded from the NCBI website (ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_01/hs_ref_chr1.gbk.gz) I receive the error message 'Out of memory'. This takes about one hour. My question is, how I can insert large genbank files in my BioSQL database using BioPerl. I do not know, what to do. Thank you for your help!!! Cheers, Andreas From pallavi.sarmah at igib.res.in Thu Jul 3 05:06:12 2008 From: pallavi.sarmah at igib.res.in (Pallavi Sarmah) Date: Thu, 3 Jul 2008 14:36:12 +0530 Subject: [Bioperl-l] not being able to install Bio-ext-1.4 References: <4C33FA201D55F743B5DE794497FCA8971F0C9C@n1ex> <1A4207F8295607498283FE9E93B775B405072F29@EX02.asurite.ad.asu.edu> Message-ID: <4C33FA201D55F743B5DE794497FCA8971F0CA1@n1ex> Hi While trying to install Bio-ext-1.5.1 I get the following error Writing Makefile for Bio::Ext::Align ERROR from evaluation of /home/pallavi/Pallavi/downloads/bioperl-ext-1.5.1/Bio/SeqIO/staden/Makefile.PL: Invalid version '' for Bio::SeqIO::staden::read. Must be of the form '#.##'. (For instance '1.23') at ./Makefile.PL line 4 pallavi -----Original Message----- From: Kevin Brown [mailto:Kevin.M.Brown at asu.edu] Sent: Wed 7/2/2008 8:40 PM To: Pallavi Sarmah; bioperl-l at bioperl.org Subject: RE: [Bioperl-l] not being able to install Bio-ext-1.4 Bioperl 1.4 is more than 5 years old. Try following the install instructions on the bioperl website for a more up2date version (v1.5.2): http://www.bioperl.org/wiki/Installing_BioPerl_on_Ubuntu_Server Or http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Pallavi Sarmah > Sent: Wednesday, July 02, 2008 12:36 AM > To: ymc at paxil.stanford.edu; birney at sanger.ac.uk; bioperl-l at bioperl.org > Subject: [Bioperl-l] not being able to install Bio-ext-1.4 > > > Hi > > I am having problem installing Bio::Ext-1.4. I have forced > installed BioPerl1.4 and now trying to install Bio::Ext but > getting the following errors in Ubuntu. This is not the full > list of errors but I am not being able to get all. Can anyone > please help me with this. I have been trying the mailing list > for quite sometime now. > > Align.c:5835: error: array subscript is not an integer > Align.c:5835: error: array subscript is not an integer > Align.c:5835: error: array subscript is not an integer > Align.c:5836: error: array subscript is not an integer > Align.c:5836: error: array subscript is not an integer > Align.c:5836: error: array subscript is not an integer > Align.c:5836: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:5838: error: 'OP' has no member named 'op_private' > Align.c:5838: error: 'OP' has no member named 'op_targ' > Align.c:5842: error: invalid operands to binary + > Align.c:5842: error: 'IV' undeclared (first use in this function) > Align.c:5842: error: expected ')' before 'RETVAL' > Align.c:5842: error: too many arguments to function 'Perl_sv_setiv' > Align.c:5842: error: 'SV' has no member named 'sv_flags' > Align.c:5844: error: expected ';' before 'tmpXSoff' > Align.c:5844: error: invalid operands to binary + > Align.c:5844: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__FileSource_filename': > Align.c:5851: error: function 'ax' is initialized like a variable > Align.c:5851: error: invalid lvalue in increment > Align.c:5851: error: function 'items' is initialized like a variable > Align.c:5852: warning: comparison between pointer and integer > Align.c:5855: error: array subscript is not an integer > Align.c:5855: error: array subscript is not an integer > Align.c:5855: error: array subscript is not an integer > Align.c:5855: error: array subscript is not an integer > Align.c:5857: error: 'OP' has no member named 'op_private' > Align.c:5857: error: 'OP' has no member named 'op_targ' > Align.c:5865: error: invalid operands to binary + > Align.c:5865: error: 'SV' has no member named 'sv_flags' > Align.c:5867: error: 'IV' undeclared (first use in this function) > Align.c:5867: error: expected ';' before 'tmpXSoff' > Align.c:5867: error: invalid operands to binary + > Align.c:5867: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__FileSource_set_input': > Align.c:5874: error: function 'ax' is initialized like a variable > Align.c:5874: error: invalid lvalue in increment > Align.c:5874: error: function 'items' is initialized like a variable > Align.c:5875: warning: comparison between pointer and integer > Align.c:5878: error: array subscript is not an integer > Align.c:5878: error: array subscript is not an integer > Align.c:5878: error: array subscript is not an integer > Align.c:5878: error: array subscript is not an integer > Align.c:5879: error: array subscript is not an integer > Align.c:5879: error: 'XPVIO' has no member named 'xio_ifp' > Align.c:5881: error: 'OP' has no member named 'op_private' > Align.c:5881: error: 'OP' has no member named 'op_targ' > Align.c:5885: error: invalid operands to binary + > Align.c:5885: error: 'IV' undeclared (first use in this function) > Align.c:5885: error: expected ')' before 'RETVAL' > Align.c:5885: error: too many arguments to function 'Perl_sv_setiv' > Align.c:5885: error: 'SV' has no member named 'sv_flags' > Align.c:5887: error: expected ';' before 'tmpXSoff' > Align.c:5887: error: invalid operands to binary + > Align.c:5887: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__FileSource_input': > Align.c:5894: error: function 'ax' is initialized like a variable > Align.c:5894: error: invalid lvalue in increment > Align.c:5894: error: function 'items' is initialized like a variable > Align.c:5895: warning: comparison between pointer and integer > Align.c:5898: error: array subscript is not an integer > Align.c:5898: error: array subscript is not an integer > Align.c:5898: error: array subscript is not an integer > Align.c:5898: error: array subscript is not an integer > Align.c:5903: error: array subscript is not an integer > Align.c:5907: warning: passing argument 3 of 'Perl_do_open' > makes pointer from integer without a cast > Align.c:5908: error: array subscript is not an integer > Align.c:5908: warning: passing argument 2 of > 'Perl_gv_stashpv' makes pointer from integer without a cast > Align.c:5908: warning: passing argument 3 of > 'Perl_sv_setsv_flags' makes pointer from integer without a cast > Align.c:5910: error: array subscript is not an integer > Align.c:5913: error: 'IV' undeclared (first use in this function) > Align.c:5913: error: expected ';' before 'tmpXSoff' > Align.c:5913: error: invalid operands to binary + > Align.c:5913: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__FileSource_set_format': > Align.c:5920: error: function 'ax' is initialized like a variable > Align.c:5920: error: invalid lvalue in increment > Align.c:5920: error: function 'items' is initialized like a variable > Align.c:5921: warning: comparison between pointer and integer > Align.c:5924: error: array subscript is not an integer > Align.c:5924: error: array subscript is not an integer > Align.c:5924: error: array subscript is not an integer > Align.c:5924: error: array subscript is not an integer > Align.c:5925: error: array subscript is not an integer > Align.c:5925: error: array subscript is not an integer > Align.c:5925: error: array subscript is not an integer > Align.c:5927: error: 'OP' has no member named 'op_private' > Align.c:5927: error: 'OP' has no member named 'op_targ' > Align.c:5931: error: invalid operands to binary + > Align.c:5931: error: 'IV' undeclared (first use in this function) > Align.c:5931: error: expected ')' before 'RETVAL' > Align.c:5931: error: too many arguments to function 'Perl_sv_setiv' > Align.c:5931: error: 'SV' has no member named 'sv_flags' > Align.c:5933: error: expected ';' before 'tmpXSoff' > Align.c:5933: error: invalid operands to binary + > Align.c:5933: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__FileSource_format': > Align.c:5940: error: function 'ax' is initialized like a variable > Align.c:5940: error: invalid lvalue in increment > Align.c:5940: error: function 'items' is initialized like a variable > Align.c:5941: warning: comparison between pointer and integer > Align.c:5944: error: array subscript is not an integer > Align.c:5944: error: array subscript is not an integer > Align.c:5944: error: array subscript is not an integer > Align.c:5944: error: array subscript is not an integer > Align.c:5946: error: 'OP' has no member named 'op_private' > Align.c:5946: error: 'OP' has no member named 'op_targ' > Align.c:5950: error: invalid operands to binary + > Align.c:5950: error: 'IV' undeclared (first use in this function) > Align.c:5950: error: expected ')' before 'RETVAL' > Align.c:5950: error: too many arguments to function 'Perl_sv_setiv' > Align.c:5950: error: 'SV' has no member named 'sv_flags' > Align.c:5952: error: expected ';' before 'tmpXSoff' > Align.c:5952: error: invalid operands to binary + > Align.c:5952: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__FileSource_set_type': > Align.c:5959: error: function 'ax' is initialized like a variable > Align.c:5959: error: invalid lvalue in increment > Align.c:5959: error: function 'items' is initialized like a variable > Align.c:5960: warning: comparison between pointer and integer > Align.c:5963: error: array subscript is not an integer > Align.c:5963: error: array subscript is not an integer > Align.c:5963: error: array subscript is not an integer > Align.c:5963: error: array subscript is not an integer > Align.c:5964: error: array subscript is not an integer > Align.c:5964: error: array subscript is not an integer > Align.c:5964: error: array subscript is not an integer > Align.c:5966: error: 'OP' has no member named 'op_private' > Align.c:5966: error: 'OP' has no member named 'op_targ' > Align.c:5970: error: invalid operands to binary + > Align.c:5970: error: 'IV' undeclared (first use in this function) > Align.c:5970: error: expected ')' before 'RETVAL' > Align.c:5970: error: too many arguments to function 'Perl_sv_setiv' > Align.c:5970: error: 'SV' has no member named 'sv_flags' > Align.c:5972: error: expected ';' before 'tmpXSoff' > Align.c:5972: error: invalid operands to binary + > Align.c:5972: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__FileSource_type': > Align.c:5979: error: function 'ax' is initialized like a variable > Align.c:5979: error: invalid lvalue in increment > Align.c:5979: error: function 'items' is initialized like a variable > Align.c:5980: warning: comparison between pointer and integer > Align.c:5983: error: array subscript is not an integer > Align.c:5983: error: array subscript is not an integer > Align.c:5983: error: array subscript is not an integer > Align.c:5983: error: array subscript is not an integer > Align.c:5985: error: 'OP' has no member named 'op_private' > Align.c:5985: error: 'OP' has no member named 'op_targ' > Align.c:5989: error: invalid operands to binary + > Align.c:5989: error: 'IV' undeclared (first use in this function) > Align.c:5989: error: expected ')' before 'RETVAL' > Align.c:5989: error: too many arguments to function 'Perl_sv_setiv' > Align.c:5989: error: 'SV' has no member named 'sv_flags' > Align.c:5991: error: expected ';' before 'tmpXSoff' > Align.c:5991: error: invalid operands to binary + > Align.c:5991: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__FileSource_new': > Align.c:5998: error: function 'ax' is initialized like a variable > Align.c:5998: error: invalid lvalue in increment > Align.c:5998: error: function 'items' is initialized like a variable > Align.c:5999: warning: comparison between pointer and integer > Align.c:6001: error: invalid operands to binary - > Align.c:6003: error: array subscript is not an integer > Align.c:6003: error: array subscript is not an integer > Align.c:6003: error: array subscript is not an integer > Align.c:6003: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.xs:3253: error: array subscript is not an integer > Align.xs:3254: error: array subscript is not an integer > Align.xs:3255: error: 'IV' undeclared (first use in this function) > Align.xs:3255: error: expected ';' before 'tmpXSoff' > Align.xs:3255: error: invalid operands to binary + > Align.xs:3255: error: 'tmpXSoff' undeclared (first use in > this function) > Align.c: In function 'XS_Bio__Ext__Align__FileSource_DESTROY': > Align.c:6021: error: function 'ax' is initialized like a variable > Align.c:6021: error: invalid lvalue in increment > Align.c:6021: error: function 'items' is initialized like a variable > Align.c:6022: warning: comparison between pointer and integer > Align.c:6025: error: array subscript is not an integer > Align.c:6025: error: array subscript is not an integer > Align.c:6025: error: array subscript is not an integer > Align.c:6025: error: array subscript is not an integer > Align.c:6030: error: 'IV' undeclared (first use in this function) > Align.c:6030: error: expected ';' before 'tmpXSoff' > Align.c:6030: error: invalid operands to binary + > Align.c:6030: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function > 'XS_Bio__Ext__Align_Align_strings_ProteinSmithWaterman': > Align.c:6037: error: function 'ax' is initialized like a variable > Align.c:6037: error: invalid lvalue in increment > Align.c:6037: error: function 'items' is initialized like a variable > Align.c:6038: warning: comparison between pointer and integer > Align.c:6041: error: array subscript is not an integer > Align.c:6041: error: array subscript is not an integer > Align.c:6041: error: array subscript is not an integer > Align.c:6041: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6042: error: array subscript is not an integer > Align.c:6042: error: array subscript is not an integer > Align.c:6042: error: array subscript is not an integer > Align.c:6042: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6043: error: array subscript is not an integer > Align.c:6043: error: array subscript is not an integer > Align.c:6043: error: array subscript is not an integer > Align.c:6043: error: array subscript is not an integer > Align.c:6044: error: array subscript is not an integer > Align.c:6044: error: array subscript is not an integer > Align.c:6044: error: array subscript is not an integer > Align.c:6045: error: array subscript is not an integer > Align.c:6045: error: array subscript is not an integer > Align.c:6045: error: array subscript is not an integer > Align.c:6050: error: array subscript is not an integer > Align.c:6051: error: array subscript is not an integer > Align.c:6054: error: 'IV' undeclared (first use in this function) > Align.c:6054: error: expected ';' before 'tmpXSoff' > Align.c:6054: error: invalid operands to binary + > Align.c:6054: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function > 'XS_Bio__Ext__Align_Align_Sequences_ProteinSmithWaterman': > Align.c:6061: error: function 'ax' is initialized like a variable > Align.c:6061: error: invalid lvalue in increment > Align.c:6061: error: function 'items' is initialized like a variable > Align.c:6062: warning: comparison between pointer and integer > Align.c:6065: error: array subscript is not an integer > Align.c:6065: error: array subscript is not an integer > Align.c:6065: error: array subscript is not an integer > Align.c:6065: error: array subscript is not an integer > Align.c:6066: error: array subscript is not an integer > Align.c:6066: error: array subscript is not an integer > Align.c:6066: error: array subscript is not an integer > Align.c:6066: error: array subscript is not an integer > Align.c:6067: error: array subscript is not an integer > Align.c:6067: error: array subscript is not an integer > Align.c:6067: error: array subscript is not an integer > Align.c:6067: error: array subscript is not an integer > Align.c:6068: error: array subscript is not an integer > Align.c:6068: error: array subscript is not an integer > Align.c:6068: error: array subscript is not an integer > Align.c:6069: error: array subscript is not an integer > Align.c:6069: error: array subscript is not an integer > Align.c:6069: error: array subscript is not an integer > Align.c:6074: error: array subscript is not an integer > Align.c:6075: error: array subscript is not an integer > Align.c:6078: error: 'IV' undeclared (first use in this function) > Align.c:6078: error: expected ';' before 'tmpXSoff' > Align.c:6078: error: invalid operands to binary + > Align.c:6078: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function > 'XS_Bio__Ext__Align_Align_Proteins_SmithWaterman': > Align.c:6085: error: function 'ax' is initialized like a variable > Align.c:6085: error: invalid lvalue in increment > Align.c:6085: error: function 'items' is initialized like a variable > Align.c:6086: warning: comparison between pointer and integer > Align.c:6089: error: array subscript is not an integer > Align.c:6089: error: array subscript is not an integer > Align.c:6089: error: array subscript is not an integer > Align.c:6089: error: array subscript is not an integer > Align.c:6090: error: array subscript is not an integer > Align.c:6090: error: array subscript is not an integer > Align.c:6090: error: array subscript is not an integer > Align.c:6090: error: array subscript is not an integer > Align.c:6091: error: array subscript is not an integer > Align.c:6091: error: array subscript is not an integer > Align.c:6091: error: array subscript is not an integer > Align.c:6091: error: array subscript is not an integer > Align.c:6092: error: array subscript is not an integer > Align.c:6092: error: array subscript is not an integer > Align.c:6092: error: array subscript is not an integer > Align.c:6093: error: array subscript is not an integer > Align.c:6093: error: array subscript is not an integer > Align.c:6093: error: array subscript is not an integer > Align.c:6098: error: array subscript is not an integer > Align.c:6099: error: array subscript is not an integer > Align.c:6102: error: 'IV' undeclared (first use in this function) > Align.c:6102: error: expected ';' before 'tmpXSoff' > Align.c:6102: error: invalid operands to binary + > Align.c:6102: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align_Align_DNA_Sequences': > Align.c:6109: error: function 'ax' is initialized like a variable > Align.c:6109: error: invalid lvalue in increment > Align.c:6109: error: function 'items' is initialized like a variable > Align.c:6110: warning: comparison between pointer and integer > Align.c:6113: error: array subscript is not an integer > Align.c:6113: error: array subscript is not an integer > Align.c:6113: error: array subscript is not an integer > Align.c:6113: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6114: error: array subscript is not an integer > Align.c:6114: error: array subscript is not an integer > Align.c:6114: error: array subscript is not an integer > Align.c:6114: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6115: error: array subscript is not an integer > Align.c:6115: error: array subscript is not an integer > Align.c:6115: error: array subscript is not an integer > Align.c:6116: error: array subscript is not an integer > Align.c:6116: error: array subscript is not an integer > Align.c:6116: error: array subscript is not an integer > Align.c:6117: error: array subscript is not an integer > Align.c:6117: error: array subscript is not an integer > Align.c:6117: error: array subscript is not an integer > Align.c:6118: error: array subscript is not an integer > Align.c:6118: error: array subscript is not an integer > Align.c:6118: error: array subscript is not an integer > Align.c:6119: error: array subscript is not an integer > Align.c:6119: error: array subscript is not an integer > Align.c:6119: error: array subscript is not an integer > Align.c:6131: error: array subscript is not an integer > Align.c:6132: error: array subscript is not an integer > Align.c:6135: error: 'IV' undeclared (first use in this function) > Align.c:6135: error: expected ';' before 'tmpXSoff' > Align.c:6135: error: invalid operands to binary + > Align.c:6135: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align_Align_Protein_Sequences': > Align.c:6142: error: function 'ax' is initialized like a variable > Align.c:6142: error: invalid lvalue in increment > Align.c:6142: error: function 'items' is initialized like a variable > Align.c:6143: warning: comparison between pointer and integer > Align.c:6146: error: array subscript is not an integer > Align.c:6146: error: array subscript is not an integer > Align.c:6146: error: array subscript is not an integer > Align.c:6146: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6147: error: array subscript is not an integer > Align.c:6147: error: array subscript is not an integer > Align.c:6147: error: array subscript is not an integer > Align.c:6147: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6148: error: array subscript is not an integer > Align.c:6148: error: array subscript is not an integer > Align.c:6148: error: array subscript is not an integer > Align.c:6148: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6153: error: array subscript is not an integer > Align.c:6154: error: array subscript is not an integer > Align.c:6157: error: 'IV' undeclared (first use in this function) > Align.c:6157: error: expected ';' before 'tmpXSoff' > Align.c:6157: error: invalid operands to binary + > Align.c:6157: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__AlignOutput_aln1': > Align.c:6164: error: function 'ax' is initialized like a variable > Align.c:6164: error: invalid lvalue in increment > Align.c:6164: error: function 'items' is initialized like a variable > Align.c:6165: warning: comparison between pointer and integer > Align.c:6168: error: array subscript is not an integer > Align.c:6168: error: array subscript is not an integer > Align.c:6168: error: array subscript is not an integer > Align.c:6168: error: array subscript is not an integer > Align.c:6170: error: 'OP' has no member named 'op_private' > Align.c:6170: error: 'OP' has no member named 'op_targ' > Align.c:6174: error: invalid operands to binary + > Align.c:6174: error: 'SV' has no member named 'sv_flags' > Align.c:6176: error: 'IV' undeclared (first use in this function) > Align.c:6176: error: expected ';' before 'tmpXSoff' > Align.c:6176: error: invalid operands to binary + > Align.c:6176: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__AlignOutput_aln2': > Align.c:6183: error: function 'ax' is initialized like a variable > Align.c:6183: error: invalid lvalue in increment > Align.c:6183: error: function 'items' is initialized like a variable > Align.c:6184: warning: comparison between pointer and integer > Align.c:6187: error: array subscript is not an integer > Align.c:6187: error: array subscript is not an integer > Align.c:6187: error: array subscript is not an integer > Align.c:6187: error: array subscript is not an integer > Align.c:6189: error: 'OP' has no member named 'op_private' > Align.c:6189: error: 'OP' has no member named 'op_targ' > Align.c:6193: error: invalid operands to binary + > Align.c:6193: error: 'SV' has no member named 'sv_flags' > Align.c:6195: error: 'IV' undeclared (first use in this function) > Align.c:6195: error: expected ';' before 'tmpXSoff' > Align.c:6195: error: invalid operands to binary + > Align.c:6195: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__AlignOutput_start1': > Align.c:6202: error: function 'ax' is initialized like a variable > Align.c:6202: error: invalid lvalue in increment > Align.c:6202: error: function 'items' is initialized like a variable > Align.c:6203: warning: comparison between pointer and integer > Align.c:6206: error: array subscript is not an integer > Align.c:6206: error: array subscript is not an integer > Align.c:6206: error: array subscript is not an integer > Align.c:6206: error: array subscript is not an integer > Align.c:6208: error: 'OP' has no member named 'op_private' > Align.c:6208: error: 'OP' has no member named 'op_targ' > Align.c:6212: error: invalid operands to binary + > Align.c:6212: error: 'IV' undeclared (first use in this function) > Align.c:6212: error: expected ')' before 'RETVAL' > Align.c:6212: error: too many arguments to function 'Perl_sv_setiv' > Align.c:6212: error: 'SV' has no member named 'sv_flags' > Align.c:6214: error: expected ';' before 'tmpXSoff' > Align.c:6214: error: invalid operands to binary + > Align.c:6214: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__AlignOutput_end1': > Align.c:6221: error: function 'ax' is initialized like a variable > Align.c:6221: error: invalid lvalue in increment > Align.c:6221: error: function 'items' is initialized like a variable > Align.c:6222: warning: comparison between pointer and integer > Align.c:6225: error: array subscript is not an integer > Align.c:6225: error: array subscript is not an integer > Align.c:6225: error: array subscript is not an integer > Align.c:6225: error: array subscript is not an integer > Align.c:6227: error: 'OP' has no member named 'op_private' > Align.c:6227: error: 'OP' has no member named 'op_targ' > Align.c:6231: error: invalid operands to binary + > Align.c:6231: error: 'IV' undeclared (first use in this function) > Align.c:6231: error: expected ')' before 'RETVAL' > Align.c:6231: error: too many arguments to function 'Perl_sv_setiv' > Align.c:6231: error: 'SV' has no member named 'sv_flags' > Align.c:6233: error: expected ';' before 'tmpXSoff' > Align.c:6233: error: invalid operands to binary + > Align.c:6233: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__AlignOutput_start2': > Align.c:6240: error: function 'ax' is initialized like a variable > Align.c:6240: error: invalid lvalue in increment > Align.c:6240: error: function 'items' is initialized like a variable > Align.c:6241: warning: comparison between pointer and integer > Align.c:6244: error: array subscript is not an integer > Align.c:6244: error: array subscript is not an integer > Align.c:6244: error: array subscript is not an integer > Align.c:6244: error: array subscript is not an integer > Align.c:6246: error: 'OP' has no member named 'op_private' > Align.c:6246: error: 'OP' has no member named 'op_targ' > Align.c:6250: error: invalid operands to binary + > Align.c:6250: error: 'IV' undeclared (first use in this function) > Align.c:6250: error: expected ')' before 'RETVAL' > Align.c:6250: error: too many arguments to function 'Perl_sv_setiv' > Align.c:6250: error: 'SV' has no member named 'sv_flags' > Align.c:6252: error: expected ';' before 'tmpXSoff' > Align.c:6252: error: invalid operands to binary + > Align.c:6252: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'XS_Bio__Ext__Align__AlignOutput_end2': > Align.c:6259: error: function 'ax' is initialized like a variable > Align.c:6259: error: invalid lvalue in increment > Align.c:6259: error: function 'items' is initialized like a variable > Align.c:6260: warning: comparison between pointer and integer > Align.c:6263: error: array subscript is not an integer > Align.c:6263: error: array subscript is not an integer > Align.c:6263: error: array subscript is not an integer > Align.c:6263: error: array subscript is not an integer > Align.c:6265: error: 'OP' has no member named 'op_private' > Align.c:6265: error: 'OP' has no member named 'op_targ' > Align.c:6269: error: invalid operands to binary + > Align.c:6269: error: 'IV' undeclared (first use in this function) > Align.c:6269: error: expected ')' before 'RETVAL' > Align.c:6269: error: too many arguments to function 'Perl_sv_setiv' > Align.c:6269: error: 'SV' has no member named 'sv_flags' > Align.c:6271: error: expected ';' before 'tmpXSoff' > Align.c:6271: error: invalid operands to binary + > Align.c:6271: error: 'tmpXSoff' undeclared (first use in this > function) > Align.c: In function 'boot_Bio__Ext__Align': > Align.c:6280: error: function 'ax' is initialized like a variable > Align.c:6280: error: invalid lvalue in increment > Align.c:6280: error: function 'items' is initialized like a variable > Align.c:6283: error: array subscript is not an integer > Align.c:6283: error: array subscript is not an integer > Align.c:6283: error: array subscript is not an integer > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: warning: comparison between pointer and integer > Align.c:6283: error: array subscript is not an integer > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6283: error: 'SV' has no member named 'sv_flags' > Align.c:6283: error: too many arguments to function > 'Perl_sv_2pv_flags' > Align.c:6595: error: array subscript is not an integer > Align.c:6595: error: 'IV' undeclared (first use in this function) > Align.c:6595: error: expected ';' before 'tmpXSoff' > Align.c:6595: error: invalid operands to binary + > Align.c:6595: error: 'tmpXSoff' undeclared (first use in this > function) > make[1]: *** [Align.o] Error 1 > make[1]: Leaving directory > `/home/pallavi/Pallavi/downloads/bioperl-ext-1.4/Bio/Ext/Align' > make: *** [subdirs] Error 2 > > > thanks > Pallavi > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From alperyilmaz at gmail.com Thu Jul 3 11:22:53 2008 From: alperyilmaz at gmail.com (Alper Yilmaz) Date: Thu, 3 Jul 2008 11:22:53 -0400 Subject: [Bioperl-l] Bio::Graphics, circular map Message-ID: Hi all, Is there a way to use Bio::Graphics module to generate circular plasmid maps? I'm using Bio::Graphics::Panel for another purpose and as far I saw in manuals and HOW-TOs, there's no circular option. Do I need to use another module? thanks, Alper Yilmaz Plant Biotechnology Center The Ohio State University From alexl at users.sourceforge.net Thu Jul 3 21:27:31 2008 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Thu, 03 Jul 2008 18:27:31 -0700 Subject: [Bioperl-l] Install help errors In-Reply-To: <628aabb70807030208y183e7ca7rb3f37f491b5fb6e3@mail.gmail.com> (Dave Messina's message of "Thu\, 3 Jul 2008 11\:08\:19 +0200") References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <536f21b00807021313l6cec00devfd452db661ec1449@mail.gmail.com> <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> <628aabb70807030208y183e7ca7rb3f37f491b5fb6e3@mail.gmail.com> Message-ID: >>>>> "DM" == Dave Messina writes: DM> Here's your problem -- bioperl 1.4 is waaaay out of date. Don't DM> use that. >> BIRNEY/bioperl-1.4.tar.gz : make_test NO Instead, use the 1.5.2_100 version of bioperl-core that matches this: >> SENDU/bioperl-db-1.5.2_100.tar.gz : make_test NO DM> Or even better, you might want to get the latest versions of each from the DM> bioperl website. DM> Look here: http://www.bioperl.org/wiki/Getting_BioPerl DM> and here: http://www.bioperl.org/wiki/Installing_BioPerl Fedora does ship the latest bioperl (1.5.2) and bioperl-run, as perl-bioperl and perl-bioperl-run, respectively see: https://admin.fedoraproject.org/pkgdb/packages/name/perl-bioperl https://admin.fedoraproject.org/pkgdb/packages/name/perl-bioperl-run but we haven't yet packaged the bioperl-db module, but I could certainly look into doing that. Is http://www.bioperl.org/wiki/Getting_BioPerl the best place to add section a section on the Fedora packages for bioperl? It would just need to say something like: To install bioperl (core) simply run (as root): yum install perl-bioperl I do keep the Fedora packages up to date, so when the next bioperl is released (any timeline for that?), it will be updated. Incidentally why is 1.5.2 still called a "developer" release and 1.4 "stable", it just confuses users who tend to assume that the "stable" release is the one they should install (and Linux distributions for that matter). 1.5.2 is now already 3 or so years old, so it should be considered the default release by now. Alex From cjfields at uiuc.edu Fri Jul 4 02:14:37 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 4 Jul 2008 01:14:37 -0500 Subject: [Bioperl-l] Memory not sufficient when storing human chromosom 1 in BioSQL In-Reply-To: <486CBCA7.8080201@uni-tuebingen.de> References: <486CBCA7.8080201@uni-tuebingen.de> Message-ID: <530CA5F3-8F26-4FA8-B611-39A6B240CA7A@uiuc.edu> Have you tried just loading the sequence into memory using Bio::SeqIO? The problem may be the size of the file itself. chris On Jul 3, 2008, at 6:48 AM, Andreas Dr?ger wrote: > Hi all, > > Recently I have successfully installed the latest version of BioPerl > and BioSQL on my computer, which has 2 GB RAM. Both works fine, but > when trying to insert the genbank file of the human chromosome 1, > which I have downloaded from the NCBI website (ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_01/hs_ref_chr1.gbk.gz > ) I receive the error message 'Out of memory'. This takes about one > hour. My question is, how I can insert large genbank files in my > BioSQL database using BioPerl. I do not know, what to do. Thank you > for your help!!! > > Cheers, > Andreas > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Marie-Claude Hofmann College of Veterinary Medicine University of Illinois Urbana-Champaign From torsten.seemann at infotech.monash.edu.au Fri Jul 4 02:54:29 2008 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Fri, 4 Jul 2008 16:54:29 +1000 Subject: [Bioperl-l] Memory not sufficient when storing human chromosom 1 in BioSQL In-Reply-To: <530CA5F3-8F26-4FA8-B611-39A6B240CA7A@uiuc.edu> References: <486CBCA7.8080201@uni-tuebingen.de> <530CA5F3-8F26-4FA8-B611-39A6B240CA7A@uiuc.edu> Message-ID: >> (ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_01/hs_ref_chr1.gbk.gz) I >> receive the error message 'Out of memory'. This takes about one hour. My > Have you tried just loading the sequence into memory using Bio::SeqIO? The > problem may be the size of the file itself. # gunzip -l hs_ref_chr1.gbk.gz compressed uncompressed ratio uncompressed_name 95180772 296770940 67.9% hs_ref_chr1.gbk # zgrep -c ^LOCUS hs_ref_chr1.gbk.gz 49 # zgrep -c -i '^ [A-Z-]' hs_ref_chr1.gbk.gz 25853 It's about 300 MB of ASCII in 49 records and 26,000 features. Not sure what that would explode to if wrapped in Bio::SeqFeature-like objects? Factor of 4 perhaps? -- --Torsten Seemann --Victorian Bioinformatics Consortium, Dept. Microbiology, Monash University From torsten.seemann at infotech.monash.edu.au Fri Jul 4 02:56:00 2008 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Fri, 4 Jul 2008 16:56:00 +1000 Subject: [Bioperl-l] Bio::Graphics, circular map In-Reply-To: References: Message-ID: > Is there a way to use Bio::Graphics module to generate circular > plasmid maps? I'm using Bio::Graphics::Panel for another purpose and > as far I saw in manuals and HOW-TOs, there's no circular option. Do I > need to use another module? I don't think there is one in BioPerl. You may want to look at PlasMapper: http://wishart.biology.ualberta.ca/PlasMapper/ -- --Torsten Seemann --Victorian Bioinformatics Consortium, Dept. Microbiology, Monash University --Tel: 9905 9010 / 0422 923 024 From bix at sendu.me.uk Fri Jul 4 05:29:05 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 04 Jul 2008 10:29:05 +0100 Subject: [Bioperl-l] Install help errors In-Reply-To: References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <536f21b00807021313l6cec00devfd452db661ec1449@mail.gmail.com> <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> <628aabb70807030208y183e7ca7rb3f37f491b5fb6e3@mail.gmail.com> Message-ID: <486DED61.9020800@sendu.me.uk> Alex Lancaster wrote: > Fedora does ship the latest bioperl (1.5.2) and bioperl-run, as > perl-bioperl and perl-bioperl-run, respectively see: > > https://admin.fedoraproject.org/pkgdb/packages/name/perl-bioperl > https://admin.fedoraproject.org/pkgdb/packages/name/perl-bioperl-run > > but we haven't yet packaged the bioperl-db module, but I could > certainly look into doing that. > > Is http://www.bioperl.org/wiki/Getting_BioPerl the best place to add > section a section on the Fedora packages for bioperl? Yup, thanks for doing that. > Incidentally why is 1.5.2 still called a "developer" release and 1.4 > "stable", it just confuses users who tend to assume that the "stable" > release is the one they should install (and Linux distributions for > that matter). 1.5.2 is now already 3 or so years old, so it should be > considered the default release by now. See http://www.bioperl.org/wiki/FAQ#What_is_the_difference_between_1.5.2_and_1.4.0.3F_What_do_you_mean_developer_release.3F While I've got you, what are your thoughts on this?: http://article.gmane.org/gmane.comp.lang.perl.bio.general/17282 Is this still an issue with recent version of Fedora? Does the problem indeed come and go with different versions? Why does Fedora suffer the problem at all? From alexl at users.sourceforge.net Fri Jul 4 06:01:00 2008 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Fri, 04 Jul 2008 03:01:00 -0700 Subject: [Bioperl-l] Install help errors In-Reply-To: <486DED61.9020800@sendu.me.uk> (Sendu Bala's message of "Fri\, 04 Jul 2008 10\:29\:05 +0100") References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <536f21b00807021313l6cec00devfd452db661ec1449@mail.gmail.com> <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> <628aabb70807030208y183e7ca7rb3f37f491b5fb6e3@mail.gmail.com> <486DED61.9020800@sendu.me.uk> Message-ID: <77vdzmvuhv.fsf@allele2.eebweb.arizona.edu> >>>>> "SB" == Sendu Bala writes: [...] SB> Yup, thanks for doing that. >> Incidentally why is 1.5.2 still called a "developer" release and >> 1.4 "stable", it just confuses users who tend to assume that the >> "stable" release is the one they should install (and Linux >> distributions for that matter). 1.5.2 is now already 3 or so years >> old, so it should be considered the default release by now. SB> See SB> http://www.bioperl.org/wiki/FAQ#What_is_the_difference_between_1.5.2_and_1.4.0.3F_What_do_you_mean_developer_release.3F Ok, but it needs to be made upfront on the download section to new users (i.e. those that don't have any existing scripts that might not be compatible with the new API in 1.5.2) that even though it is a "developer" release, they should still get 1.5.2 as I've seen a few several threads on this mailing list that go like this: User: something doesn't work in bioperl! Dev: what version are you using? U: I'm using bioperl 1.4! D: what!? that's way old, you should be using 1.5.2 U: but I'm using the stable version listed: 1.4 SB> While I've got you, what are your thoughts on this?: SB> http://article.gmane.org/gmane.comp.lang.perl.bio.general/17282 SB> Is this still an issue with recent version of Fedora? Does the SB> problem indeed come and go with different versions? Why does SB> Fedora suffer the problem at all? I don't know exactly what "the problem" is that you are referring to. Which version of Fedora and what version of perl-bioperl? Is this an issue with bioperl-sql? That bit isn't packaged yet. The current version of Task::Weaken package (in F-8, at least) is: perl-Task-Weaken-1.02-2.fc8 And looking at http://search.cpan.org/dist/Task-Weaken/ it seems to be the most recent. I never saw a requirement for that package in the original Build.PL, should it be made a requirement for bioperl (core) or bioperl-run? If it is a "soft requirement", then it should be able to be installed using yum: yum install perl-Task-Weaken Also, I would never recommend overwriting the files from RPMs with the files from manually-compiled CPAN Perl packages, it will cause endless headaches down the road. The cleanest way to "overwrite" non-RPM packaged CPAN packages is to first remove the Fedora RPM: yum remove perl-foobar then install the CPAN package using the perl system, but make sure that they are installed in /usr/local/ not /usr to avoid stepping on any system-managed files. Alex From bix at sendu.me.uk Fri Jul 4 06:10:53 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 04 Jul 2008 11:10:53 +0100 Subject: [Bioperl-l] Memory not sufficient when storing human chromosom 1 in BioSQL In-Reply-To: <530CA5F3-8F26-4FA8-B611-39A6B240CA7A@uiuc.edu> References: <486CBCA7.8080201@uni-tuebingen.de> <530CA5F3-8F26-4FA8-B611-39A6B240CA7A@uiuc.edu> Message-ID: <486DF72D.7080803@sendu.me.uk> [CC:ing Gabrielle who had an identical problem] Chris Fields wrote: > On Jul 3, 2008, at 6:48 AM, Andreas Dr?ger wrote: >> Recently I have successfully installed the latest version of BioPerl >> and BioSQL on my computer, which has 2 GB RAM. Both works fine, but >> when trying to insert the genbank file of the human chromosome 1, >> which I have downloaded from the NCBI website >> (ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_01/hs_ref_chr1.gbk.gz) I >> receive the error message 'Out of memory'. This takes about one hour. >> My question is, how I can insert large genbank files in my BioSQL >> database using BioPerl. I do not know, what to do. Thank you for your >> help!!! > > Have you tried just loading the sequence into memory using Bio::SeqIO? > The problem may be the size of the file itself. Just looping through: perl -MBio::SeqIO -e '$i Bio::SeqIO->new(-file => "hs_ref_chr1.gbk"); while ($seq = $i->next_seq) { $ac = $seq->accession; }' This gave me a variable memory usage, typically around 360MB, peaking up to 980MB before dropping back down again. Seems a little high to me, but it doesn't seem to be a memory leak? Keeping every seq object in memory: perl -MBio::SeqIO -e '$i Bio::SeqIO->new(-file => "hs_ref_chr1.gbk"); @seqs; while ($seq = $i->next_seq) { push(@seqs, $seq); }' This used up to 810MB. I didn't notice any peakiness, but it may have been there. SeqIO by itself shouldn't be causing any out of memory errors on 2 and 4GB machines. What does bioperl-db do as it enters sequences into the db? How does it currently deal with species information? From vttran at i3s.unice.fr Fri Jul 4 10:00:28 2008 From: vttran at i3s.unice.fr (Tran Trang) Date: Fri, 4 Jul 2008 16:00:28 +0200 (CEST) Subject: [Bioperl-l] install Perl Message-ID: <3139.134.59.129.240.1215180028.squirrel@webmail.i3s.unice.fr> Dear: I followed the instruction "INSTALLING BIOPERL THE EASY WAY USING 'Build.PL'" at the website http://bio.perl.org/wiki/Installing_Bioperl_for_Unix for installing the BIOPERL package. When I do the command >perl Build.PL I obtained the following lines. I seems that is not good and I did not win to install this package? I have the same problem when installing BIOPERL-RUN package. Could you please help me how can i do it now? Thank you in advance! Best regard, Trang ------------------------------- Installation BIOPERL version bioperl-1.5.2_102 gives: ... Manifying blib/lib/Module/Build/Compat.pm -> blib/libdoc/Module::Build::Compat.3pm /usr/bin/make -- OK Running make test /usr/bin/perl Build --makefile_env_macros 1 test t/basic...............ok t/compat..............ok t/destinations........ok 8/113 skipped: various reasons t/ext.................ok t/extend..............ok t/files...............ok t/help................ok t/install.............ok t/manifypods..........ok t/mbyaml..............ok t/metadata............ok 8/47 skipped: YAML_support feature is not enabled t/metadata2...........ok 4/18 skipped: YAML_support feature is not enabled t/moduleinfo..........ok t/new_from_context....ok t/notes...............ok t/par.................skipped all skipped: C_support not enabled t/parents.............ok t/pod_parser..........ok t/ppm.................skipped all skipped: C_support not enabled t/runthrough..........ok 11/32 skipped: various reasons t/signature...........skipped all skipped: $ENV{TEST_SIGNATURE} is not set t/test_type...........ok t/test_types..........ok t/tilde...............ok t/versions............ok t/xs..................skipped all skipped: C_support not enabled All tests successful, 4 tests and 31 subtests skipped. Files=26, Tests=750, 14 wallclock secs ( 5.77 cusr + 8.16 csys = 13.93 CPU) /usr/bin/make test -- OK Running make install /usr/bin/perl Build --makefile_env_macros 1 install mkdir /usr/local/man/man1: Permission non accord�e at /usr/share/perl/5.8/ExtUtils/Install.pm line 112 make: *** [install] Erreur 13 /usr/bin/make install -- NOT OK Couldn't install Module::Build, giving up. BEGIN failed--compilation aborted at ModuleBuildBioperl.pm line 51. Compilation failed in require at Build.PL line 14. BEGIN failed--compilation aborted at Build.PL line 14. -------------------------------------------------- Installation BIOPERL-RUN version bioperl-1.5.2_100 gives: Manifying blib/lib/Module/Build/Compat.pm -> blib/libdoc/Module::Build::Compat.3pm /usr/bin/make -- OK Running make test /usr/bin/perl Build --makefile_env_macros 1 test t/basic...............ok t/compat..............ok t/destinations........ok 8/113 skipped: various reasons t/ext.................ok t/extend..............ok t/files...............ok t/help................ok t/install.............ok t/manifypods..........ok t/mbyaml..............ok t/metadata............ok 8/47 skipped: YAML_support feature is not enabled t/metadata2...........ok 4/18 skipped: YAML_support feature is not enabled t/moduleinfo..........ok t/new_from_context....ok t/notes...............ok t/par.................skipped all skipped: C_support not enabled t/parents.............ok t/pod_parser..........ok t/ppm.................skipped all skipped: C_support not enabled t/runthrough..........ok 11/32 skipped: various reasons t/signature...........skipped all skipped: $ENV{TEST_SIGNATURE} is not set t/test_type...........ok t/test_types..........ok t/tilde...............ok t/versions............ok t/xs..................skipped all skipped: C_support not enabled All tests successful, 4 tests and 31 subtests skipped. Files=26, Tests=750, 15 wallclock secs ( 5.65 cusr + 8.28 csys = 13.93 CPU) /usr/bin/make test -- OK Running make install /usr/bin/perl Build --makefile_env_macros 1 install mkdir /usr/local/man/man1: Permission non accord�e at /usr/share/perl/5.8/ExtUtils/Install.pm line 112 make: *** [install] Erreur 13 /usr/bin/make install -- NOT OK Couldn't install Module::Build, giving up. BEGIN failed--compilation aborted at ModuleBuildBioperl.pm line 51. Compilation failed in require at Build.PL line 10. BEGIN failed--compilation aborted at Build.PL line 10. From simon.andrews at bbsrc.ac.uk Fri Jul 4 10:15:33 2008 From: simon.andrews at bbsrc.ac.uk (Simon Andrews) Date: Fri, 4 Jul 2008 15:15:33 +0100 Subject: [Bioperl-l] install Perl In-Reply-To: <3139.134.59.129.240.1215180028.squirrel@webmail.i3s.unice.fr> References: <3139.134.59.129.240.1215180028.squirrel@webmail.i3s.unice.fr> Message-ID: <20BFD82C-B82A-4E27-B716-315FFF2F7E58@bbsrc.ac.uk> On 4 Jul 2008, at 15:00, Tran Trang wrote: > Dear: > > I followed the instruction "INSTALLING BIOPERL THE EASY WAY USING > 'Build.PL'" at the website > http://bio.perl.org/wiki/Installing_Bioperl_for_Unix for installing > the > BIOPERL package. When I do the command > >> perl Build.PL > > I obtained the following lines. I seems that is not good and I did > not win > to install this package? I have the same problem when installing > BIOPERL-RUN package. > > > Files=26, Tests=750, 14 wallclock secs ( 5.77 cusr + 8.16 csys = > 13.93 CPU) > /usr/bin/make test -- OK > Running make install > /usr/bin/perl Build --makefile_env_macros 1 install > mkdir /usr/local/man/man1: Permission non accord�e at > /usr/share/perl/5.8/ExtUtils/Install.pm line 112 It looks like you're running this as a user who doesn't have enough permissions to install the perl modules into the necessary system directories. All the tests are OK, you just can't copy the files at the end. Try running it as root (either directly or via sudo) and it should work OK. TTFN Simon. From roy.chaudhuri at gmail.com Fri Jul 4 10:26:04 2008 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Fri, 04 Jul 2008 15:26:04 +0100 Subject: [Bioperl-l] install Perl In-Reply-To: <20BFD82C-B82A-4E27-B716-315FFF2F7E58@bbsrc.ac.uk> References: <3139.134.59.129.240.1215180028.squirrel@webmail.i3s.unice.fr> <20BFD82C-B82A-4E27-B716-315FFF2F7E58@bbsrc.ac.uk> Message-ID: <486E32FC.5060003@gmail.com> Also, if you don't have root access and can't persuade your sysadmin to install it for you, see: http://bio.perl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_IN_A_PERSONAL_MODULE_AREA Roy. -- Dr. Roy Chaudhuri Department of Veterinary Medicine University of Cambridge, U.K. Simon Andrews wrote: > On 4 Jul 2008, at 15:00, Tran Trang wrote: > >> Dear: >> >> I followed the instruction "INSTALLING BIOPERL THE EASY WAY USING >> 'Build.PL'" at the website >> http://bio.perl.org/wiki/Installing_Bioperl_for_Unix for installing >> the >> BIOPERL package. When I do the command >> >>> perl Build.PL >> I obtained the following lines. I seems that is not good and I did >> not win >> to install this package? I have the same problem when installing >> BIOPERL-RUN package. >> >> >> Files=26, Tests=750, 14 wallclock secs ( 5.77 cusr + 8.16 csys = >> 13.93 CPU) >> /usr/bin/make test -- OK >> Running make install >> /usr/bin/perl Build --makefile_env_macros 1 install >> mkdir /usr/local/man/man1: Permission non accord�e at >> /usr/share/perl/5.8/ExtUtils/Install.pm line 112 > > It looks like you're running this as a user who doesn't have enough > permissions to install the perl modules into the necessary system > directories. All the tests are OK, you just can't copy the files at > the end. > > Try running it as root (either directly or via sudo) and it should > work OK. > > TTFN > > Simon. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at uiuc.edu Fri Jul 4 11:01:15 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 4 Jul 2008 10:01:15 -0500 Subject: [Bioperl-l] Install help errors In-Reply-To: <77vdzmvuhv.fsf@allele2.eebweb.arizona.edu> References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <536f21b00807021313l6cec00devfd452db661ec1449@mail.gmail.com> <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> <628aabb70807030208y183e7ca7rb3f37f491b5fb6e3@mail.gmail.com> <486DED61.9020800@sendu.me.uk> <77vdzmvuhv.fsf@allele2.eebweb.arizona.edu> Message-ID: On Jul 4, 2008, at 5:01 AM, Alex Lancaster wrote: >>>>>> "SB" == Sendu Bala writes: > > [...] > > SB> Yup, thanks for doing that. > >>> Incidentally why is 1.5.2 still called a "developer" release and >>> 1.4 "stable", it just confuses users who tend to assume that the >>> "stable" release is the one they should install (and Linux >>> distributions for that matter). 1.5.2 is now already 3 or so years >>> old, so it should be considered the default release by now. > > SB> See > SB> http://www.bioperl.org/wiki/FAQ#What_is_the_difference_between_1.5.2_and_1.4.0.3F_What_do_you_mean_developer_release.3F > > Ok, but it needs to be made upfront on the download section to new > users (i.e. those that don't have any existing scripts that might not > be compatible with the new API in 1.5.2) that even though it is a > "developer" release, they should still get 1.5.2 as I've seen a few > several threads on this mailing list that go like this: > > User: something doesn't work in bioperl! > Dev: what version are you using? > U: I'm using bioperl 1.4! > D: what!? that's way old, you should be using 1.5.2 > U: but I'm using the stable version listed: 1.4 That happens anyway regardless of where we put a notice. I don't think we can dump the 'stable' vs. 'dev' versioning systemjust for aesthetic reasons. However, I think we could fix a minimal set of problems at this point (bugs, etc) and release a new stable version fairly quickly. I would be up for that. > SB> While I've got you, what are your thoughts on this?: > SB> http://article.gmane.org/gmane.comp.lang.perl.bio.general/17282 > > SB> Is this still an issue with recent version of Fedora? Does the > SB> problem indeed come and go with different versions? Why does > SB> Fedora suffer the problem at all? > > I don't know exactly what "the problem" is that you are referring to. > Which version of Fedora and what version of perl-bioperl? Is this an > issue with bioperl-sql? That bit isn't packaged yet. > > The current version of Task::Weaken package (in F-8, at least) is: > > perl-Task-Weaken-1.02-2.fc8 > > And looking at http://search.cpan.org/dist/Task-Weaken/ it seems to be > the most recent. I never saw a requirement for that package in the > original Build.PL, should it be made a requirement for bioperl (core) > or bioperl-run? > > If it is a "soft requirement", then it should be able to be installed > using yum: > > yum install perl-Task-Weaken > > Also, I would never recommend overwriting the files from RPMs with the > files from manually-compiled CPAN Perl packages, it will cause endless > headaches down the road. The cleanest way to "overwrite" non-RPM > packaged CPAN packages is to first remove the Fedora RPM: > > yum remove perl-foobar > > then install the CPAN package using the perl system, but make sure > that they are installed in /usr/local/ not /usr to avoid stepping on > any system-managed files. > > Alex The problem is actually with Scalar::Util and weaken(). The link to Task::Weaken describes the problem: some versions of Red Hat Linux (and I'm assuming Fedora as well) ship with a broken version of Scalar::Util that does not pass tests due to issues with the XS-based weaken(). The only option is to add Task::Weaken as a dependency, which catches the problem if it exists and indicates the next possible step (generally to reinstall Scalar::Util or install a user-specific version of perl). I'm surprised we haven't seen this more often, but IIRC the user in that link was using a newer version of Fedora. chris From vttran at i3s.unice.fr Fri Jul 4 11:14:05 2008 From: vttran at i3s.unice.fr (Tran Trang) Date: Fri, 4 Jul 2008 17:14:05 +0200 (CEST) Subject: [Bioperl-l] install Perl In-Reply-To: <486E32FC.5060003@gmail.com> References: <3139.134.59.129.240.1215180028.squirrel@webmail.i3s.unice.fr> <20BFD82C-B82A-4E27-B716-315FFF2F7E58@bbsrc.ac.uk> <486E32FC.5060003@gmail.com> Message-ID: <3848.134.59.129.240.1215184445.squirrel@webmail.i3s.unice.fr> I won! Many thanks for your helps! Trang > Also, if you don't have root access and can't persuade your sysadmin to > install it for you, see: > http://bio.perl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_IN_A_PERSONAL_MODULE_AREA > > Roy. > -- > Dr. Roy Chaudhuri > Department of Veterinary Medicine > University of Cambridge, U.K. > > Simon Andrews wrote: >> On 4 Jul 2008, at 15:00, Tran Trang wrote: >> >>> Dear: >>> >>> I followed the instruction "INSTALLING BIOPERL THE EASY WAY USING >>> 'Build.PL'" at the website >>> http://bio.perl.org/wiki/Installing_Bioperl_for_Unix for installing >>> the >>> BIOPERL package. When I do the command >>> >>>> perl Build.PL >>> I obtained the following lines. I seems that is not good and I did >>> not win >>> to install this package? I have the same problem when installing >>> BIOPERL-RUN package. >>> >>> >>> Files=26, Tests=750, 14 wallclock secs ( 5.77 cusr + 8.16 csys = >>> 13.93 CPU) >>> /usr/bin/make test -- OK >>> Running make install >>> /usr/bin/perl Build --makefile_env_macros 1 install >>> mkdir /usr/local/man/man1: Permission non accord�e at >>> /usr/share/perl/5.8/ExtUtils/Install.pm line 112 >> >> It looks like you're running this as a user who doesn't have enough >> permissions to install the perl modules into the necessary system >> directories. All the tests are OK, you just can't copy the files at >> the end. >> >> Try running it as root (either directly or via sudo) and it should >> work OK. >> >> TTFN >> >> Simon. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at uiuc.edu Fri Jul 4 11:31:05 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 4 Jul 2008 10:31:05 -0500 Subject: [Bioperl-l] Memory not sufficient when storing human chromosom 1 in BioSQL In-Reply-To: <486DF72D.7080803@sendu.me.uk> References: <486CBCA7.8080201@uni-tuebingen.de> <530CA5F3-8F26-4FA8-B611-39A6B240CA7A@uiuc.edu> <486DF72D.7080803@sendu.me.uk> Message-ID: <13EBEBE2-7FA1-424B-92E1-4BB05D45BDD3@uiuc.edu> On Jul 4, 2008, at 5:10 AM, Sendu Bala wrote: > [CC:ing Gabrielle who had an identical problem] > > Chris Fields wrote: >> On Jul 3, 2008, at 6:48 AM, Andreas Dr?ger wrote: >>> Recently I have successfully installed the latest version of >>> BioPerl and BioSQL on my computer, which has 2 GB RAM. Both works >>> fine, but when trying to insert the genbank file of the human >>> chromosome 1, which I have downloaded from the NCBI website (ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_01/hs_ref_chr1.gbk.gz >>> ) I receive the error message 'Out of memory'. This takes about >>> one hour. My question is, how I can insert large genbank files in >>> my BioSQL database using BioPerl. I do not know, what to do. Thank >>> you for your help!!! >> >> Have you tried just loading the sequence into memory using >> Bio::SeqIO? The problem may be the size of the file itself. > > Just looping through: > perl -MBio::SeqIO -e '$i Bio::SeqIO->new(-file => > "hs_ref_chr1.gbk"); while ($seq = $i->next_seq) { $ac = $seq- > >accession; }' > > This gave me a variable memory usage, typically around 360MB, > peaking up to 980MB before dropping back down again. Seems a little > high to me, but it doesn't seem to be a memory leak? > > > Keeping every seq object in memory: > perl -MBio::SeqIO -e '$i Bio::SeqIO->new(-file => > "hs_ref_chr1.gbk"); @seqs; while ($seq = $i->next_seq) { push(@seqs, > $seq); }' > > This used up to 810MB. I didn't notice any peakiness, but it may > have been there. > > SeqIO by itself shouldn't be causing any out of memory errors on 2 > and 4GB machines. > > > What does bioperl-db do as it enters sequences into the db? How does > it currently deal with species information? Are the 'latest versions of bioperl/bioperl-db' Andreas indicated above the latest versions from Subversion, or 1.5.2? I can't recall whether 1.5.2 shipped with the memory issue fixes re: Bio::Species (I think it did, but maybe Sendu knows better than I). Some more info from Andreas would also help, such as OS, RDBMS, etc. Cold this be a combination of RDBMS, bioperl-db, and bioperl memory issues? Of course that would depend on how the local MySQL/Pg/Oracle is set up, but if the memory peaks out at 980MB (or 810MB for all sequences) for Bio::SeqIO alone, I could see how bioperl-db and the RDBMS may add quite a bit more to that. If anyone has a local bioperl-db set up we should try replicating this. Speaking of, does anyone know if we have set up bioperl-db testing on dev (or wherever it was to be hosted)? This was discussed at one point. chris From hartzell at alerce.com Fri Jul 4 15:46:09 2008 From: hartzell at alerce.com (George Hartzell) Date: Fri, 4 Jul 2008 12:46:09 -0700 Subject: [Bioperl-l] Memory not sufficient when storing human chromosom 1 in BioSQL In-Reply-To: <530CA5F3-8F26-4FA8-B611-39A6B240CA7A@uiuc.edu> References: <486CBCA7.8080201@uni-tuebingen.de> <530CA5F3-8F26-4FA8-B611-39A6B240CA7A@uiuc.edu> Message-ID: <18542.32257.772558.123807@almost.alerce.com> Chris Fields writes: > Have you tried just loading the sequence into memory using > Bio::SeqIO? The problem may be the size of the file itself. > > chris > > On Jul 3, 2008, at 6:48 AM, Andreas Dr?ger wrote: > > > Hi all, > > > > Recently I have successfully installed the latest version of BioPerl > > and BioSQL on my computer, which has 2 GB RAM. Both works fine, but > > when trying to insert the genbank file of the human chromosome 1, > > which I have downloaded from the NCBI website (ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_01/hs_ref_chr1.gbk.gz > > ) I receive the error message 'Out of memory'. This takes about one > > hour. My question is, how I can insert large genbank files in my > > BioSQL database using BioPerl. I do not know, what to do. Thank you > > for your help!!! I didn't catch the original question, so I don't know if you provided any of the specifics of your configuration. It's possible you really are running out of memory, is there a lot of other activity on the box or does e.g. top show a lot of free memory? My first guess is that you're running up against per-process limits. Check out the man pages for csh and/or bash and read about limit and/or ulimit. In the [t]csh world, run 'limit' and reflect on it's output. In the bash world, try 'ulimit -a' and think about what it has to say. If you're in the *BSD world you may be being constrained by limits imposed by your login class, I remember that the various linux flavors have similar mechanisms for configuring limits. Finally, it'd be nice to know how large the perl process gets before it goes blooey. You could just watch the output from top, or you could wrap up a little scriptlet that uses ps and grep to stash the data to a file somewhere. g. From alexl at users.sourceforge.net Fri Jul 4 22:13:05 2008 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Fri, 04 Jul 2008 19:13:05 -0700 Subject: [Bioperl-l] Install help errors In-Reply-To: (Chris Fields's message of "Fri\, 4 Jul 2008 10\:01\:15 -0500") References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <536f21b00807021313l6cec00devfd452db661ec1449@mail.gmail.com> <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> <628aabb70807030208y183e7ca7rb3f37f491b5fb6e3@mail.gmail.com> <486DED61.9020800@sendu.me.uk> <77vdzmvuhv.fsf@allele2.eebweb.arizona.edu> Message-ID: >>>>> "CF" == Chris Fields writes: CF> On Jul 4, 2008, at 5:01 AM, Alex Lancaster wrote: >>>>>> "SB" == Sendu Bala writes: [...] >> User: something doesn't work in bioperl! Dev: what version are you >> using? U: I'm using bioperl 1.4! D: what!? that's way old, you >> should be using 1.5.2 U: but I'm using the stable version listed: >> 1.4 CF> That happens anyway regardless of where we put a notice. Not necessarily, the notice needs to be made much more prominent in the section: http://www.bioperl.org/wiki/Getting_BioPerl#Bioperl_1.5.2.2C_Developer_Release however, because people are unlikely to click on FAQ page because (especially experienced) users will think they already know the difference between developer and stable. Perhaps something like: Which version should I get? 1. If you are just starting with bioperl, you should download the developer release as it is the most currently maintained release. 2. If you have older scripts and are concerned about API compatibility, you may want install the stable bioperl. CF> I don't think we can dump the 'stable' vs. 'dev' versioning CF> systemjust for aesthetic reasons. However, I think we could fix a CF> minimal set of problems at this point (bugs, etc) and release a CF> new stable version fairly quickly. I would be up for that. Sure, sounds good. [...] CF> The problem is actually with Scalar::Util and weaken(). The link CF> to Task::Weaken describes the problem: some versions of Red Hat CF> Linux (and I'm assuming Fedora as well) ship with a broken version CF> of Scalar::Util that does not pass tests due to issues with the CF> XS-based weaken(). The only option is to add Task::Weaken as a CF> dependency, which catches the problem if it exists and indicates CF> the next possible step (generally to reinstall Scalar::Util or CF> install a user-specific version of perl). If this is still a major issue in Fedora 9 (F-9) or rawhide, then the best way to handle this would be to open up a bug on: http://bugzilla.redhat.com/ and file it against the perl component, which appears to provide Scalar::Util: $ rpm -q --whatprovides 'perl(Scalar::Util)' perl-5.10.0-27.fc9.i386 Feel free to Cc me on the bug. Once fixed in perl 5.10, we could look into backporting the fix to F-8 which still ships with perl 5.8. CF> I'm surprised we haven't seen this more often, but IIRC the user CF> in that link was using a newer version of Fedora. F-9 ships with perl-5.10. Not sure if this is still a problem in that version. Alex From cjfields at uiuc.edu Fri Jul 4 23:41:15 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 4 Jul 2008 22:41:15 -0500 Subject: [Bioperl-l] Install help errors In-Reply-To: References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <536f21b00807021313l6cec00devfd452db661ec1449@mail.gmail.com> <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> <628aabb70807030208y183e7ca7rb3f37f491b5fb6e3@mail.gmail.com> <486DED61.9020800@sendu.me.uk> <77vdzmvuhv.fsf@allele2.eebweb.arizona.edu> Message-ID: <7713F291-EA5E-45CD-91EE-338DFBFF7BF4@uiuc.edu> On Jul 4, 2008, at 9:13 PM, Alex Lancaster wrote: >>>>>> "CF" == Chris Fields writes: >>> ... > > CF> That happens anyway regardless of where we put a notice. > > Not necessarily, the notice needs to be made much more prominent in > the section: > > http://www.bioperl.org/wiki/Getting_BioPerl#Bioperl_1.5.2.2C_Developer_Release > > however, because people are unlikely to click on FAQ page because > (especially experienced) users will think they already know the > difference between developer and stable. Perhaps something like: > > Which version should I get? > > 1. If you are just starting with bioperl, you should download the > developer release as it is the most currently maintained release. > > 2. If you have older scripts and are concerned about API > compatibility, you may want install the stable bioperl. Added to the wiki. > ... > CF> The problem is actually with Scalar::Util and weaken(). The link > CF> to Task::Weaken describes the problem: some versions of Red Hat > CF> Linux (and I'm assuming Fedora as well) ship with a broken version > CF> of Scalar::Util that does not pass tests due to issues with the > CF> XS-based weaken(). The only option is to add Task::Weaken as a > CF> dependency, which catches the problem if it exists and indicates > CF> the next possible step (generally to reinstall Scalar::Util or > CF> install a user-specific version of perl). > > If this is still a major issue in Fedora 9 (F-9) or rawhide, then > the best way to handle this would be to open up a bug on: > > http://bugzilla.redhat.com/ > > and file it against the perl component, which appears to provide > Scalar::Util: > > $ rpm -q --whatprovides 'perl(Scalar::Util)' > perl-5.10.0-27.fc9.i386 > > Feel free to Cc me on the bug. Once fixed in perl 5.10, we could look > into backporting the fix to F-8 which still ships with perl 5.8. > > CF> I'm surprised we haven't seen this more often, but IIRC the user > CF> in that link was using a newer version of Fedora. > > F-9 ships with perl-5.10. Not sure if this is still a problem in that > version. > > Alex Scalar::Util bug reports have already been posted several times, both with Fedora 8 and RHEL 5: https://bugzilla.redhat.com/show_bug.cgi?id=375621 https://bugzilla.redhat.com/show_bug.cgi?id=335481 https://bugzilla.redhat.com/show_bug.cgi?id=434574 The first bug apparently is still pending. This doesn't include duplicate reports either. Unfortunately this appears to be a common issue with Fedora/RH. I'm not sure why they consistently ship perl with an apparently broken Scalar::Util (which is part of the perl core lib since 5.8 and is tested for weaken() and other XS-based methods, so should fail). The module apparently compiles w/o problems. chris From alexl at users.sourceforge.net Sat Jul 5 00:05:48 2008 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Fri, 04 Jul 2008 21:05:48 -0700 Subject: [Bioperl-l] Install help errors In-Reply-To: <7713F291-EA5E-45CD-91EE-338DFBFF7BF4@uiuc.edu> (Chris Fields's message of "Fri\, 4 Jul 2008 22\:41\:15 -0500") References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <536f21b00807021313l6cec00devfd452db661ec1449@mail.gmail.com> <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> <628aabb70807030208y183e7ca7rb3f37f491b5fb6e3@mail.gmail.com> <486DED61.9020800@sendu.me.uk> <77vdzmvuhv.fsf@allele2.eebweb.arizona.edu> <7713F291-EA5E-45CD-91EE-338DFBFF7BF4@uiuc.edu> Message-ID: >>>>> "CF" == Chris Fields writes: [...] >> $ rpm -q --whatprovides 'perl(Scalar::Util)' >> perl-5.10.0-27.fc9.i386 >> Feel free to Cc me on the bug. Once fixed in perl 5.10, we could >> look into backporting the fix to F-8 which still ships with perl >> 5.8. [...] CF> Scalar::Util bug reports have already been posted several times, CF> both with Fedora 8 and RHEL 5: OK, thanks for the bugzilla pointers. CF> https://bugzilla.redhat.com/show_bug.cgi?id=375621 That's a RHEL bug. Not much a Fedora contributor can do to influence that bug, unfortunately, hopefully they will fix it in time (also perl-bioperl hasn't been branched for EPEL, which is "Extras for RHEL" as yet). CF> https://bugzilla.redhat.com/show_bug.cgi?id=335481 That bug seems to have been closed as not a bug, possibly because of mixing between CPAN and Fedora compiled bits. CF> https://bugzilla.redhat.com/show_bug.cgi?id=434574 This bug seems to indicate that the problem was fixed in perl-5.8.8-36.fc8 which was released back in March. CF> The first bug apparently is still pending. This doesn't include CF> duplicate reports either. CF> Unfortunately this appears to be a common issue with Fedora/RH. CF> I'm not sure why they consistently ship perl with an apparently CF> broken Scalar::Util (which is part of the perl core lib since 5.8 CF> and is tested for weaken() and other XS-based methods, so should CF> fail). The module apparently compiles w/o problems. If this this can be duplicated on Fedora in Perl later than perl-5.8.8-36.fc8 then https://bugzilla.redhat.com/show_bug.cgi?id=434574 should probably be re-opened, but at least looking at that bug it seems the issue *was* fixed in that version, so hopefully Fedora hasn't "consistently" been shipping a broken version of Perl since then. Alex From bix at sendu.me.uk Sat Jul 5 05:43:02 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Sat, 05 Jul 2008 10:43:02 +0100 Subject: [Bioperl-l] Install help errors In-Reply-To: References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <536f21b00807021313l6cec00devfd452db661ec1449@mail.gmail.com> <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> <628aabb70807030208y183e7ca7rb3f37f491b5fb6e3@mail.gmail.com> <486DED61.9020800@sendu.me.uk> <77vdzmvuhv.fsf@allele2.eebweb.arizona.edu> <7713F291-EA5E-45CD-91EE-338DFBFF7BF4@uiuc.edu> Message-ID: <486F4226.4040302@sendu.me.uk> Alex Lancaster wrote: > should probably be re-opened, but at least looking at that bug it > seems the issue *was* fixed in that version, so hopefully Fedora > hasn't "consistently" been shipping a broken version of Perl since > then. So, advice to people with the problem should be? yum update perl ?? is this likely to solve the issue regardless of what version of fedora they're using? If that doesn't work: cpan force install Scalar::Util From alexl at users.sourceforge.net Sat Jul 5 06:13:43 2008 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Sat, 05 Jul 2008 03:13:43 -0700 Subject: [Bioperl-l] Install help errors In-Reply-To: <486F4226.4040302@sendu.me.uk> (Sendu Bala's message of "Sat\, 05 Jul 2008 10\:43\:02 +0100") References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <536f21b00807021313l6cec00devfd452db661ec1449@mail.gmail.com> <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> <628aabb70807030208y183e7ca7rb3f37f491b5fb6e3@mail.gmail.com> <486DED61.9020800@sendu.me.uk> <77vdzmvuhv.fsf@allele2.eebweb.arizona.edu> <7713F291-EA5E-45CD-91EE-338DFBFF7BF4@uiuc.edu> <486F4226.4040302@sendu.me.uk> Message-ID: <9lk0gtz8o.fsf@allele2.eebweb.arizona.edu> >>>>> "SB" == Sendu Bala writes: SB> Alex Lancaster wrote: >> should probably be re-opened, but at least looking at that bug it >> seems the issue *was* fixed in that version, so hopefully Fedora >> hasn't "consistently" been shipping a broken version of Perl since >> then. SB> So, advice to people with the problem should be? Without knowing what version of Perl and Fedora they are using it's hard to say (see below). SB> yum update perl ?? Just: "yum update". In general, people should be continually updating their system, so if they are up-to-date they should be fine. F-7: the last update of Perl appears to be perl-5.8.8-30.fc7, which doesn't appear to have the fix. F-7 is now end-of-lifed, so no new updates to fix this are possible, all users are advised to upgrade to at least F-8, but preferrably F-9. F-8: current update is perl-5.8.8-40 and the fix was introduced into perl-5.8.8-35, so if the F-8 is system is up to date you should be good to go, I ran the test suggested in one this bug report: https://bugzilla.redhat.com/show_bug.cgi?id=434574 on my F-8 box: $ perl -MCompress::Zlib -e 0 and it runs without error. F-9: ships with perl-5.10, not sure if this problem affects perl 5.10, but "perl -MCompress::Zlib -e 0" also runs without error on my F-9 box. SB> is this likely to solve the issue regardless of what version of SB> fedora they're using? Bottom line: assuming the fix in perl-5.8.8-35 (and later) did the trick, then just make sure your are running on F-8 or later and be fully up to date (using "yum update" or pup/packagekit, which should be standard practice for all Fedora users anyway). SB> If that doesn't work: SB> cpan force install Scalar::Util Please don't recommend that they do that because it will mess up the installed Perl. If they are on F-7, upgrade to F-8 or later. If there is still an error, ask them to re-open this bug: https://bugzilla.redhat.com/show_bug.cgi?id=434574 Alex From hlapp at gmx.net Sun Jul 6 19:10:24 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Sun, 6 Jul 2008 19:10:24 -0400 Subject: [Bioperl-l] Install help errors In-Reply-To: <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <536f21b00807021313l6cec00devfd452db661ec1449@mail.gmail.com> <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> Message-ID: <3B7F44AA-1950-472C-B2D5-5AFEA360D431@gmx.net> Thanks to everyone who chimed in on this report. Snoze Pa - let us know if the responses didn't resolve the issue for you. -hilmar On Jul 2, 2008, at 4:49 PM, snoze pa wrote: > I used the latest rpm shipped with fedora 9. > > Next I removed the bioperl from fedora 9 and try to installed it from > the CPAN.. it worked fine but thr bioperl-db again give me following > messages using cpan. Seems nothing working properly! > > thanks a lot for your help. > > > > Test Summary Report > ------------------- > t/01dbadaptor (Wstat: 512 Tests: 0 Failed: 0) > Non-zero exit status: 2 > Parse errors: Bad plan. You planned 19 tests but ran 0. > t/02species (Wstat: 512 Tests: 0 Failed: 0) > Non-zero exit status: 2 > Parse errors: Bad plan. You planned 65 tests but ran 0. > t/03simpleseq (Wstat: 512 Tests: 0 Failed: 0) > Non-zero exit status: 2 > Parse errors: Bad plan. You planned 59 tests but ran 0. > t/04swiss (Wstat: 512 Tests: 0 Failed: 0) > Non-zero exit status: 2 > Parse errors: Bad plan. You planned 52 tests but ran 0. > t/05seqfeature (Wstat: 512 Tests: 0 Failed: 0) > Non-zero exit status: 2 > Parse errors: Bad plan. You planned 48 tests but ran 0. > t/06comment (Wstat: 512 Tests: 0 Failed: 0) > Non-zero exit status: 2 > Parse errors: Bad plan. You planned 11 tests but ran 0. > t/07dblink (Wstat: 512 Tests: 0 Failed: 0) > Non-zero exit status: 2 > Parse errors: Bad plan. You planned 18 tests but ran 0. > t/08genbank (Wstat: 512 Tests: 0 Failed: 0) > Non-zero exit status: 2 > Parse errors: Bad plan. You planned 18 tests but ran 0. > t/09fuzzy2 (Wstat: 512 Tests: 0 Failed: 0) > Non-zero exit status: 2 > Parse errors: Bad plan. You planned 21 tests but ran 0. > t/10ensembl (Wstat: 512 Tests: 0 Failed: 0) > Non-zero exit status: 2 > Parse errors: Bad plan. You planned 15 tests but ran 0. > t/11locuslink (Wstat: 512 Tests: 0 Failed: 0) > Non-zero exit status: 2 > Parse errors: Bad plan. You planned 110 tests but ran 0. > t/12ontology (Wstat: 512 Tests: 0 Failed: 0) > Non-zero exit status: 2 > Parse errors: Bad plan. You planned 738 tests but ran 0. > t/13remove (Wstat: 512 Tests: 0 Failed: 0) > Non-zero exit status: 2 > Parse errors: Bad plan. You planned 59 tests but ran 0. > t/14query (Wstat: 512 Tests: 0 Failed: 0) > Non-zero exit status: 2 > Parse errors: Bad plan. You planned 18 tests but ran 0. > t/15cluster (Wstat: 512 Tests: 0 Failed: 0) > Non-zero exit status: 2 > Parse errors: Bad plan. You planned 160 tests but ran 0. > t/16obda (Wstat: 512 Tests: 0 Failed: 0) > Non-zero exit status: 2 > Parse errors: Bad plan. You planned 12 tests but ran 0. > Files=16, Tests=0, 2 wallclock secs ( 0.09 usr 0.06 sys + 1.19 cusr > 0.20 csys = 1.54 CPU) > Result: FAIL > Failed 16/16 test programs. 0/0 subtests failed. > SENDU/bioperl-db-1.5.2_100.tar.gz > ./Build test -- NOT OK > //hint// to see the cpan-testers results for installing this module, > try: > reports SENDU/bioperl-db-1.5.2_100.tar.gz > Warning (usually harmless): 'YAML' not installed, will not store > persistent state > Running Build install > make test had returned bad status, won't install without force > Failed during this command: > BIRNEY/bioperl-1.4.tar.gz : make_test NO > SENDU/bioperl-db-1.5.2_100.tar.gz : make_test NO > > On Wed, Jul 2, 2008 at 3:13 PM, Scott Cain > wrote: >> Hello, >> >> When you say you installed the BioPerl RPM, do you mean the one at >> biopackages.net? It is very old and the likely problem you are >> running into is that it is too old to work with the version of BioSQL >> you have. >> >> Scott >> >> >> On Wed, Jul 2, 2008 at 3:56 PM, snoze pa wrote: >>> Dear Users, >>> I am trying to install bioperl in fedora machine. I am using >>> precompiled rpm from fedora repo. it is installed. Next I download >>> the >>> biosql and put in a dir /usr/local/biosql >>> create a database bioseqdb and load the scema. >>> >>> However the bioperl-db is not working.. it is giving lots of >>> error. I >>> used CPAN and also the perl Build.PL. following are the results >>> >>> Please help me. >>> thank you. >>> >>> >>> Test Summary Report >>> ------------------- >>> t/04swiss (Wstat: 65280 Tests: 5 Failed: 0) >>> Non-zero exit status: 255 >>> Parse errors: Bad plan. You planned 52 tests but ran 5. >>> t/05seqfeature (Wstat: 65280 Tests: 3 Failed: 0) >>> Non-zero exit status: 255 >>> Parse errors: Bad plan. You planned 48 tests but ran 3. >>> t/06comment (Wstat: 65280 Tests: 2 Failed: 0) >>> Non-zero exit status: 255 >>> Parse errors: Bad plan. You planned 11 tests but ran 2. >>> t/07dblink (Wstat: 65280 Tests: 2 Failed: 0) >>> Non-zero exit status: 255 >>> Parse errors: Bad plan. You planned 18 tests but ran 2. >>> t/08genbank (Wstat: 65280 Tests: 2 Failed: 0) >>> Non-zero exit status: 255 >>> Parse errors: Bad plan. You planned 18 tests but ran 2. >>> t/09fuzzy2 (Wstat: 65280 Tests: 2 Failed: 0) >>> Non-zero exit status: 255 >>> Parse errors: Bad plan. You planned 21 tests but ran 2. >>> t/10ensembl (Wstat: 65280 Tests: 2 Failed: 0) >>> Non-zero exit status: 255 >>> Parse errors: Bad plan. You planned 15 tests but ran 2. >>> t/11locuslink (Wstat: 65280 Tests: 4 Failed: 0) >>> Non-zero exit status: 255 >>> Parse errors: Bad plan. You planned 110 tests but ran 4. >>> t/12ontology (Wstat: 65280 Tests: 4 Failed: 0) >>> Non-zero exit status: 255 >>> Parse errors: Bad plan. You planned 738 tests but ran 4. >>> t/13remove (Wstat: 0 Tests: 4 Failed: 1) >>> Failed test: 4 >>> Parse errors: Bad plan. You planned 59 tests but ran 4. >>> t/15cluster (Wstat: 65280 Tests: 5 Failed: 0) >>> Non-zero exit status: 255 >>> Parse errors: Bad plan. You planned 160 tests but ran 5. >>> t/16obda (Wstat: 65280 Tests: 2 Failed: 0) >>> Non-zero exit status: 255 >>> Parse errors: Bad plan. You planned 12 tests but ran 2. >>> Files=16, Tests=198, 26 wallclock secs ( 0.21 usr 0.07 sys + 22.81 >>> cusr 1.25 csys = 24.34 CPU) >>> Result: FAIL >>> Failed 12/16 test programs. 1/198 subtests failed. >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. cain.cshl at gmail.com >> GMOD Coordinator (http://www.gmod.org/) 216-392-3087 >> Cold Spring Harbor Laboratory >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From snoze.pa at gmail.com Mon Jul 7 12:23:21 2008 From: snoze.pa at gmail.com (snoze pa) Date: Mon, 7 Jul 2008 11:23:21 -0500 Subject: [Bioperl-l] Install help errors In-Reply-To: <3B7F44AA-1950-472C-B2D5-5AFEA360D431@gmx.net> References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <536f21b00807021313l6cec00devfd452db661ec1449@mail.gmail.com> <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> <3B7F44AA-1950-472C-B2D5-5AFEA360D431@gmx.net> Message-ID: <10f848910807070923m5d1d2f53l75035a46905252a6@mail.gmail.com> Dear Users, Thank you very much for you timely support. I highly appreciate your help in installing the software. Meanwhile during the installation of bioperl-db and loading load_seqdatabase.pl, it ask me to use the dbname "biosql" while the database created in during bioperl installation is "bioseqdb". Shall I use bioseqdb instead of biosql as dbname. Thank you, s On Sun, Jul 6, 2008 at 6:10 PM, Hilmar Lapp wrote: > Thanks to everyone who chimed in on this report. > > Snoze Pa - let us know if the responses didn't resolve the issue for you. > > -hilmar > > On Jul 2, 2008, at 4:49 PM, snoze pa wrote: > >> I used the latest rpm shipped with fedora 9. >> >> Next I removed the bioperl from fedora 9 and try to installed it from >> the CPAN.. it worked fine but thr bioperl-db again give me following >> messages using cpan. Seems nothing working properly! >> >> thanks a lot for your help. >> >> >> >> Test Summary Report >> ------------------- >> t/01dbadaptor (Wstat: 512 Tests: 0 Failed: 0) >> Non-zero exit status: 2 >> Parse errors: Bad plan. You planned 19 tests but ran 0. >> t/02species (Wstat: 512 Tests: 0 Failed: 0) >> Non-zero exit status: 2 >> Parse errors: Bad plan. You planned 65 tests but ran 0. >> t/03simpleseq (Wstat: 512 Tests: 0 Failed: 0) >> Non-zero exit status: 2 >> Parse errors: Bad plan. You planned 59 tests but ran 0. >> t/04swiss (Wstat: 512 Tests: 0 Failed: 0) >> Non-zero exit status: 2 >> Parse errors: Bad plan. You planned 52 tests but ran 0. >> t/05seqfeature (Wstat: 512 Tests: 0 Failed: 0) >> Non-zero exit status: 2 >> Parse errors: Bad plan. You planned 48 tests but ran 0. >> t/06comment (Wstat: 512 Tests: 0 Failed: 0) >> Non-zero exit status: 2 >> Parse errors: Bad plan. You planned 11 tests but ran 0. >> t/07dblink (Wstat: 512 Tests: 0 Failed: 0) >> Non-zero exit status: 2 >> Parse errors: Bad plan. You planned 18 tests but ran 0. >> t/08genbank (Wstat: 512 Tests: 0 Failed: 0) >> Non-zero exit status: 2 >> Parse errors: Bad plan. You planned 18 tests but ran 0. >> t/09fuzzy2 (Wstat: 512 Tests: 0 Failed: 0) >> Non-zero exit status: 2 >> Parse errors: Bad plan. You planned 21 tests but ran 0. >> t/10ensembl (Wstat: 512 Tests: 0 Failed: 0) >> Non-zero exit status: 2 >> Parse errors: Bad plan. You planned 15 tests but ran 0. >> t/11locuslink (Wstat: 512 Tests: 0 Failed: 0) >> Non-zero exit status: 2 >> Parse errors: Bad plan. You planned 110 tests but ran 0. >> t/12ontology (Wstat: 512 Tests: 0 Failed: 0) >> Non-zero exit status: 2 >> Parse errors: Bad plan. You planned 738 tests but ran 0. >> t/13remove (Wstat: 512 Tests: 0 Failed: 0) >> Non-zero exit status: 2 >> Parse errors: Bad plan. You planned 59 tests but ran 0. >> t/14query (Wstat: 512 Tests: 0 Failed: 0) >> Non-zero exit status: 2 >> Parse errors: Bad plan. You planned 18 tests but ran 0. >> t/15cluster (Wstat: 512 Tests: 0 Failed: 0) >> Non-zero exit status: 2 >> Parse errors: Bad plan. You planned 160 tests but ran 0. >> t/16obda (Wstat: 512 Tests: 0 Failed: 0) >> Non-zero exit status: 2 >> Parse errors: Bad plan. You planned 12 tests but ran 0. >> Files=16, Tests=0, 2 wallclock secs ( 0.09 usr 0.06 sys + 1.19 cusr >> 0.20 csys = 1.54 CPU) >> Result: FAIL >> Failed 16/16 test programs. 0/0 subtests failed. >> SENDU/bioperl-db-1.5.2_100.tar.gz >> ./Build test -- NOT OK >> //hint// to see the cpan-testers results for installing this module, try: >> reports SENDU/bioperl-db-1.5.2_100.tar.gz >> Warning (usually harmless): 'YAML' not installed, will not store >> persistent state >> Running Build install >> make test had returned bad status, won't install without force >> Failed during this command: >> BIRNEY/bioperl-1.4.tar.gz : make_test NO >> SENDU/bioperl-db-1.5.2_100.tar.gz : make_test NO >> >> On Wed, Jul 2, 2008 at 3:13 PM, Scott Cain wrote: >>> >>> Hello, >>> >>> When you say you installed the BioPerl RPM, do you mean the one at >>> biopackages.net? It is very old and the likely problem you are >>> running into is that it is too old to work with the version of BioSQL >>> you have. >>> >>> Scott >>> >>> >>> On Wed, Jul 2, 2008 at 3:56 PM, snoze pa wrote: >>>> >>>> Dear Users, >>>> I am trying to install bioperl in fedora machine. I am using >>>> precompiled rpm from fedora repo. it is installed. Next I download the >>>> biosql and put in a dir /usr/local/biosql >>>> create a database bioseqdb and load the scema. >>>> >>>> However the bioperl-db is not working.. it is giving lots of error. I >>>> used CPAN and also the perl Build.PL. following are the results >>>> >>>> Please help me. >>>> thank you. >>>> >>>> >>>> Test Summary Report >>>> ------------------- >>>> t/04swiss (Wstat: 65280 Tests: 5 Failed: 0) >>>> Non-zero exit status: 255 >>>> Parse errors: Bad plan. You planned 52 tests but ran 5. >>>> t/05seqfeature (Wstat: 65280 Tests: 3 Failed: 0) >>>> Non-zero exit status: 255 >>>> Parse errors: Bad plan. You planned 48 tests but ran 3. >>>> t/06comment (Wstat: 65280 Tests: 2 Failed: 0) >>>> Non-zero exit status: 255 >>>> Parse errors: Bad plan. You planned 11 tests but ran 2. >>>> t/07dblink (Wstat: 65280 Tests: 2 Failed: 0) >>>> Non-zero exit status: 255 >>>> Parse errors: Bad plan. You planned 18 tests but ran 2. >>>> t/08genbank (Wstat: 65280 Tests: 2 Failed: 0) >>>> Non-zero exit status: 255 >>>> Parse errors: Bad plan. You planned 18 tests but ran 2. >>>> t/09fuzzy2 (Wstat: 65280 Tests: 2 Failed: 0) >>>> Non-zero exit status: 255 >>>> Parse errors: Bad plan. You planned 21 tests but ran 2. >>>> t/10ensembl (Wstat: 65280 Tests: 2 Failed: 0) >>>> Non-zero exit status: 255 >>>> Parse errors: Bad plan. You planned 15 tests but ran 2. >>>> t/11locuslink (Wstat: 65280 Tests: 4 Failed: 0) >>>> Non-zero exit status: 255 >>>> Parse errors: Bad plan. You planned 110 tests but ran 4. >>>> t/12ontology (Wstat: 65280 Tests: 4 Failed: 0) >>>> Non-zero exit status: 255 >>>> Parse errors: Bad plan. You planned 738 tests but ran 4. >>>> t/13remove (Wstat: 0 Tests: 4 Failed: 1) >>>> Failed test: 4 >>>> Parse errors: Bad plan. You planned 59 tests but ran 4. >>>> t/15cluster (Wstat: 65280 Tests: 5 Failed: 0) >>>> Non-zero exit status: 255 >>>> Parse errors: Bad plan. You planned 160 tests but ran 5. >>>> t/16obda (Wstat: 65280 Tests: 2 Failed: 0) >>>> Non-zero exit status: 255 >>>> Parse errors: Bad plan. You planned 12 tests but ran 2. >>>> Files=16, Tests=198, 26 wallclock secs ( 0.21 usr 0.07 sys + 22.81 >>>> cusr 1.25 csys = 24.34 CPU) >>>> Result: FAIL >>>> Failed 12/16 test programs. 1/198 subtests failed. >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> >>> >>> -- >>> ------------------------------------------------------------------------ >>> Scott Cain, Ph. D. cain.cshl at gmail.com >>> GMOD Coordinator (http://www.gmod.org/) 216-392-3087 >>> Cold Spring Harbor Laboratory >>> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > From hlapp at gmx.net Mon Jul 7 16:12:32 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 7 Jul 2008 16:12:32 -0400 Subject: [Bioperl-l] Install help errors In-Reply-To: <10f848910807070923m5d1d2f53l75035a46905252a6@mail.gmail.com> References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <536f21b00807021313l6cec00devfd452db661ec1449@mail.gmail.com> <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> <3B7F44AA-1950-472C-B2D5-5AFEA360D431@gmx.net> <10f848910807070923m5d1d2f53l75035a46905252a6@mail.gmail.com> Message-ID: <3A1A91BC-253F-4883-A833-0127300B5DD1@gmx.net> You may use any name for the database - is there some piece of documentation that prompted you to conclude that this parameter isn't under your control? There should be a command-line parameter (-- namespace) in load_seqdatabase.pl -hilmar On Jul 7, 2008, at 12:23 PM, snoze pa wrote: > Dear Users, > Thank you very much for you timely support. I highly appreciate your > help in installing the software. Meanwhile during the installation > of bioperl-db and loading load_seqdatabase.pl, it ask me to use the > dbname "biosql" while the database created in during bioperl > installation is "bioseqdb". Shall I use bioseqdb instead of biosql as > dbname. > Thank you, > s > > > On Sun, Jul 6, 2008 at 6:10 PM, Hilmar Lapp wrote: >> Thanks to everyone who chimed in on this report. >> >> Snoze Pa - let us know if the responses didn't resolve the issue >> for you. >> >> -hilmar >> >> On Jul 2, 2008, at 4:49 PM, snoze pa wrote: >> >>> I used the latest rpm shipped with fedora 9. >>> >>> Next I removed the bioperl from fedora 9 and try to installed it >>> from >>> the CPAN.. it worked fine but thr bioperl-db again give me following >>> messages using cpan. Seems nothing working properly! >>> >>> thanks a lot for your help. >>> >>> >>> >>> Test Summary Report >>> ------------------- >>> t/01dbadaptor (Wstat: 512 Tests: 0 Failed: 0) >>> Non-zero exit status: 2 >>> Parse errors: Bad plan. You planned 19 tests but ran 0. >>> t/02species (Wstat: 512 Tests: 0 Failed: 0) >>> Non-zero exit status: 2 >>> Parse errors: Bad plan. You planned 65 tests but ran 0. >>> t/03simpleseq (Wstat: 512 Tests: 0 Failed: 0) >>> Non-zero exit status: 2 >>> Parse errors: Bad plan. You planned 59 tests but ran 0. >>> t/04swiss (Wstat: 512 Tests: 0 Failed: 0) >>> Non-zero exit status: 2 >>> Parse errors: Bad plan. You planned 52 tests but ran 0. >>> t/05seqfeature (Wstat: 512 Tests: 0 Failed: 0) >>> Non-zero exit status: 2 >>> Parse errors: Bad plan. You planned 48 tests but ran 0. >>> t/06comment (Wstat: 512 Tests: 0 Failed: 0) >>> Non-zero exit status: 2 >>> Parse errors: Bad plan. You planned 11 tests but ran 0. >>> t/07dblink (Wstat: 512 Tests: 0 Failed: 0) >>> Non-zero exit status: 2 >>> Parse errors: Bad plan. You planned 18 tests but ran 0. >>> t/08genbank (Wstat: 512 Tests: 0 Failed: 0) >>> Non-zero exit status: 2 >>> Parse errors: Bad plan. You planned 18 tests but ran 0. >>> t/09fuzzy2 (Wstat: 512 Tests: 0 Failed: 0) >>> Non-zero exit status: 2 >>> Parse errors: Bad plan. You planned 21 tests but ran 0. >>> t/10ensembl (Wstat: 512 Tests: 0 Failed: 0) >>> Non-zero exit status: 2 >>> Parse errors: Bad plan. You planned 15 tests but ran 0. >>> t/11locuslink (Wstat: 512 Tests: 0 Failed: 0) >>> Non-zero exit status: 2 >>> Parse errors: Bad plan. You planned 110 tests but ran 0. >>> t/12ontology (Wstat: 512 Tests: 0 Failed: 0) >>> Non-zero exit status: 2 >>> Parse errors: Bad plan. You planned 738 tests but ran 0. >>> t/13remove (Wstat: 512 Tests: 0 Failed: 0) >>> Non-zero exit status: 2 >>> Parse errors: Bad plan. You planned 59 tests but ran 0. >>> t/14query (Wstat: 512 Tests: 0 Failed: 0) >>> Non-zero exit status: 2 >>> Parse errors: Bad plan. You planned 18 tests but ran 0. >>> t/15cluster (Wstat: 512 Tests: 0 Failed: 0) >>> Non-zero exit status: 2 >>> Parse errors: Bad plan. You planned 160 tests but ran 0. >>> t/16obda (Wstat: 512 Tests: 0 Failed: 0) >>> Non-zero exit status: 2 >>> Parse errors: Bad plan. You planned 12 tests but ran 0. >>> Files=16, Tests=0, 2 wallclock secs ( 0.09 usr 0.06 sys + 1.19 >>> cusr >>> 0.20 csys = 1.54 CPU) >>> Result: FAIL >>> Failed 16/16 test programs. 0/0 subtests failed. >>> SENDU/bioperl-db-1.5.2_100.tar.gz >>> ./Build test -- NOT OK >>> //hint// to see the cpan-testers results for installing this >>> module, try: >>> reports SENDU/bioperl-db-1.5.2_100.tar.gz >>> Warning (usually harmless): 'YAML' not installed, will not store >>> persistent state >>> Running Build install >>> make test had returned bad status, won't install without force >>> Failed during this command: >>> BIRNEY/bioperl-1.4.tar.gz : make_test NO >>> SENDU/bioperl-db-1.5.2_100.tar.gz : make_test NO >>> >>> On Wed, Jul 2, 2008 at 3:13 PM, Scott Cain >>> wrote: >>>> >>>> Hello, >>>> >>>> When you say you installed the BioPerl RPM, do you mean the one at >>>> biopackages.net? It is very old and the likely problem you are >>>> running into is that it is too old to work with the version of >>>> BioSQL >>>> you have. >>>> >>>> Scott >>>> >>>> >>>> On Wed, Jul 2, 2008 at 3:56 PM, snoze pa >>>> wrote: >>>>> >>>>> Dear Users, >>>>> I am trying to install bioperl in fedora machine. I am using >>>>> precompiled rpm from fedora repo. it is installed. Next I >>>>> download the >>>>> biosql and put in a dir /usr/local/biosql >>>>> create a database bioseqdb and load the scema. >>>>> >>>>> However the bioperl-db is not working.. it is giving lots of >>>>> error. I >>>>> used CPAN and also the perl Build.PL. following are the results >>>>> >>>>> Please help me. >>>>> thank you. >>>>> >>>>> >>>>> Test Summary Report >>>>> ------------------- >>>>> t/04swiss (Wstat: 65280 Tests: 5 Failed: 0) >>>>> Non-zero exit status: 255 >>>>> Parse errors: Bad plan. You planned 52 tests but ran 5. >>>>> t/05seqfeature (Wstat: 65280 Tests: 3 Failed: 0) >>>>> Non-zero exit status: 255 >>>>> Parse errors: Bad plan. You planned 48 tests but ran 3. >>>>> t/06comment (Wstat: 65280 Tests: 2 Failed: 0) >>>>> Non-zero exit status: 255 >>>>> Parse errors: Bad plan. You planned 11 tests but ran 2. >>>>> t/07dblink (Wstat: 65280 Tests: 2 Failed: 0) >>>>> Non-zero exit status: 255 >>>>> Parse errors: Bad plan. You planned 18 tests but ran 2. >>>>> t/08genbank (Wstat: 65280 Tests: 2 Failed: 0) >>>>> Non-zero exit status: 255 >>>>> Parse errors: Bad plan. You planned 18 tests but ran 2. >>>>> t/09fuzzy2 (Wstat: 65280 Tests: 2 Failed: 0) >>>>> Non-zero exit status: 255 >>>>> Parse errors: Bad plan. You planned 21 tests but ran 2. >>>>> t/10ensembl (Wstat: 65280 Tests: 2 Failed: 0) >>>>> Non-zero exit status: 255 >>>>> Parse errors: Bad plan. You planned 15 tests but ran 2. >>>>> t/11locuslink (Wstat: 65280 Tests: 4 Failed: 0) >>>>> Non-zero exit status: 255 >>>>> Parse errors: Bad plan. You planned 110 tests but ran 4. >>>>> t/12ontology (Wstat: 65280 Tests: 4 Failed: 0) >>>>> Non-zero exit status: 255 >>>>> Parse errors: Bad plan. You planned 738 tests but ran 4. >>>>> t/13remove (Wstat: 0 Tests: 4 Failed: 1) >>>>> Failed test: 4 >>>>> Parse errors: Bad plan. You planned 59 tests but ran 4. >>>>> t/15cluster (Wstat: 65280 Tests: 5 Failed: 0) >>>>> Non-zero exit status: 255 >>>>> Parse errors: Bad plan. You planned 160 tests but ran 5. >>>>> t/16obda (Wstat: 65280 Tests: 2 Failed: 0) >>>>> Non-zero exit status: 255 >>>>> Parse errors: Bad plan. You planned 12 tests but ran 2. >>>>> Files=16, Tests=198, 26 wallclock secs ( 0.21 usr 0.07 sys + >>>>> 22.81 >>>>> cusr 1.25 csys = 24.34 CPU) >>>>> Result: FAIL >>>>> Failed 12/16 test programs. 1/198 subtests failed. >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> >>>> >>>> >>>> -- >>>> ------------------------------------------------------------------------ >>>> Scott Cain, Ph. D. cain.cshl at gmail.com >>>> GMOD Coordinator (http://www.gmod.org/) 216-392-3087 >>>> Cold Spring Harbor Laboratory >>>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >> =========================================================== >> >> >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From bix at sendu.me.uk Mon Jul 7 17:20:23 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 07 Jul 2008 22:20:23 +0100 Subject: [Bioperl-l] Install help errors In-Reply-To: <3A1A91BC-253F-4883-A833-0127300B5DD1@gmx.net> References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <536f21b00807021313l6cec00devfd452db661ec1449@mail.gmail.com> <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> <3B7F44AA-1950-472C-B2D5-5AFEA360D431@gmx.net> <10f848910807070923m5d1d2f53l75035a46905252a6@mail.gmail.com> <3A1A91BC-253F-4883-A833-0127300B5DD1@gmx.net> Message-ID: <48728897.7090103@sendu.me.uk> Hilmar Lapp wrote: > You may use any name for the database - is there some piece of > documentation that prompted you to conclude that this parameter isn't > under your control? There should be a command-line parameter > (--namespace) in load_seqdatabase.pl For what its worth, I was caught out by this as well. It would be a little more friendly if the documentation for biosql and bioperl-db were consistent in their suggestions for what to call the database. When you don't really have any idea what's going on, you at least want to be able to copy/paste the suggested commands/code ;) > On Jul 7, 2008, at 12:23 PM, snoze pa wrote: > >> Dear Users, >> Thank you very much for you timely support. I highly appreciate your >> help in installing the software. Meanwhile during the installation >> of bioperl-db and loading load_seqdatabase.pl, it ask me to use the >> dbname "biosql" while the database created in during bioperl >> installation is "bioseqdb". Shall I use bioseqdb instead of biosql as >> dbname. From snoze.pa at gmail.com Tue Jul 8 11:29:49 2008 From: snoze.pa at gmail.com (snoze pa) Date: Tue, 8 Jul 2008 10:29:49 -0500 Subject: [Bioperl-l] Install help errors In-Reply-To: <48728897.7090103@sendu.me.uk> References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <536f21b00807021313l6cec00devfd452db661ec1449@mail.gmail.com> <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> <3B7F44AA-1950-472C-B2D5-5AFEA360D431@gmx.net> <10f848910807070923m5d1d2f53l75035a46905252a6@mail.gmail.com> <3A1A91BC-253F-4883-A833-0127300B5DD1@gmx.net> <48728897.7090103@sendu.me.uk> Message-ID: <10f848910807080829v111a1072p63bd82e546cc9c6a@mail.gmail.com> I agree with you. There is no clean installation help of the bioperl/biosql/bioperl-db available. If you read the biosql INSTALL file and follow what is written then you will find database name biosql. However if you read the mysql entry in same page then you will find the name of the data base is bioseqdb. For new bee in the area it is not only difficult but also confusing. I am trying a clean installation of bioperl/biosql/bioseqdb but still there is no success. If I assume the installation is done then it always crash on DBSOURCE entry. The load_sequencedb.pl crashes every time when I encounter with sequences like LOCUS P27912 792 aa linear VRL 10-JUN-2008 DEFINITION Genome polyprotein [Contains: Protein C (Core protein) (Capsid protein); prM; Peptide pr; Small envelope protein M (Matrix protein); Envelope protein E; Non-structural protein 1 (NS1)]. ACCESSION P27912 VERSION P27912.1 GI:130422 DBSOURCE swissprot: locus POLG_DEN1A, accession P27912; class: standard. created: Aug 1, 1992. sequence updated: Aug 1, 1992. annotation updated: Jun 10, 2008. xrefs: D00502.1, BAA00394.1, B32401 xrefs (non-sequence databases): HSSP:Q88653, SMR:P27912, GO:0005789, InterPro:IPR011999, InterPro:IPR013754, InterPro:IPR001122, InterPro:IPR000069, InterPro:IPR001157, InterPro:IPR002535, InterPro:IPR000336, Gene3D:G3DSA:2.60.98.10, Gene3D:G3DSA:2.60.40.350, Pfam:PF01003, Pfam:PF02832, Pfam:PF00869, Pfam:PF01004, Pfam:PF00948, Pfam:PF01570 KEYWORDS Capsid protein; Cleavage on pair of basic residues; Endoplasmic reticulum; Envelope protein; Glycoprotein; Membrane; Secreted; Transmembrane; Viral nucleoprotein; Virion. It can not parse the DBSOURCE entry. May be I am doing something wrong but It will great if someone can try to load P27912, entry of genbank to bioseqdb database. Please let me know if you can load the this genbank file. Thank you all for your Help. Best S On Mon, Jul 7, 2008 at 4:20 PM, Sendu Bala wrote: > Hilmar Lapp wrote: >> >> You may use any name for the database - is there some piece of >> documentation that prompted you to conclude that this parameter isn't under >> your control? There should be a command-line parameter (--namespace) in >> load_seqdatabase.pl > > For what its worth, I was caught out by this as well. It would be a little > more friendly if the documentation for biosql and bioperl-db were consistent > in their suggestions for what to call the database. > > When you don't really have any idea what's going on, you at least want to be > able to copy/paste the suggested commands/code ;) > > >> On Jul 7, 2008, at 12:23 PM, snoze pa wrote: >> >>> Dear Users, >>> Thank you very much for you timely support. I highly appreciate your >>> help in installing the software. Meanwhile during the installation >>> of bioperl-db and loading load_seqdatabase.pl, it ask me to use the >>> dbname "biosql" while the database created in during bioperl >>> installation is "bioseqdb". Shall I use bioseqdb instead of biosql as >>> dbname. > From hlapp at gmx.net Tue Jul 8 14:35:38 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 8 Jul 2008 14:35:38 -0400 Subject: [Bioperl-l] Install help errors In-Reply-To: <10f848910807080829v111a1072p63bd82e546cc9c6a@mail.gmail.com> References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <536f21b00807021313l6cec00devfd452db661ec1449@mail.gmail.com> <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> <3B7F44AA-1950-472C-B2D5-5AFEA360D431@gmx.net> <10f848910807070923m5d1d2f53l75035a46905252a6@mail.gmail.com> <3A1A91BC-253F-4883-A833-0127300B5DD1@gmx.net> <48728897.7090103@sendu.me.uk> <10f848910807080829v111a1072p63bd82e546cc9c6a@mail.gmail.com> Message-ID: <87B902CC-42E7-4646-844A-F047CC7CB7BF@gmx.net> On Jul 8, 2008, at 11:29 AM, snoze pa wrote: > I agree with you. There is no clean installation help of the > bioperl/biosql/bioperl-db available. If you read the biosql INSTALL > file and follow what is written then you will find database name > biosql. However if you read the mysql entry in same page then you will > find the name of the data base is bioseqdb. For new bee in the area it > is not only difficult but also confusing. That's useful feedback. In fact it sounds like there is a documentation bug (inconsistent documentation is a bug, IMHO). Would you mind filing a bug report (BioSQL has its own queue now)? > > > I am trying a clean installation of bioperl/biosql/bioseqdb but still > there is no success. If I assume the installation is done then it > always crash on DBSOURCE entry. The load_sequencedb.pl crashes every > time when I encounter with sequences like Could you post the error message? The entry you quote in reality is a Swissprot (or Uniprot) entry sucked up into GenPept, so it's possible that it's the BioPerl genbank parser that's failing, not bioperl-db. I recall that we've had issues with these records before, though I don't recall what the actual cause was, nor the recommended fix. Is there a requirement that prevents you from loading these entries in their native Uniprot format? -hilmar > > > LOCUS P27912 792 aa linear VRL > 10-JUN-2008 > DEFINITION Genome polyprotein [Contains: Protein C (Core protein) > (Capsid > protein); prM; Peptide pr; Small envelope protein M (Matrix > protein); Envelope protein E; Non-structural protein 1 > (NS1)]. > ACCESSION P27912 > VERSION P27912.1 GI:130422 > DBSOURCE swissprot: locus POLG_DEN1A, accession P27912; > class: standard. > created: Aug 1, 1992. > sequence updated: Aug 1, 1992. > annotation updated: Jun 10, 2008. > xrefs: D00502.1, BAA00394.1, B32401 > xrefs (non-sequence databases): HSSP:Q88653, SMR:P27912, > GO:0005789, InterPro:IPR011999, InterPro:IPR013754, > InterPro:IPR001122, InterPro:IPR000069, InterPro:IPR001157, > InterPro:IPR002535, InterPro:IPR000336, Gene3D:G3DSA: > 2.60.98.10, > Gene3D:G3DSA:2.60.40.350, Pfam:PF01003, Pfam:PF02832, > Pfam:PF00869, > Pfam:PF01004, Pfam:PF00948, Pfam:PF01570 > KEYWORDS Capsid protein; Cleavage on pair of basic residues; > Endoplasmic > reticulum; Envelope protein; Glycoprotein; Membrane; > Secreted; > Transmembrane; Viral nucleoprotein; Virion. > > > It can not parse the DBSOURCE entry. May be I am doing something > wrong but It will great if someone can try to load > P27912, entry of genbank to bioseqdb database. Please let me know if > you can load the this genbank file. > > Thank you all for your Help. > Best S > > > > On Mon, Jul 7, 2008 at 4:20 PM, Sendu Bala wrote: >> Hilmar Lapp wrote: >>> >>> You may use any name for the database - is there some piece of >>> documentation that prompted you to conclude that this parameter >>> isn't under >>> your control? There should be a command-line parameter (-- >>> namespace) in >>> load_seqdatabase.pl >> >> For what its worth, I was caught out by this as well. It would be a >> little >> more friendly if the documentation for biosql and bioperl-db were >> consistent >> in their suggestions for what to call the database. >> >> When you don't really have any idea what's going on, you at least >> want to be >> able to copy/paste the suggested commands/code ;) >> >> >>> On Jul 7, 2008, at 12:23 PM, snoze pa wrote: >>> >>>> Dear Users, >>>> Thank you very much for you timely support. I highly appreciate >>>> your >>>> help in installing the software. Meanwhile during the >>>> installation >>>> of bioperl-db and loading load_seqdatabase.pl, it ask me to use >>>> the >>>> dbname "biosql" while the database created in during bioperl >>>> installation is "bioseqdb". Shall I use bioseqdb instead of >>>> biosql as >>>> dbname. >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From snoze.pa at gmail.com Tue Jul 8 15:00:05 2008 From: snoze.pa at gmail.com (snoze pa) Date: Tue, 8 Jul 2008 14:00:05 -0500 Subject: [Bioperl-l] Install help errors In-Reply-To: <87B902CC-42E7-4646-844A-F047CC7CB7BF@gmx.net> References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <536f21b00807021313l6cec00devfd452db661ec1449@mail.gmail.com> <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> <3B7F44AA-1950-472C-B2D5-5AFEA360D431@gmx.net> <10f848910807070923m5d1d2f53l75035a46905252a6@mail.gmail.com> <3A1A91BC-253F-4883-A833-0127300B5DD1@gmx.net> <48728897.7090103@sendu.me.uk> <10f848910807080829v111a1072p63bd82e546cc9c6a@mail.gmail.com> <87B902CC-42E7-4646-844A-F047CC7CB7BF@gmx.net> Message-ID: <10f848910807081200q21d78b1q2e65b8a767844135@mail.gmail.com> Hilmar, I really had tough time dealing with bioperl-db and then loading the sequences. As we discussed earlier(long back) that DBSOURCE is crashing every time so I removed the gen bank installation. Currently I am loading uniprot_sprot.dat file which I downloaded from swissprot site. Based on the guideline in bio-perl website I am able to manage the bioperl/biosql/bioperl-db/ installation and then try to load the swissprot file, uniprot_sprot.dat, officially uniprot_sprot.dat.gz latest release july 7th 2008. It always give me a warning "insert in Bio::DB::BioSQL::SeqFeatureAdaptor (driver) failed," which I think okie as long the loading seq is fine. I can see it from SELECT * FROM biosequence but now it also crashes after loading 214 sequence from uniprot_sprot.dat file. Here is the error message --------------------------------------------------- Could not store P21215: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: The supplied lineage does not start near 'Clostridium sp.' (I was supplied 'sp. ATCC29733 | Clostridium | Clostridiaceae | Clostridiales | Clostridia |Firmicutes | Bacteria') STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/lib/perl5/site_perl/5.10.0/Bio/Root/Root.pm:359 STACK: Bio::Species::classification /usr/local/lib/perl5/site_perl/5.10.0/Bio/Species.pm:174 STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:552 STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/SpeciesAdaptor.pm:281 STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1305 STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:973 STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:852 STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:182 STACK: Bio::DB::Persistent::PersistentObject::create /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:244 STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:169 STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251 STACK: Bio::DB::Persistent::PersistentObject::store /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:271 STACK: /usr/local/bioperl-db/scripts/biosql/load_seqdatabase.pl:630 ----------------------------------------------------------- at /usr/local/bioperl-db/scripts/biosql/load_seqdatabase.pl line 643 If I remove this entry from uniprot_sprot.dat file then it gives similar error in other IDs Any Idea, Thanks a lot for your reply and help On Tue, Jul 8, 2008 at 1:35 PM, Hilmar Lapp wrote: > > On Jul 8, 2008, at 11:29 AM, snoze pa wrote: > >> I agree with you. There is no clean installation help of the >> bioperl/biosql/bioperl-db available. If you read the biosql INSTALL >> file and follow what is written then you will find database name >> biosql. However if you read the mysql entry in same page then you will >> find the name of the data base is bioseqdb. For new bee in the area it >> is not only difficult but also confusing. > > That's useful feedback. In fact it sounds like there is a documentation bug > (inconsistent documentation is a bug, IMHO). Would you mind filing a bug > report (BioSQL has its own queue now)? > >> >> >> I am trying a clean installation of bioperl/biosql/bioseqdb but still >> there is no success. If I assume the installation is done then it >> always crash on DBSOURCE entry. The load_sequencedb.pl crashes every >> time when I encounter with sequences like > > Could you post the error message? The entry you quote in reality is a > Swissprot (or Uniprot) entry sucked up into GenPept, so it's possible that > it's the BioPerl genbank parser that's failing, not bioperl-db. I recall > that we've had issues with these records before, though I don't recall what > the actual cause was, nor the recommended fix. Is there a requirement that > prevents you from loading these entries in their native Uniprot format? > > -hilmar > >> >> >> LOCUS P27912 792 aa linear VRL >> 10-JUN-2008 >> DEFINITION Genome polyprotein [Contains: Protein C (Core protein) (Capsid >> protein); prM; Peptide pr; Small envelope protein M (Matrix >> protein); Envelope protein E; Non-structural protein 1 (NS1)]. >> ACCESSION P27912 >> VERSION P27912.1 GI:130422 >> DBSOURCE swissprot: locus POLG_DEN1A, accession P27912; >> class: standard. >> created: Aug 1, 1992. >> sequence updated: Aug 1, 1992. >> annotation updated: Jun 10, 2008. >> xrefs: D00502.1, BAA00394.1, B32401 >> xrefs (non-sequence databases): HSSP:Q88653, SMR:P27912, >> GO:0005789, InterPro:IPR011999, InterPro:IPR013754, >> InterPro:IPR001122, InterPro:IPR000069, InterPro:IPR001157, >> InterPro:IPR002535, InterPro:IPR000336, Gene3D:G3DSA:2.60.98.10, >> Gene3D:G3DSA:2.60.40.350, Pfam:PF01003, Pfam:PF02832, >> Pfam:PF00869, >> Pfam:PF01004, Pfam:PF00948, Pfam:PF01570 >> KEYWORDS Capsid protein; Cleavage on pair of basic residues; >> Endoplasmic >> reticulum; Envelope protein; Glycoprotein; Membrane; Secreted; >> Transmembrane; Viral nucleoprotein; Virion. >> >> >> It can not parse the DBSOURCE entry. May be I am doing something >> wrong but It will great if someone can try to load >> P27912, entry of genbank to bioseqdb database. Please let me know if >> you can load the this genbank file. >> >> Thank you all for your Help. >> Best S >> >> >> >> On Mon, Jul 7, 2008 at 4:20 PM, Sendu Bala wrote: >>> >>> Hilmar Lapp wrote: >>>> >>>> You may use any name for the database - is there some piece of >>>> documentation that prompted you to conclude that this parameter isn't >>>> under >>>> your control? There should be a command-line parameter (--namespace) in >>>> load_seqdatabase.pl >>> >>> For what its worth, I was caught out by this as well. It would be a >>> little >>> more friendly if the documentation for biosql and bioperl-db were >>> consistent >>> in their suggestions for what to call the database. >>> >>> When you don't really have any idea what's going on, you at least want to >>> be >>> able to copy/paste the suggested commands/code ;) >>> >>> >>>> On Jul 7, 2008, at 12:23 PM, snoze pa wrote: >>>> >>>>> Dear Users, >>>>> Thank you very much for you timely support. I highly appreciate your >>>>> help in installing the software. Meanwhile during the installation >>>>> of bioperl-db and loading load_seqdatabase.pl, it ask me to use the >>>>> dbname "biosql" while the database created in during bioperl >>>>> installation is "bioseqdb". Shall I use bioseqdb instead of biosql as >>>>> dbname. >>> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > From bix at sendu.me.uk Tue Jul 8 16:24:54 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 08 Jul 2008 21:24:54 +0100 Subject: [Bioperl-l] Install help errors In-Reply-To: <10f848910807081200q21d78b1q2e65b8a767844135@mail.gmail.com> References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <536f21b00807021313l6cec00devfd452db661ec1449@mail.gmail.com> <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> <3B7F44AA-1950-472C-B2D5-5AFEA360D431@gmx.net> <10f848910807070923m5d1d2f53l75035a46905252a6@mail.gmail.com> <3A1A91BC-253F-4883-A833-0127300B5DD1@gmx.net> <48728897.7090103@sendu.me.uk> <10f848910807080829v111a1072p63bd82e546cc9c6a@mail.gmail.com> <87B902CC-42E7-4646-844A-F047CC7CB7BF@gmx.net> <10f848910807081200q21d78b1q2e65b8a767844135@mail.gmail.com> Message-ID: <4873CD16.7040409@sendu.me.uk> snoze pa wrote: > Here is the error message > > --------------------------------------------------- > Could not store P21215: > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: The supplied lineage does not start near 'Clostridium sp.' (I was > supplied 'sp. ATCC29733 | Clostridium | Clostridiaceae | Clostridiales > | Clostridia |Firmicutes | Bacteria') This problem (in BioPerl) was only fixed quite recently, so you'll have to use the very latest BioPerl from SVN: http://www.bioperl.org/DIST/nightly_builds/bioperl-live.tar.gz From cjfields at uiuc.edu Tue Jul 8 16:41:38 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 8 Jul 2008 15:41:38 -0500 Subject: [Bioperl-l] Nightly build archives now available In-Reply-To: <4873CDBB.30208@sendu.me.uk> References: <4873CDBB.30208@sendu.me.uk> Message-ID: <6643F0F4-C848-4274-8E42-A33BA4A4C494@uiuc.edu> Thanks. I'll look into it; under such conditions I would just remove and run a clean co. chris On Jul 8, 2008, at 3:27 PM, Sendu Bala wrote: > Chris Fields wrote: >> We now have nightly bundled archives for bioperl-live, bioperl-db, >> bioperl-run, and bioperl-network running; these will be updated ~ >> 1:00 am every night. >> http://www.bioperl.org/DIST/nightly_builds/ > > I just noticed that > http://www.bioperl.org/DIST/nightly_builds/nightly_log > is complaining about locked working copies. I don't know if this is > significant or causes any problems, just thought I would mention it. From bix at sendu.me.uk Tue Jul 8 16:27:39 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 08 Jul 2008 21:27:39 +0100 Subject: [Bioperl-l] Nightly build archives now available In-Reply-To: References: Message-ID: <4873CDBB.30208@sendu.me.uk> Chris Fields wrote: > We now have nightly bundled archives for bioperl-live, bioperl-db, > bioperl-run, and bioperl-network running; these will be updated ~ 1:00 > am every night. > > http://www.bioperl.org/DIST/nightly_builds/ I just noticed that http://www.bioperl.org/DIST/nightly_builds/nightly_log is complaining about locked working copies. I don't know if this is significant or causes any problems, just thought I would mention it. From cjfields at uiuc.edu Tue Jul 8 18:55:45 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 8 Jul 2008 17:55:45 -0500 Subject: [Bioperl-l] Nightly build archives now available In-Reply-To: <4873CDBB.30208@sendu.me.uk> References: <4873CDBB.30208@sendu.me.uk> Message-ID: On Jul 8, 2008, at 3:27 PM, Sendu Bala wrote: > Chris Fields wrote: >> We now have nightly bundled archives for bioperl-live, bioperl-db, >> bioperl-run, and bioperl-network running; these will be updated ~ >> 1:00 am every night. >> http://www.bioperl.org/DIST/nightly_builds/ > > I just noticed that > http://www.bioperl.org/DIST/nightly_builds/nightly_log > is complaining about locked working copies. I don't know if this is > significant or causes any problems, just thought I would mention it. I don't think the archives were affected, but I went ahead and cleaned out the old svn directory and restarted the script. I'll work on bullet-proofing it a bit more as I mentioned before. Not sure why it locked up but it could have something to do with server- side issues on portal. chris From Russell.Smithies at agresearch.co.nz Tue Jul 8 22:37:16 2008 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Wed, 9 Jul 2008 14:37:16 +1200 Subject: [Bioperl-l] public qblast servers? Message-ID: Hi all, Not a BioPerl question, but does anyone know of any public qblast servers? DB's of interest would be at: Wormbase: http://www.wormbase.org/ Nematode Net: http://www.nematode.net/ H. contortus: http://www.sanger.ac.uk/Projects/H_contortus/ We have a script that fakes qblast internally so Vector NTI will work with it but some of our users would like to blast elsewhere. Thanx, Russell Smithies ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From hlapp at gmx.net Tue Jul 8 20:59:50 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 8 Jul 2008 20:59:50 -0400 Subject: [Bioperl-l] Install help errors In-Reply-To: <10f848910807081200q21d78b1q2e65b8a767844135@mail.gmail.com> References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <536f21b00807021313l6cec00devfd452db661ec1449@mail.gmail.com> <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> <3B7F44AA-1950-472C-B2D5-5AFEA360D431@gmx.net> <10f848910807070923m5d1d2f53l75035a46905252a6@mail.gmail.com> <3A1A91BC-253F-4883-A833-0127300B5DD1@gmx.net> <48728897.7090103@sendu.me.uk> <10f848910807080829v111a1072p63bd82e546cc9c6a@mail.gmail.com> <87B902CC-42E7-4646-844A-F047CC7CB7BF@gmx.net> <10f848910807081200q21d78b1q2e65b8a767844135@mail.gmail.com> Message-ID: On Jul 8, 2008, at 3:00 PM, snoze pa wrote: > It always give me a warning > > "insert in Bio::DB::BioSQL::SeqFeatureAdaptor (driver) failed," This should be followed by a string similar to "values were (a,b,c,d) FKs (1,2,3)" where a, b, c, d are the actual seqfeature values that the adaptor tried to bind to the INSERT statement, and 1, 2, and 3 would be the foreign keys to the bioentry (i.e., the primary key of the bioentry to which the seqfeature belongs) and the primary and source tag terms. This should be followed by the actual error message that was raised by the database driver. We will need that full error message to have any clue about why that feature fails to successfully store. You can identify the sequence record to which the feature belongs by issuing the following SQL query: sql> SELECT * FROM bioentry WHERE bioentry_id = 123456; where 123456 is the first actual number between the parentheses followed by FK. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From snoze.pa at gmail.com Wed Jul 9 16:32:51 2008 From: snoze.pa at gmail.com (snoze pa) Date: Wed, 9 Jul 2008 15:32:51 -0500 Subject: [Bioperl-l] Install help errors In-Reply-To: References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> <3B7F44AA-1950-472C-B2D5-5AFEA360D431@gmx.net> <10f848910807070923m5d1d2f53l75035a46905252a6@mail.gmail.com> <3A1A91BC-253F-4883-A833-0127300B5DD1@gmx.net> <48728897.7090103@sendu.me.uk> <10f848910807080829v111a1072p63bd82e546cc9c6a@mail.gmail.com> <87B902CC-42E7-4646-844A-F047CC7CB7BF@gmx.net> <10f848910807081200q21d78b1q2e65b8a767844135@mail.gmail.com> Message-ID: <10f848910807091332l51ffceadta6e4b7953bd951b1@mail.gmail.com> Hilmar, Here are results of fresh bioperl installation from cvs. Seems it is not even installing the bioperl properly. >perl -MCPAN -e shell cpan>install Bundle::CPAN cpan>q >cpan cpan>install Module::Build cpan>o conf prefer_installer MB cpan>o conf commit cpan>q >cpan cpan[1]> d /bioperl/ CPAN: Storable loaded ok (v2.18) Going to read /root/.cpan/Metadata Database was generated on Wed, 09 Jul 2008 19:02:50 GMT CPAN: YAML loaded ok (v0.66) Going to read /root/.cpan/build/ ............................................................................DONE Found 16 old builds, restored the state of 10 Distribution BIRNEY/bioperl-1.2.1.tar.gz Distribution BIRNEY/bioperl-1.2.2.tar.gz Distribution BIRNEY/bioperl-1.2.3.tar.gz Distribution BIRNEY/bioperl-1.2.tar.gz Distribution BIRNEY/bioperl-1.4.tar.gz Distribution BIRNEY/bioperl-db-0.1.tar.gz Distribution BIRNEY/bioperl-ext-1.4.tar.gz Distribution BIRNEY/bioperl-gui-0.7.tar.gz Distribution BIRNEY/bioperl-run-1.2.2.tar.gz Distribution BIRNEY/bioperl-run-1.4.tar.gz Distribution BOZO/Fry-Lib-BioPerl-0.15.tar.gz Distribution CRAFFI/Bundle-BioPerl-2.1.8.tar.gz Distribution SENDU/bioperl-1.5.2_102.tar.gz Distribution SENDU/bioperl-db-1.5.2_100.tar.gz 14 items found cpan[2]> install S/SE/SENDU/bioperl-1.5.2_102.tar.gz Running Build for S/SE/SENDU/bioperl-1.5.2_102.tar.gz Has already been unwrapped into directory /root/.cpan/build/bioperl-1.5.2_102-Dx59Dg Has already been made Running Build test Test Summary Report ------------------- t/Biblio_eutils (Wstat: 0 Tests: 6 Failed: 1) Failed test: 6 Parse errors: Bad plan. You planned 5 tests but ran 6. t/BioFetch_DB (Wstat: 0 Tests: 27 Failed: 1) Failed test: 27 t/HtSNP (Wstat: 65280 Tests: 0 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 7 tests but ran 0. Files=236, Tests=12000, 366 wallclock secs ( 7.79 usr 1.28 sys + 174.92 cusr 10.07 csys = 194.06 CPU) Result: FAIL Failed 3/236 test programs. 2/12000 subtests failed. SENDU/bioperl-1.5.2_102.tar.gz ./Build test -- NOT OK //hint// to see the cpan-testers results for installing this module, try: reports SENDU/bioperl-1.5.2_102.tar.gz Running Build install Already done Failed during this command: SENDU/bioperl-1.5.2_102.tar.gz : make_test NO Any Idea From hlapp at gmx.net Wed Jul 9 17:40:01 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 9 Jul 2008 17:40:01 -0400 Subject: [Bioperl-l] Install help errors In-Reply-To: <10f848910807091332l51ffceadta6e4b7953bd951b1@mail.gmail.com> References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <10f848910807021349h70ea876dj9436a7892a5ed6af@mail.gmail.com> <3B7F44AA-1950-472C-B2D5-5AFEA360D431@gmx.net> <10f848910807070923m5d1d2f53l75035a46905252a6@mail.gmail.com> <3A1A91BC-253F-4883-A833-0127300B5DD1@gmx.net> <48728897.7090103@sendu.me.uk> <10f848910807080829v111a1072p63bd82e546cc9c6a@mail.gmail.com> <87B902CC-42E7-4646-844A-F047CC7CB7BF@gmx.net> <10f848910807081200q21d78b1q2e65b8a767844135@mail.gmail.com> <10f848910807091332l51ffceadta6e4b7953bd951b1@mail.gmail.com> Message-ID: I don't understand what's going wrong in your install but note that Sendu said you need to install a /nightly build/ (which by definition you can't pull from CPAN) because the fix to the issue you tripped over is so recent. Nightly builds are at http://www.bioperl.org/DIST/nightly_builds/bioperl-live.tar.gz -hilmar On Jul 9, 2008, at 4:32 PM, snoze pa wrote: > Hilmar, > > Here are results of fresh bioperl installation from cvs. Seems it is > not even installing the bioperl properly. > >> perl -MCPAN -e shell > cpan>install Bundle::CPAN > cpan>q > >> cpan > cpan>install Module::Build > cpan>o conf prefer_installer MB > cpan>o conf commit > cpan>q > >> cpan > cpan[1]> d /bioperl/ > CPAN: Storable loaded ok (v2.18) > Going to read /root/.cpan/Metadata > Database was generated on Wed, 09 Jul 2008 19:02:50 GMT > CPAN: YAML loaded ok (v0.66) > Going to read /root/.cpan/build/ > ............................................................................DONE > Found 16 old builds, restored the state of 10 > Distribution BIRNEY/bioperl-1.2.1.tar.gz > Distribution BIRNEY/bioperl-1.2.2.tar.gz > Distribution BIRNEY/bioperl-1.2.3.tar.gz > Distribution BIRNEY/bioperl-1.2.tar.gz > Distribution BIRNEY/bioperl-1.4.tar.gz > Distribution BIRNEY/bioperl-db-0.1.tar.gz > Distribution BIRNEY/bioperl-ext-1.4.tar.gz > Distribution BIRNEY/bioperl-gui-0.7.tar.gz > Distribution BIRNEY/bioperl-run-1.2.2.tar.gz > Distribution BIRNEY/bioperl-run-1.4.tar.gz > Distribution BOZO/Fry-Lib-BioPerl-0.15.tar.gz > Distribution CRAFFI/Bundle-BioPerl-2.1.8.tar.gz > Distribution SENDU/bioperl-1.5.2_102.tar.gz > Distribution SENDU/bioperl-db-1.5.2_100.tar.gz > 14 items found > > cpan[2]> install S/SE/SENDU/bioperl-1.5.2_102.tar.gz > Running Build for S/SE/SENDU/bioperl-1.5.2_102.tar.gz > Has already been unwrapped into directory > /root/.cpan/build/bioperl-1.5.2_102-Dx59Dg > Has already been made > Running Build test > > Test Summary Report > ------------------- > t/Biblio_eutils (Wstat: 0 Tests: 6 Failed: 1) > Failed test: 6 > Parse errors: Bad plan. You planned 5 tests but ran 6. > t/BioFetch_DB (Wstat: 0 Tests: 27 Failed: 1) > Failed test: 27 > t/HtSNP (Wstat: 65280 Tests: 0 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 7 tests but ran 0. > Files=236, Tests=12000, 366 wallclock secs ( 7.79 usr 1.28 sys + > 174.92 cusr 10.07 csys = 194.06 CPU) > Result: FAIL > Failed 3/236 test programs. 2/12000 subtests failed. > SENDU/bioperl-1.5.2_102.tar.gz > ./Build test -- NOT OK > //hint// to see the cpan-testers results for installing this module, > try: > reports SENDU/bioperl-1.5.2_102.tar.gz > Running Build install > Already done > Failed during this command: > SENDU/bioperl-1.5.2_102.tar.gz : make_test NO > > Any Idea > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From snoze.pa at gmail.com Thu Jul 10 11:13:39 2008 From: snoze.pa at gmail.com (snoze pa) Date: Thu, 10 Jul 2008 10:13:39 -0500 Subject: [Bioperl-l] Install help errors In-Reply-To: References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <10f848910807070923m5d1d2f53l75035a46905252a6@mail.gmail.com> <3A1A91BC-253F-4883-A833-0127300B5DD1@gmx.net> <48728897.7090103@sendu.me.uk> <10f848910807080829v111a1072p63bd82e546cc9c6a@mail.gmail.com> <87B902CC-42E7-4646-844A-F047CC7CB7BF@gmx.net> <10f848910807081200q21d78b1q2e65b8a767844135@mail.gmail.com> <10f848910807091332l51ffceadta6e4b7953bd951b1@mail.gmail.com> Message-ID: <10f848910807100813p1b29c798hdf3f52abbeedbecd@mail.gmail.com> Hilmar, thanks a lot for your help. I will clean the bioperl from my computer and install the fresh nightly build. I will update you with installation. Earlier I tested it with FC8 and FC9 but no luck. s On Wed, Jul 9, 2008 at 4:40 PM, Hilmar Lapp wrote: > I don't understand what's going wrong in your install but note that Sendu > said you need to install a /nightly build/ (which by definition you can't > pull from CPAN) because the fix to the issue you tripped over is so recent. > > Nightly builds are at > > http://www.bioperl.org/DIST/nightly_builds/bioperl-live.tar.gz > > -hilmar > > On Jul 9, 2008, at 4:32 PM, snoze pa wrote: > >> Hilmar, >> >> Here are results of fresh bioperl installation from cvs. Seems it is >> not even installing the bioperl properly. >> >>> perl -MCPAN -e shell >> >> cpan>install Bundle::CPAN >> cpan>q >> >>> cpan >> >> cpan>install Module::Build >> cpan>o conf prefer_installer MB >> cpan>o conf commit >> cpan>q >> >>> cpan >> >> cpan[1]> d /bioperl/ >> CPAN: Storable loaded ok (v2.18) >> Going to read /root/.cpan/Metadata >> Database was generated on Wed, 09 Jul 2008 19:02:50 GMT >> CPAN: YAML loaded ok (v0.66) >> Going to read /root/.cpan/build/ >> >> ............................................................................DONE >> Found 16 old builds, restored the state of 10 >> Distribution BIRNEY/bioperl-1.2.1.tar.gz >> Distribution BIRNEY/bioperl-1.2.2.tar.gz >> Distribution BIRNEY/bioperl-1.2.3.tar.gz >> Distribution BIRNEY/bioperl-1.2.tar.gz >> Distribution BIRNEY/bioperl-1.4.tar.gz >> Distribution BIRNEY/bioperl-db-0.1.tar.gz >> Distribution BIRNEY/bioperl-ext-1.4.tar.gz >> Distribution BIRNEY/bioperl-gui-0.7.tar.gz >> Distribution BIRNEY/bioperl-run-1.2.2.tar.gz >> Distribution BIRNEY/bioperl-run-1.4.tar.gz >> Distribution BOZO/Fry-Lib-BioPerl-0.15.tar.gz >> Distribution CRAFFI/Bundle-BioPerl-2.1.8.tar.gz >> Distribution SENDU/bioperl-1.5.2_102.tar.gz >> Distribution SENDU/bioperl-db-1.5.2_100.tar.gz >> 14 items found >> >> cpan[2]> install S/SE/SENDU/bioperl-1.5.2_102.tar.gz >> Running Build for S/SE/SENDU/bioperl-1.5.2_102.tar.gz >> Has already been unwrapped into directory >> /root/.cpan/build/bioperl-1.5.2_102-Dx59Dg >> Has already been made >> Running Build test >> >> Test Summary Report >> ------------------- >> t/Biblio_eutils (Wstat: 0 Tests: 6 Failed: 1) >> Failed test: 6 >> Parse errors: Bad plan. You planned 5 tests but ran 6. >> t/BioFetch_DB (Wstat: 0 Tests: 27 Failed: 1) >> Failed test: 27 >> t/HtSNP (Wstat: 65280 Tests: 0 Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 7 tests but ran 0. >> Files=236, Tests=12000, 366 wallclock secs ( 7.79 usr 1.28 sys + >> 174.92 cusr 10.07 csys = 194.06 CPU) >> Result: FAIL >> Failed 3/236 test programs. 2/12000 subtests failed. >> SENDU/bioperl-1.5.2_102.tar.gz >> ./Build test -- NOT OK >> //hint// to see the cpan-testers results for installing this module, try: >> reports SENDU/bioperl-1.5.2_102.tar.gz >> Running Build install >> Already done >> Failed during this command: >> SENDU/bioperl-1.5.2_102.tar.gz : make_test NO >> >> Any Idea >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > From snoze.pa at gmail.com Thu Jul 10 14:46:05 2008 From: snoze.pa at gmail.com (snoze pa) Date: Thu, 10 Jul 2008 13:46:05 -0500 Subject: [Bioperl-l] Install help errors In-Reply-To: <10f848910807100813p1b29c798hdf3f52abbeedbecd@mail.gmail.com> References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <3A1A91BC-253F-4883-A833-0127300B5DD1@gmx.net> <48728897.7090103@sendu.me.uk> <10f848910807080829v111a1072p63bd82e546cc9c6a@mail.gmail.com> <87B902CC-42E7-4646-844A-F047CC7CB7BF@gmx.net> <10f848910807081200q21d78b1q2e65b8a767844135@mail.gmail.com> <10f848910807091332l51ffceadta6e4b7953bd951b1@mail.gmail.com> <10f848910807100813p1b29c798hdf3f52abbeedbecd@mail.gmail.com> Message-ID: <10f848910807101146o4d3d4c71xcda88438fa912c09@mail.gmail.com> With minor warning, It seems the nightly build pack of bioperl working. Atleast this time it is not crashing. I checked the sequence information in the DB, and all are there. Thanks a lot for your help. best s some warnings are MSG: The supplied lineage does not start near ' and Use of get_dblinks is deprecated. Note that prior use of this method could return either simple scalar values or Bio::Annotation::DBLink instances; only Bio::Annotation::DBLink is now supported. Use get_dbxrefs() instead STACK Bio::Ontology::Term::get_dblinks /usr/local/lib/perl5/site_perl/5.10.0/Bio/Ontology/Term.pm:437 STACK Bio::DB::Persistent::PersistentObject::AUTOLOAD /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:552 STACK Bio::DB::BioSQL::TermAdaptor::store_children /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/TermAdaptor.pm:280 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214 STACK Bio::DB::Persistent::PersistentObject::create /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:244 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:169 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251 STACK Bio::DB::Persistent::PersistentObject::store /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:271 STACK Bio::DB::BioSQL::SeqAdaptor::store_children /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/SeqAdaptor.pm:244 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251 STACK Bio::DB::Persistent::PersistentObject::store /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:271 STACK (eval) /usr/local/bin/bp_load_seqdatabase.pl:623 STACK toplevel /usr/local/bin/bp_load_seqdatabase.pl:605 From cjfields at uiuc.edu Thu Jul 10 14:54:33 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 10 Jul 2008 13:54:33 -0500 Subject: [Bioperl-l] Install help errors In-Reply-To: <10f848910807101146o4d3d4c71xcda88438fa912c09@mail.gmail.com> References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <3A1A91BC-253F-4883-A833-0127300B5DD1@gmx.net> <48728897.7090103@sendu.me.uk> <10f848910807080829v111a1072p63bd82e546cc9c6a@mail.gmail.com> <87B902CC-42E7-4646-844A-F047CC7CB7BF@gmx.net> <10f848910807081200q21d78b1q2e65b8a767844135@mail.gmail.com> <10f848910807091332l51ffceadta6e4b7953bd951b1@mail.gmail.com> <10f848910807100813p1b29c798hdf3f52abbeedbecd@mail.gmail.com> <10f848910807101146o4d3d4c71xcda88438fa912c09@mail.gmail.com> Message-ID: Okay, that's a bug related to some changes I made. I can look into it; should be easy to fix. chris On Jul 10, 2008, at 1:46 PM, snoze pa wrote: > With minor warning, It seems the nightly build pack of bioperl > working. Atleast this time it is not crashing. I checked the sequence > information in the DB, and all are there. > Thanks a lot for your help. > best s > > some warnings are > > MSG: The supplied lineage does not start near ' > > and > > Use of get_dblinks is deprecated. Note that prior use > of this method could return either simple scalar values > or Bio::Annotation::DBLink instances; only > Bio::Annotation::DBLink is now supported. > Use get_dbxrefs() instead > STACK Bio::Ontology::Term::get_dblinks > /usr/local/lib/perl5/site_perl/5.10.0/Bio/Ontology/Term.pm:437 > STACK Bio::DB::Persistent::PersistentObject::AUTOLOAD > /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/Persistent/ > PersistentObject.pm:552 > STACK Bio::DB::BioSQL::TermAdaptor::store_children > /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/TermAdaptor.pm:280 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create > /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:214 > STACK Bio::DB::Persistent::PersistentObject::create > /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/Persistent/ > PersistentObject.pm:244 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create > /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:169 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store > /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:251 > STACK Bio::DB::Persistent::PersistentObject::store > /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/Persistent/ > PersistentObject.pm:271 > STACK Bio::DB::BioSQL::SeqAdaptor::store_children > /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/SeqAdaptor.pm:244 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create > /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:214 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store > /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:251 > STACK Bio::DB::Persistent::PersistentObject::store > /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/Persistent/ > PersistentObject.pm:271 > STACK (eval) /usr/local/bin/bp_load_seqdatabase.pl:623 > STACK toplevel /usr/local/bin/bp_load_seqdatabase.pl:605 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Marie-Claude Hofmann College of Veterinary Medicine University of Illinois Urbana-Champaign From cjfields at uiuc.edu Fri Jul 11 08:40:25 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 11 Jul 2008 07:40:25 -0500 Subject: [Bioperl-l] Install help errors In-Reply-To: References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <3A1A91BC-253F-4883-A833-0127300B5DD1@gmx.net> <48728897.7090103@sendu.me.uk> <10f848910807080829v111a1072p63bd82e546cc9c6a@mail.gmail.com> <87B902CC-42E7-4646-844A-F047CC7CB7BF@gmx.net> <10f848910807081200q21d78b1q2e65b8a767844135@mail.gmail.com> <10f848910807091332l51ffceadta6e4b7953bd951b1@mail.gmail.com> <10f848910807100813p1b29c798hdf3f52abbeedbecd@mail.gmail.com> <10f848910807101146o4d3d4c71xcda88438fa912c09@mail.gmail.com> Message-ID: <14221C54-C180-4B07-8057-2C7C19B18567@uiuc.edu> Make sure you have an updated bioperl-db as well. The call to get_dblinks() was changed to get_xrefs a while back and, IIRC, so was 'The supplied lineage does not start near...' message, which is related to Bio::Species changes. chris On Jul 10, 2008, at 1:54 PM, Chris Fields wrote: > Okay, that's a bug related to some changes I made. I can look into > it; should be easy to fix. > > chris > > On Jul 10, 2008, at 1:46 PM, snoze pa wrote: > >> With minor warning, It seems the nightly build pack of bioperl >> working. Atleast this time it is not crashing. I checked the sequence >> information in the DB, and all are there. >> Thanks a lot for your help. >> best s >> >> some warnings are >> >> MSG: The supplied lineage does not start near ' >> >> and >> >> Use of get_dblinks is deprecated. Note that prior use >> of this method could return either simple scalar values >> or Bio::Annotation::DBLink instances; only >> Bio::Annotation::DBLink is now supported. >> Use get_dbxrefs() instead >> STACK Bio::Ontology::Term::get_dblinks >> /usr/local/lib/perl5/site_perl/5.10.0/Bio/Ontology/Term.pm:437 >> STACK Bio::DB::Persistent::PersistentObject::AUTOLOAD >> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/Persistent/ >> PersistentObject.pm:552 >> STACK Bio::DB::BioSQL::TermAdaptor::store_children >> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/TermAdaptor.pm: >> 280 >> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create >> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/ >> BasePersistenceAdaptor.pm:214 >> STACK Bio::DB::Persistent::PersistentObject::create >> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/Persistent/ >> PersistentObject.pm:244 >> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create >> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/ >> BasePersistenceAdaptor.pm:169 >> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store >> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/ >> BasePersistenceAdaptor.pm:251 >> STACK Bio::DB::Persistent::PersistentObject::store >> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/Persistent/ >> PersistentObject.pm:271 >> STACK Bio::DB::BioSQL::SeqAdaptor::store_children >> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/SeqAdaptor.pm:244 >> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create >> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/ >> BasePersistenceAdaptor.pm:214 >> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store >> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/ >> BasePersistenceAdaptor.pm:251 >> STACK Bio::DB::Persistent::PersistentObject::store >> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/Persistent/ >> PersistentObject.pm:271 >> STACK (eval) /usr/local/bin/bp_load_seqdatabase.pl:623 >> STACK toplevel /usr/local/bin/bp_load_seqdatabase.pl:605 >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Marie-Claude Hofmann > College of Veterinary Medicine > University of Illinois Urbana-Champaign > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Marie-Claude Hofmann College of Veterinary Medicine University of Illinois Urbana-Champaign From bernd.web at gmail.com Fri Jul 11 12:25:56 2008 From: bernd.web at gmail.com (Bernd Web) Date: Fri, 11 Jul 2008 18:25:56 +0200 Subject: [Bioperl-l] wiki example scripts Message-ID: <716af09c0807110925s2694a8a8tb168333a49e49184@mail.gmail.com> Hi, At the moment the Bioperl_scripts page on the WIKI, http://www.bioperl.org/wiki/Bioperl_scripts is completely emty. Did something change? Regards, Bernd From mauricio at open-bio.org Fri Jul 11 13:17:35 2008 From: mauricio at open-bio.org (Mauricio Herrera Cuadra) Date: Fri, 11 Jul 2008 12:17:35 -0500 Subject: [Bioperl-l] wiki example scripts In-Reply-To: <716af09c0807110925s2694a8a8tb168333a49e49184@mail.gmail.com> References: <716af09c0807110925s2694a8a8tb168333a49e49184@mail.gmail.com> Message-ID: <487795AF.6080509@open-bio.org> [Sending to OBF support] The usual Apache stop/restart trick doesn't work for this. The rest of the wiki works fine, except for the page that Bernd points out. Seems like we would need to increment the allowed memory size in the PHP config: ---------------------------------------------------------------------- [Fri Jul 11 13:07:08 2008] [error] [client 209.131.62.115] PHP Fatal error: Allowed memory size of 25165824 bytes exhausted (tried to allocate 18583148 bytes) in /home/websites/cross-site-stuff/mediaWiki_base/mediawiki-REL1_12/includes/Preprocessor_Hash.php on line 1354 ---------------------------------------------------------------------- Nor ps, top or mytop showed significant memory usage by other applications in portal. Mauricio. Bernd Web wrote: > Hi, > > At the moment the Bioperl_scripts page on the WIKI, > http://www.bioperl.org/wiki/Bioperl_scripts > is completely emty. Did something change? > > Regards, > Bernd > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From jay at jays.net Fri Jul 11 13:13:51 2008 From: jay at jays.net (Jay Hannah) Date: Fri, 11 Jul 2008 12:13:51 -0500 Subject: [Bioperl-l] wiki example scripts In-Reply-To: <716af09c0807110925s2694a8a8tb168333a49e49184@mail.gmail.com> References: <716af09c0807110925s2694a8a8tb168333a49e49184@mail.gmail.com> Message-ID: <668F2D9D-AA85-4876-8E91-3AA80D652790@jays.net> On Jul 11, 2008, at 11:25 AM, Bernd Web wrote: > At the moment the Bioperl_scripts page on the WIKI, > http://www.bioperl.org/wiki/Bioperl_scripts > is completely emty. Did something change? Woof. Looks like a server issue. Heads up helpdesk. :) j From snoze.pa at gmail.com Fri Jul 11 15:24:48 2008 From: snoze.pa at gmail.com (snoze pa) Date: Fri, 11 Jul 2008 14:24:48 -0500 Subject: [Bioperl-l] Install help errors In-Reply-To: <14221C54-C180-4B07-8057-2C7C19B18567@uiuc.edu> References: <10f848910807021256l56d2fff8v82c6452fb9bd9850@mail.gmail.com> <87B902CC-42E7-4646-844A-F047CC7CB7BF@gmx.net> <10f848910807081200q21d78b1q2e65b8a767844135@mail.gmail.com> <10f848910807091332l51ffceadta6e4b7953bd951b1@mail.gmail.com> <10f848910807100813p1b29c798hdf3f52abbeedbecd@mail.gmail.com> <10f848910807101146o4d3d4c71xcda88438fa912c09@mail.gmail.com> <14221C54-C180-4B07-8057-2C7C19B18567@uiuc.edu> Message-ID: <10f848910807111224p3232eda8v9a0e7f4a2624b4d2@mail.gmail.com> Thanks Chris and all bioperl developers On Fri, Jul 11, 2008 at 7:40 AM, Chris Fields wrote: > Make sure you have an updated bioperl-db as well. The call to get_dblinks() > was changed to get_xrefs a while back and, IIRC, so was 'The supplied > lineage does not start near...' message, which is related to Bio::Species > changes. > > chris > > On Jul 10, 2008, at 1:54 PM, Chris Fields wrote: > >> Okay, that's a bug related to some changes I made. I can look into it; >> should be easy to fix. >> >> chris >> >> On Jul 10, 2008, at 1:46 PM, snoze pa wrote: >> >>> With minor warning, It seems the nightly build pack of bioperl >>> working. Atleast this time it is not crashing. I checked the sequence >>> information in the DB, and all are there. >>> Thanks a lot for your help. >>> best s >>> >>> some warnings are >>> >>> MSG: The supplied lineage does not start near ' >>> >>> and >>> >>> Use of get_dblinks is deprecated. Note that prior use >>> of this method could return either simple scalar values >>> or Bio::Annotation::DBLink instances; only >>> Bio::Annotation::DBLink is now supported. >>> Use get_dbxrefs() instead >>> STACK Bio::Ontology::Term::get_dblinks >>> /usr/local/lib/perl5/site_perl/5.10.0/Bio/Ontology/Term.pm:437 >>> STACK Bio::DB::Persistent::PersistentObject::AUTOLOAD >>> >>> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:552 >>> STACK Bio::DB::BioSQL::TermAdaptor::store_children >>> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/TermAdaptor.pm:280 >>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create >>> >>> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214 >>> STACK Bio::DB::Persistent::PersistentObject::create >>> >>> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:244 >>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create >>> >>> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:169 >>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store >>> >>> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251 >>> STACK Bio::DB::Persistent::PersistentObject::store >>> >>> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:271 >>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children >>> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/SeqAdaptor.pm:244 >>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create >>> >>> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214 >>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store >>> >>> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251 >>> STACK Bio::DB::Persistent::PersistentObject::store >>> >>> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/Persistent/PersistentObject.pm:271 >>> STACK (eval) /usr/local/bin/bp_load_seqdatabase.pl:623 >>> STACK toplevel /usr/local/bin/bp_load_seqdatabase.pl:605 >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Marie-Claude Hofmann >> College of Veterinary Medicine >> University of Illinois Urbana-Champaign >> >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Marie-Claude Hofmann > College of Veterinary Medicine > University of Illinois Urbana-Champaign > > > > > From Samantha.Thompson at greenbiologics.com Mon Jul 14 12:36:27 2008 From: Samantha.Thompson at greenbiologics.com (Samantha Thompson) Date: Mon, 14 Jul 2008 17:36:27 +0100 Subject: [Bioperl-l] Form validating and Bio::Seq objects.. Message-ID: Hi, I'm trying to incorporate some bioperl functionality into webpages. For example I'm hoping to make a BLAST server that can be accessed by pasting/typing a sequence into a form on one of my own pages. I'm wondering, if I read the contents into a Bio::Seq object (initialising it to use format as fasta) will bioperl edit out all the white space and nonsensical characters from the sequence before I use it in a BLAST query, or do I need to validate it with a perl routine first? Thanks ST From alperyilmaz at gmail.com Mon Jul 14 17:34:26 2008 From: alperyilmaz at gmail.com (Alper Yilmaz) Date: Mon, 14 Jul 2008 17:34:26 -0400 Subject: [Bioperl-l] Bio::Graphics - several Message-ID: Hi, I have couple questions about Bio::Graphics. a- even though I played around with start, end, width, length values, I wasn't able to make a ruler which starts from -1600 and ends at 0 (promoter region). How can I make a ruler, which has negative values and decreases towards right? In such a case, what happens to start and end values of the box glyphs? How can I adjust start and end values of an element located at 1500bp so that it's shown at -100bp, in other words are negative values taken as is or interpreted as "less than start" ? b- some of the recognized variables for -link argument are $name, $id, etc. $name corresponds to -display_name of Bio::SeqFeature::Generic.What does $id correspond to? I tried to assign value to $id but it was not successful -link=> sub { my $element = shift; my $id = $element->seq_id; return 'http://database/address.html?promoter_id=$id'; }, In this statement even if I try to print $id within sub, it does not print anything. c- I didn't come accross any scripts or tutorials about including pan or zoom button (as in GBrowser). How can I add those functionalities to already available graphics generated by Bio::Graphics ? From David.Messina at sbc.su.se Tue Jul 15 03:08:23 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 15 Jul 2008 09:08:23 +0200 Subject: [Bioperl-l] Form validating and Bio::Seq objects.. In-Reply-To: References: Message-ID: <628aabb70807150008m13ffef59g29c11513ce03a128@mail.gmail.com> Hi Samantha, Bio::SeqIO will strip out whitespace and newlines when it reads in a sequence, but it won't validate the alphabet for you -- you'll need to do that on your own. This topic came up on this mailing list recently, and Arshad Mohammed came up with some draft code to do this. See here: http://www.nabble.com/Format-Validator-td17444139.html Dave From Samantha.Thompson at greenbiologics.com Tue Jul 15 05:24:28 2008 From: Samantha.Thompson at greenbiologics.com (Samantha Thompson) Date: Tue, 15 Jul 2008 10:24:28 +0100 Subject: [Bioperl-l] Form validating and Bio::Seq objects.. References: <628aabb70807150008m13ffef59g29c11513ce03a128@mail.gmail.com> Message-ID: Thanks for this it was helpful. I have two related questions: 1) From the HTML
to cgi script the sequence text is sent as a string variable. As such, can Bio::SeqIO be initialised with a variable rather than a file? (I had been using the sequence to directly initialise a Bio::Seq object, although this wouldn?t take into account someone pasting multiple FASTA sequences into the text box). 2) Is there a definition of the FASTA format anywhere set in stone? .. is the initial line/title always between a > and a single newline char? Can there be white space before the ?>? for example. Thanks, ST From: dave at davemessina.com [mailto:dave at davemessina.com] On Behalf Of Dave Messina Sent: 15 July 2008 08:08 To: Samantha Thompson Cc: bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] Form validating and Bio::Seq objects.. Hi Samantha, Bio::SeqIO will strip out whitespace and newlines when it reads in a sequence, but it won't validate the alphabet for you -- you'll need to do that on your own. This topic came up on this mailing list recently, and Arshad Mohammed came up with some draft code to do this. See here: http://www.nabble.com/Format-Validator-td17444139.html Dave From simon.andrews at bbsrc.ac.uk Tue Jul 15 05:48:18 2008 From: simon.andrews at bbsrc.ac.uk (Simon Andrews) Date: Tue, 15 Jul 2008 10:48:18 +0100 Subject: [Bioperl-l] Form validating and Bio::Seq objects.. In-Reply-To: References: <628aabb70807150008m13ffef59g29c11513ce03a128@mail.gmail.com> Message-ID: <149016ED-13AF-48EA-926A-3A42092226FC@bbsrc.ac.uk> On 15 Jul 2008, at 10:24, Samantha Thompson wrote: > Thanks for this it was helpful. > > I have two related questions: > > 1) From the HTML to cgi script the sequence text is > sent as a string variable. As such, can Bio::SeqIO be initialised > with a variable rather than a file? (I had been using the sequence > to directly initialise a Bio::Seq object, although this wouldn?t > take into account someone pasting multiple FASTA sequences into the > text box). You can use IO::Scalar to make your variable act like a filehandle and then pass that to SeqIO. Simon. From David.Messina at sbc.su.se Tue Jul 15 07:27:24 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 15 Jul 2008 13:27:24 +0200 Subject: [Bioperl-l] Form validating and Bio::Seq objects.. In-Reply-To: References: <628aabb70807150008m13ffef59g29c11513ce03a128@mail.gmail.com> Message-ID: <628aabb70807150427p8e25441o992f28ecf7fec5fe@mail.gmail.com> > > 2) Is there a definition of the FASTA format anywhere set in stone? See here: http://www.bioperl.org/wiki/FASTA_sequence_format and here: http://en.wikipedia.org/wiki/Fasta_format > is the initial line/title always between a > and a single newline char? Yes. > Can there be white space before the '>' for example. > No, although if you'd like to be forgiving, it's easy enough to handle with $fasta_header_line =~ s/^\s+>/>/; Dave Dave From erin_ashurei at hotmail.com Tue Jul 15 19:39:43 2008 From: erin_ashurei at hotmail.com (Leigh Bender) Date: Tue, 15 Jul 2008 19:39:43 -0400 Subject: [Bioperl-l] problem - installing bioperl-ext Message-ID: Hi I faced a problem installing bioperl-ext package. (1.5.1) I followed direction from http://bio.perl.org/wiki/Installing_Bioperl_on_Windows under Installation using CPAN or manual installation. At the end of the step 12, it said "bioperl-ext is not installed or is installed incorrectly", "3 tests and 161 subtests skipped", and "Failed 5/268 test programs. 12/11786 subtests failed." I proceeded to step 13, installation, anyways but the ext package does not seem to work even after installation. I intended to use the module Bio::Ext::Align, Bio::AlignIO, Bio::SimpleAlign and Bio::Tools::dpAlign - however, perl keeps on telling me either that I need to install the ext package or that it cannot locate the ext modules I am trying to use, even after installation suggesting that the ext package is not installed successfully. What is the problem and how would I go about fixing it? Thanks a bunch! Leigh _________________________________________________________________ Find hidden words, unscramble celebrity names, or try the ultimate crossword puzzle with Live Search Games. Play now! http://g.msn.ca/ca55/212 From sidd.basu at gmail.com Wed Jul 16 10:37:06 2008 From: sidd.basu at gmail.com (Siddhartha Basu) Date: Wed, 16 Jul 2008 09:37:06 -0500 Subject: [Bioperl-l] Re: Bio::Graphics - several In-Reply-To: References: Message-ID: <487e0794.30e4220a.4aa2.ffffc116@mx.google.com> Hi, On Mon, 14 Jul 2008, Alper Yilmaz wrote: > Hi, > I have couple questions about Bio::Graphics. > a- even though I played around with start, end, width, length values, > I wasn't able to make a ruler which starts from -1600 and ends at 0 > (promoter region). How can I make a ruler, which has negative values > and decreases towards right? This post might answer your question .... http://article.gmane.org/gmane.comp.lang.perl.bio.general/14956/ -siddhartha > In such a case, what happens to start and end values of the box > glyphs? How can I adjust start and end values of an element located at > 1500bp so that it's shown at -100bp, in other words are negative > values taken as is or interpreted as "less than start" ? > > b- some of the recognized variables for -link argument are $name, $id, etc. > $name corresponds to -display_name of Bio::SeqFeature::Generic.What > does $id correspond to? I tried to assign value to $id but it was not > successful > -link=> sub { > my $element = shift; > my $id = $element->seq_id; > return 'http://database/address.html?promoter_id=$id'; > }, > In this statement even if I try to print $id within sub, it does not > print anything. > > c- I didn't come accross any scripts or tutorials about including pan > or zoom button (as in GBrowser). How can I add those functionalities > to already available graphics generated by Bio::Graphics ? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at uiuc.edu Tue Jul 15 09:01:22 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 15 Jul 2008 08:01:22 -0500 Subject: [Bioperl-l] parsing of codeml In-Reply-To: <034024EC-C35C-4390-9C1B-021219C4BC53@bioperl.org> References: <346817.88438.qm@web36405.mail.mud.yahoo.com> <034024EC-C35C-4390-9C1B-021219C4BC53@bioperl.org> Message-ID: I agree, the mailing list is the place to ask. However, it would be best to add the files as a bug report in bugzilla. Mailing list info: http://www.bioperl.org/wiki/Mailing_lists bioperl-l at lists.open-bio.org chris On Jul 15, 2008, at 12:25 AM, Jason Stajich wrote: > Are you really sure you want to use runmode=2 ? we have never really > tested or tried to support that combination. > It is much better to just provide your own tree - Yang talks about > this in the handbook that PAML is not a good tree building program. > > I would still encourage you to submit this as bug to bugzilla with > the files you sent me. > Honestly, I don't really know when I'll have much time to look into > this. I'll try but no promises. I really encourage you to use the > mailing list to see if you can get help from other developers as well. > > -jason > > On Jul 9, 2008, at 6:23 PM, Tannistha wrote: > >> Hi Jason, >> >> Hope you have received my earlier email having input file and >> results. Please let me know if I am to provide with any further >> information. >> >> Thanking you >> >> Best Regards >> Tannistha >> >> Dr. Tannistha Nandi email: tannistha3 at yahoo.com >> >> --- On Thu, 7/3/08, Jason Stajich wrote: >> From: Jason Stajich >> Subject: Re: parsing of codeml >> To: "Tannistha" >> Date: Thursday, July 3, 2008, 8:54 PM >> >> It is more useful to also send the data and/or codeml report file so >> I can actually duplicate the parsing problem directly. >> Best scenario is to submit it as a bug to the bugzilla as well >> http:// >> bugzilla.open-bio.org/ >> >> I'm still on the road @ another conference but if you can send the >> data I'll take a look at debugging when I have a free moment. >> >> thanks for your patience. >> -jason >> On Jul 3, 2008, at 12:45 AM, Tannistha wrote: >> >>> Hi Jason, >>> >>> I think I am able to narrow down my problem. Now the issue is when >>> I use runmode =2, seqtype =1, and Mgene =1 for a set of 8 genes >>> (multiple sequence alignment), it is not able to parse the result >>> generated by codeml. >>> I sending the runPAML.pl script I am using. Apart from this I am >>> using the SVN code of PAML.pm and codeml.pm. I am running on red >>> hat linux using Bioperl 1.5.2 and PAML4. >>> I will be grateful if you could spare some time of yours to look >>> into my problem. >>> >>> Thanking you >>> >>> Best Regards >>> Tannistha >>> >>> >>> Dr. Tannistha Nandi >>> email: tannistha3 at yahoo.com >>> >>> --- On Wed, 6/25/08, Jason Stajich wrote: >>> >>> From: Jason Stajich >>> Subject: Re: Please take a look in this issue >>> To: tannistha3 at yahoo.com >>> Date: Wednesday, June 25, 2008, 1:18 PM >>> >>> >>> i'm sorry, i'm away for the next 2 weeks, I'm not sure when I >> can >>> look into your issue. I would ask the list again if you don't get a >>> response in a few days or try and also use the code from SVN >>> directly. >>> >>> >>> On 6/25/08, Tannistha wrote: >>> Hi Jason >>> >>> I have posted my query in the forum, but no luck yet. >>> >>> I am using your new PAML script updated 4 days back, but its giving >>> error in these line in PAML.pm >>> -------------------------- >>> return unless (/^Nei\s*\&\s*Gojobori/); >>> # skip the next line is ver > 3.15 >>> $self->_readline if ($ver > 3.14); >>> ------------------------------------------------ >>> >>> Use of uninitialized value in pattern match (m//) at /usr/lib/perl5/ >>> site_perl/5.8.5/Bio/Tools/Phylo/PAML.pm line 745, line 90. >>> >>> Please help me to fix this. I am using Bioperl 1.5.2 and PAML4 >>> >>> Thanking you >>> >>> Regards >>> Tannistha >>> >>> >>> Dr. Tannistha Nandi >>> email: tannistha3 at yahoo.com >>> >>> --- On Mon, 6/23/08, Jason Stajich wrote: >>> >>> From: Jason Stajich >>> Subject: Fwd: PAML through BIOPERL - parsing error >>> To: tannistha3 at yahoo.com >>> Cc: "bioperl list" >>> Date: Monday, June 23, 2008, 11:02 PM >>> >>> >>> You'll have to report what version of BioPerl and PAML you are >>> using, only certain versions work together because the report >>> output from PAML changes in each version. We have tried to fix it >>> for PAML4 in the latest code in SVN and I believe PAML 3.15 should >>> work with what is in 1.5.2 release of BioPerl but I'm not sure. >>> >>> >>> Please direct your questions to the mailing list to insure someone >>> has a chance to look at it. >>> >>> >>> >>> -jason >>> >>> >>> >>> >>> Begin forwarded message: >>> >>> >>> From: Tannistha >>> Date: June 22, 2008 10:43:41 PM PDT >>> To: jason at bioperl.org >>> Subject: PAML through BIOPERL - parsing error >>> Reply-To: tannistha3 at yahoo.com >>> >>> >>> >>> >>> Hi Jason, >>> >>> I am using PAML through BIOPERL. My input in multiple CDS sequence. >>> I am getting an error while parsing my codeml result. >>> The error is: >>> Use of uninitialized value in pattern match (m//) at /usr/lib/perl5/ >>> site_perl/5.8.5/Bio/Tools/Phylo/PAML.pm line 615, line 90. >>> >>> >>> Please suggest how to eliminate this error. >>> >>> Thanking you >>> >>> Regards >>> >>> >>> Dr. Tannistha Nandi >>> email: tannistha3 at yahoo.com >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> -- >>> Jason Stajich >>> jason at bioperl.org >>> http://bioperl.org/wiki/User:Jason >>> >>> >>> >> >> > Christopher Fields Postdoctoral Researcher Lab of Dr. Marie-Claude Hofmann College of Veterinary Medicine University of Illinois Urbana-Champaign From potterbond007 at gmail.com Thu Jul 17 00:27:30 2008 From: potterbond007 at gmail.com (#Raul#~~ WeAtHerEd~~) Date: Thu, 17 Jul 2008 05:27:30 +0100 Subject: [Bioperl-l] PHYLIP problem. Message-ID: <87ec85590807162127k56396f64j3998604ee29f1a6a@mail.gmail.com> I have been trying for 2 days to make the prodist work for my clustalw PHYLIP output file but even after following the documentation perfectly, the distance matrix is just not being calculated. use Bio::Tools::Run::Phylo::Phylip::ProtDist; my $inputfilename = '/home/rc174/pro/align.phy'; @params = ('MODEL' => 'PAM'); my $prodistfactory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params); my ($matrix)= $prodistfactory->run($inputfile); I am writing the basic code that should work for this program. I am also attaching my alignment file ( align.phy ). Can you write a program where this alignment file outputs a phylogenetic tree based on the Kimura model. Thanks, Rahul -------------- next part -------------- A non-text attachment was scrubbed... Name: align.phy Type: application/octet-stream Size: 1482 bytes Desc: not available URL: From David.Messina at sbc.su.se Thu Jul 17 05:59:31 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Thu, 17 Jul 2008 11:59:31 +0200 Subject: [Bioperl-l] PHYLIP problem. In-Reply-To: <87ec85590807162127k56396f64j3998604ee29f1a6a@mail.gmail.com> References: <87ec85590807162127k56396f64j3998604ee29f1a6a@mail.gmail.com> Message-ID: <628aabb70807170259p6536dfa0oe70579f291c011a0@mail.gmail.com> Rahul, Using your input file and your code, BioPerl and PHYLIP run correctly. Despite your "following the documentation perfectly", I believe you may have missed this line: print $matrix->print_matrix; Dave From Alicia.Amadoz at uv.es Thu Jul 17 05:17:16 2008 From: Alicia.Amadoz at uv.es (Alicia Amadoz) Date: Thu, 17 Jul 2008 11:17:16 +0200 (CEST) Subject: [Bioperl-l] Bio_Tools_Run_RemoteBlast error: 500 Can't connect to www.ncbi.nlm.nih.gov:80 Message-ID: <6952626984amadoz@uv.es> Hi, I am installing my bioperl script into a new server and I have an error that I don't know how to solve. Once I have launched my script at the new server, it appears a file named "delete" that has the following error: -------------------- WARNING --------------------- MSG: req was POST http://www.ncbi.nlm.nih.gov/blast/Blast.cgi User-Agent: bioperl-Bio_Tools_Run_RemoteBlast/1.005002102 Content-Length: 610 Content-Type: application/x-www-form-urlencoded DATABASE=nr&QUERY=%3Ee3768n+%0Aggtgcccactggggagtcctagcgggcatagcgtatttctccatggtg gggaactgggcgaaggtcctgctagtgctgttgttgtttgccggcgtcgatgcggaaacctacatcaccggg ggggccgtcgccaaggccgcgcttggattcactgggtttttcacttcgggccccaagcaggacatccagctaatcaactccaacgg cagttggcacatcaatcgtactgccttgaactgtaatgcgagcctcgaaaccggctggatagcgg ggctcctctatcacaacagattcaactcttcaggctgccccgagaggatggccagctgtagacccctcgccgacttcgaccagggct ggggccctatcagctacgccaacggaagcggccccgatcaccgcccc&COMPOSITION_BASE D_STATISTICS=off&EXPECT=10&SERVICE=plain&FORMAT_OBJECT=Alignment&ALIGNMENTS= Pairwise&CMD=Put&FILTER=m&DESCRIPTIONS=100&PROGRAM=blastn&ALIGNMENT_VIEW=P a irwise An Error Occurred

An Error Occurred

500 Can't connect to www.ncbi.nlm.nih.gov:80 (Bad hostname 'www.ncbi.nlm.nih.gov') --------------------------------------------------- My script works ok in my current machine, a fedora 5 with bioperl 1.4 installed through cpan. The new server is a fedora 8 and we installed bioperl and bioperl run 1.5.2 through yumex installer. Both machines have perl 5.8.8 installed. Any idea of how to solve this error?? Thank you very much in advance. Alicia Here you are a part of my script: #!/usr/bin/perl use Bio::Seq; use Bio::SeqIO; use Bio::SearchIO; use Bio::DB::GenBank; use Bio::Tools::Run::RemoteBlast; use POSIX; use strict; use File::Copy; # Blast using RemoteBlast # get php variables my $query_filename = $ARGV[0]; my $query_filepath = $ARGV[1]; my $database = $ARGV[2]; my $program = $ARGV[3]; my $ALIGNMENTS = $ARGV[5]; my $ALIGNMENT_VIEW = $ARGV[5]; my $DESCRIPTIONS = $ARGV[6]; my $EXPECT = $ARGV[7]; # maybe "novar" variables my $FILTER_1 = $ARGV[8]; my $FILTER_2 = $ARGV[9]; my $LCASE_MASK = $ARGV[10]; my $MEGABLAST = $ARGV[11]; my $UNGAPPED_ALIGNMENT = $ARGV[12]; my $user_name = $ARGV[13]; my $perlfunc_path = $ARGV[14]; my $input = $ARGV[15]; my $format = $ARGV[16]; my $ENTREZ_QUERY = $ARGV[17]; my @params = ('-prog' => $program, '-data' => $database, '-expect' => $EXPECT, '- readmethod' => 'SearchIO'); my $remote = Bio::Tools::Run::RemoteBlast->new(@params); # change query parameters $Bio::Tools::Run::RemoteBlast::HEADER{'ALIGNMENTS'} = $ALIGNMENTS; $Bio::Tools::Run::RemoteBlast::HEADER{'ALIGNMENT_VIEW'} = $ALIGNMENT_VIEW; $Bio::Tools::Run::RemoteBlast::HEADER{'DESCRIPTIONS'} = $DESCRIPTIONS; .. From David.Messina at sbc.su.se Thu Jul 17 11:57:36 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Thu, 17 Jul 2008 17:57:36 +0200 Subject: [Bioperl-l] PHYLIP problem. In-Reply-To: <87ec85590807170734v2f24b5c1n962b15e22b067896@mail.gmail.com> References: <87ec85590807162127k56396f64j3998604ee29f1a6a@mail.gmail.com> <628aabb70807170259p6536dfa0oe70579f291c011a0@mail.gmail.com> <87ec85590807170734v2f24b5c1n962b15e22b067896@mail.gmail.com> Message-ID: <628aabb70807170857u19300dd7md079878f6fd38e75@mail.gmail.com> Hi Rahul, Please keep the mailing list on the Cc so that this discussion can be archived and others can see it. There's an error in your program -- you change the variable for the input file from $inputfilename in one place to $inputfile in another. It's a good idea to always use warnings and use strict with Perl. With warnings, the first error shown is: Name "main::inputfile" used only once: possible typo at test.pl line 9. which indicates that there is something wrong with $inputfile. Here's the complete program I ran: #!/usr/bin/perl use warnings; use strict; use Bio::Tools::Run::Phylo::Phylip::ProtDist; my $inputfilename = 'align.phy'; my $prodistfactory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(); my ($matrix)= $prodistfactory->run($inputfilename); print $matrix->print_matrix; Note that your perl may be in a different location than mine, so the first line may need to be changed. Also note that I changed the location of the input file -- it was in the same directory as my Perl script. The error you saw about 'protdist did not create matrix correctly' is unfortunately vague. It simply means that, for some reason, protdist didn't produce any output that BioPerl could see. A likely reason for this to occur is that protdist didn't run at all. Have you installed PHYLIP (and specifically protdist), and have you tried running it outside of BioPerl? Dave On Thu, Jul 17, 2008 at 16:34, #Raul#~~ WeAtHerEd~~ wrote: > Dear Dave, > > I added the print line and the error message that I used to receive changed > but the program is still refusing to run. > > Modified program > > use Bio::Tools::Run::Phylo::Phylip::ProtDist; > > my $inputfilename = '/home/rc174/pro/align.phy'; > #@params = ('MODEL' => 'PAM'); > my $prodistfactory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(); > my ($matrix)= $prodistfactory->run($inputfile); > print $matrix->print_matrix; > > > The error I receive is now > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Problems setting up for protdist. Probably bad input data in ! > STACK: Error::throw > STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:328 > STACK: Bio::Tools::Run::Phylo::Phylip::ProtDist::run > /usr/local/share/perl/5.8.8/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm:362 > STACK: phylip2.pl:6 > > The error I used to receive before I inserted the line was, > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: protdist did not create matrix correctly (/tmp/S3a5QG6CCd/outfile) > STACK: Error::throw > STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:328 > STACK: Bio::Tools::Run::Phylo::Phylip::ProtDist::_run > /usr/local/share/perl/5.8.8/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm:409 > STACK: Bio::Tools::Run::Phylo::Phylip::ProtDist::run > /usr/local/share/perl/5.8.8/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm:366 > STACK: phylip.pl:55 > ----------------------------------------------------------- > > Is this because I have missed out any specific packages for installation. I > use an Ubuntu Linux computer version 7.10 . I am not sure of the bioperl > version. I am trying to learn a bit of bioperl on my own so if you could > send me a model program for getting a tree so that I could work out the > issues I am facing I would be grateful. > > Cheers, > Rahul > From cjfields at uiuc.edu Thu Jul 17 22:12:10 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 17 Jul 2008 21:12:10 -0500 Subject: [Bioperl-l] Bio_Tools_Run_RemoteBlast error: 500 Can't connect to www.ncbi.nlm.nih.gov:80 In-Reply-To: <6952626984amadoz@uv.es> References: <6952626984amadoz@uv.es> Message-ID: You need to update to a recent version of bioperl (1.4 is too old). chris On Jul 17, 2008, at 4:17 AM, Alicia Amadoz wrote: > Hi, > > I am installing my bioperl script into a new server and I have an > error that I don't know how > to solve. Once I have launched my script at the new server, it > appears a file named "delete" > that has the following error: > > -------------------- WARNING --------------------- > MSG: req was POST http://www.ncbi.nlm.nih.gov/blast/Blast.cgi > User-Agent: bioperl-Bio_Tools_Run_RemoteBlast/1.005002102 > Content-Length: 610 > Content-Type: application/x-www-form-urlencoded > > DATABASE=nr&QUERY=%3Ee3768n+ > %0Aggtgcccactggggagtcctagcgggcatagcgtatttctccatggtg > gggaactgggcgaaggtcctgctagtgctgttgttgtttgccggcgtcgatgcggaaacctacatcaccggg > ggggccgtcgccaaggccgcgcttggattcactgggtttttcacttcgggccccaagcaggacatccagctaatcaactccaacgg > cagttggcacatcaatcgtactgccttgaactgtaatgcgagcctcgaaaccggctggatagcgg > ggctcctctatcacaacagattcaactcttcaggctgccccgagaggatggccagctgtagacccctcgccgacttcgaccagggct > ggggccctatcagctacgccaacggaagcggccccgatcaccgcccc&COMPOSITION_BASE > D_STATISTICS > =off&EXPECT=10&SERVICE=plain&FORMAT_OBJECT=Alignment&ALIGNMENTS= > Pairwise > &CMD=Put&FILTER=m&DESCRIPTIONS=100&PROGRAM=blastn&ALIGNMENT_VIEW=P > a > irwise > > > An Error Occurred > >

An Error Occurred

> 500 Can't connect to www.ncbi.nlm.nih.gov:80 (Bad hostname 'www.ncbi.nlm.nih.gov > ') > > > > --------------------------------------------------- > > My script works ok in my current machine, a fedora 5 with bioperl > 1.4 installed through > cpan. The new server is a fedora 8 and we installed bioperl and > bioperl run 1.5.2 through > yumex installer. Both machines have perl 5.8.8 installed. > > Any idea of how to solve this error?? Thank you very much in advance. > > Alicia > > Here you are a part of my script: > > #!/usr/bin/perl > > use Bio::Seq; > use Bio::SeqIO; > use Bio::SearchIO; > use Bio::DB::GenBank; > use Bio::Tools::Run::RemoteBlast; > use POSIX; > use strict; > use File::Copy; > > # Blast using RemoteBlast > # get php variables > > my $query_filename = $ARGV[0]; > my $query_filepath = $ARGV[1]; > my $database = $ARGV[2]; > my $program = $ARGV[3]; > my $ALIGNMENTS = $ARGV[5]; > my $ALIGNMENT_VIEW = $ARGV[5]; > my $DESCRIPTIONS = $ARGV[6]; > my $EXPECT = $ARGV[7]; > # maybe "novar" variables > my $FILTER_1 = $ARGV[8]; > my $FILTER_2 = $ARGV[9]; > my $LCASE_MASK = $ARGV[10]; > my $MEGABLAST = $ARGV[11]; > my $UNGAPPED_ALIGNMENT = $ARGV[12]; > my $user_name = $ARGV[13]; > my $perlfunc_path = $ARGV[14]; > my $input = $ARGV[15]; > my $format = $ARGV[16]; > > my $ENTREZ_QUERY = $ARGV[17]; > > my @params = ('-prog' => $program, '-data' => $database, '-expect' > => $EXPECT, '- > readmethod' => 'SearchIO'); > > my $remote = Bio::Tools::Run::RemoteBlast->new(@params); > # change query parameters > $Bio::Tools::Run::RemoteBlast::HEADER{'ALIGNMENTS'} = $ALIGNMENTS; > $Bio::Tools::Run::RemoteBlast::HEADER{'ALIGNMENT_VIEW'} = > $ALIGNMENT_VIEW; > $Bio::Tools::Run::RemoteBlast::HEADER{'DESCRIPTIONS'} = $DESCRIPTIONS; > > .. > > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Marie-Claude Hofmann College of Veterinary Medicine University of Illinois Urbana-Champaign From Alicia.Amadoz at uv.es Fri Jul 18 04:25:08 2008 From: Alicia.Amadoz at uv.es (Alicia Amadoz) Date: Fri, 18 Jul 2008 10:25:08 +0200 (CEST) Subject: [Bioperl-l] Bio_Tools_Run_RemoteBlast error: 500 Can't connect to www.ncbi.nlm.nih.gov:80 In-Reply-To: References: Message-ID: <5551614511amadoz@uv.es> Hi Chris, Thank you very much for your comment. The thing is that my script doesn't run in the most recent version of bioperl (1.5.2) and it works with the previous version (1.4). So, I would like to know if anything related to Bio::Tools:Run::RemoteBlast has changed that could throw me the error of > > 500 Can't connect to www.ncbi.nlm.nih.gov:80 (Bad hostname 'www.ncbi.nlm.nih.gov > > ') Or anyone has an idea of why it gives this error? Thank you very much in advance. Alicia > You need to update to a recent version of bioperl (1.4 is too old). > > chris > > On Jul 17, 2008, at 4:17 AM, Alicia Amadoz wrote: > > > Hi, > > > > I am installing my bioperl script into a new server and I have an > > error that I don't know how > > to solve. Once I have launched my script at the new server, it > > appears a file named "delete" > > that has the following error: > > > > -------------------- WARNING --------------------- > > MSG: req was POST http://www.ncbi.nlm.nih.gov/blast/Blast.cgi > > User-Agent: bioperl-Bio_Tools_Run_RemoteBlast/1.005002102 > > Content-Length: 610 > > Content-Type: application/x-www-form-urlencoded > > > > DATABASE=nr&QUERY=%3Ee3768n+ > > %0Aggtgcccactggggagtcctagcgggcatagcgtatttctccatggtg > > gggaactgggcgaaggtcctgctagtgctgttgttgtttgccggcgtcgatgcggaaacctacatcaccggg > > ggggccgtcgccaaggccgcgcttggattcactgggtttttcacttcgggccccaagcaggacatccagctaatcaactccaacgg > > cagttggcacatcaatcgtactgccttgaactgtaatgcgagcctcgaaaccggctggatagcgg > > ggctcctctatcacaacagattcaactcttcaggctgccccgagaggatggccagctgtagacccctcgccgacttcgaccagggct > > ggggccctatcagctacgccaacggaagcggccccgatcaccgcccc&COMPOSITION_BASE > > D_STATISTICS > > =off&EXPECT=10&SERVICE=plain&FORMAT_OBJECT=Alignment&ALIGNMENTS= > > Pairwise > > &CMD=Put&FILTER=m&DESCRIPTIONS=100&PROGRAM=blastn&ALIGNMENT_VIEW=P > > a > > irwise > > > > > > An Error Occurred > > > >

An Error Occurred

> > 500 Can't connect to www.ncbi.nlm.nih.gov:80 (Bad hostname 'www.ncbi.nlm.nih.gov > > ') > > > > > > > > --------------------------------------------------- > > > > My script works ok in my current machine, a fedora 5 with bioperl > > 1.4 installed through > > cpan. The new server is a fedora 8 and we installed bioperl and > > bioperl run 1.5.2 through > > yumex installer. Both machines have perl 5.8.8 installed. > > > > Any idea of how to solve this error?? Thank you very much in advance. > > > > Alicia > > > > Here you are a part of my script: > > > > #!/usr/bin/perl > > > > use Bio::Seq; > > use Bio::SeqIO; > > use Bio::SearchIO; > > use Bio::DB::GenBank; > > use Bio::Tools::Run::RemoteBlast; > > use POSIX; > > use strict; > > use File::Copy; > > > > # Blast using RemoteBlast > > # get php variables > > > > my $query_filename = $ARGV[0]; > > my $query_filepath = $ARGV[1]; > > my $database = $ARGV[2]; > > my $program = $ARGV[3]; > > my $ALIGNMENTS = $ARGV[5]; > > my $ALIGNMENT_VIEW = $ARGV[5]; > > my $DESCRIPTIONS = $ARGV[6]; > > my $EXPECT = $ARGV[7]; > > # maybe "novar" variables > > my $FILTER_1 = $ARGV[8]; > > my $FILTER_2 = $ARGV[9]; > > my $LCASE_MASK = $ARGV[10]; > > my $MEGABLAST = $ARGV[11]; > > my $UNGAPPED_ALIGNMENT = $ARGV[12]; > > my $user_name = $ARGV[13]; > > my $perlfunc_path = $ARGV[14]; > > my $input = $ARGV[15]; > > my $format = $ARGV[16]; > > > > my $ENTREZ_QUERY = $ARGV[17]; > > > > my @params = ('-prog' => $program, '-data' => $database, '-expect' > > => $EXPECT, '- > > readmethod' => 'SearchIO'); > > > > my $remote = Bio::Tools::Run::RemoteBlast->new(@params); > > # change query parameters > > $Bio::Tools::Run::RemoteBlast::HEADER{'ALIGNMENTS'} = $ALIGNMENTS; > > $Bio::Tools::Run::RemoteBlast::HEADER{'ALIGNMENT_VIEW'} = > > $ALIGNMENT_VIEW; > > $Bio::Tools::Run::RemoteBlast::HEADER{'DESCRIPTIONS'} = $DESCRIPTIONS; > > > > .. > > > > > > > > > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Marie-Claude Hofmann > College of Veterinary Medicine > University of Illinois Urbana-Champaign > > > > > > From Alicia.Amadoz at uv.es Fri Jul 18 06:25:07 2008 From: Alicia.Amadoz at uv.es (Alicia Amadoz) Date: Fri, 18 Jul 2008 12:25:07 +0200 (CEST) Subject: [Bioperl-l] Bio_Tools_Run_RemoteBlast error: 500 Can't connect to www.ncbi.nlm.nih.gov:80 In-Reply-To: References: Message-ID: <3383116578amadoz@uv.es> Hi again, I have been checking my script and when I have my $submit = $remote->submit_blast($query_filepath."/".$query_filename); $query_filepath."/".$query_filename variables have the following value: File: /tmp/alicia_blast_query.fastaR83qbr and $submit has -1 value. So, I think it isn't a problem of installing bioperl in my server because it recognises perl and bioperl installations. I have read documentation at http://doc.bioperl.org/releases/bioperl-current/bioperl- live/Bio/Tools/Run/RemoteBlast.html#POD10 and I think -1 value means an error while sending the request, but what kind of error? it could be some configuration of my server? Thanks for your help, Alicia From mheusel at gmail.com Fri Jul 18 06:42:45 2008 From: mheusel at gmail.com (Martin Heusel) Date: Fri, 18 Jul 2008 12:42:45 +0200 Subject: [Bioperl-l] Bio_Tools_Run_RemoteBlast error: 500 Can't connect to www.ncbi.nlm.nih.gov:80 In-Reply-To: <5551614511amadoz@uv.es> References: <5551614511amadoz@uv.es> Message-ID: <6127fc200807180342r49c6b1f7ubaf5e2e8a6a232cd@mail.gmail.com> >> > 500 Can't connect to www.ncbi.nlm.nih.gov:80 (Bad hostname 'www.ncbi.nlm.nih.gov >> > ') This looks like a DNS Problem?. What does a ping www.ncbi.nlm.nih.gov on the server? -- + Two bosons walk into a bar. The first one orders a beer. + The second one says, "I'll have what he's having." From cjfields at uiuc.edu Fri Jul 18 08:59:51 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 18 Jul 2008 07:59:51 -0500 Subject: [Bioperl-l] Bio_Tools_Run_RemoteBlast error: 500 Can't connect to www.ncbi.nlm.nih.gov:80 In-Reply-To: <3383116578amadoz@uv.es> References: <3383116578amadoz@uv.es> Message-ID: <511B6BA4-95B5-4B47-A7C9-7BD34966F113@uiuc.edu> Actually, your user agent indicated you are using 1.5.2: >> User-Agent: bioperl-Bio_Tools_Run_RemoteBlast/1.005002102 Also, the BLAST URL is the latest one (I changed it late last year; bioperl-1.4 is 4 years old so and didn't have this update). I would try Martin's suggestion of using ping and let us know what happens. chris On Jul 18, 2008, at 5:25 AM, Alicia Amadoz wrote: > Hi again, > > I have been checking my script and when I have > > my $submit = $remote->submit_blast($query_filepath."/". > $query_filename); > > $query_filepath."/".$query_filename variables have the following > value: > File: /tmp/alicia_blast_query.fastaR83qbr > > and $submit has -1 value. > > So, I think it isn't a problem of installing bioperl in my server > because it recognises perl and > bioperl installations. > > I have read documentation at http://doc.bioperl.org/releases/bioperl-current/bioperl- > live/Bio/Tools/Run/RemoteBlast.html#POD10 and I think -1 value means > an error while > sending the request, but what kind of error? it could be some > configuration of my server? > > Thanks for your help, > Alicia > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Marie-Claude Hofmann College of Veterinary Medicine University of Illinois Urbana-Champaign From Alicia.Amadoz at uv.es Fri Jul 18 11:32:32 2008 From: Alicia.Amadoz at uv.es (Alicia Amadoz) Date: Fri, 18 Jul 2008 17:32:32 +0200 (CEST) Subject: [Bioperl-l] Bio_Tools_Run_RemoteBlast error: 500 Can't connect to www.ncbi.nlm.nih.gov:80 In-Reply-To: <511B6BA4-95B5-4B47-A7C9-7BD34966F113@uiuc.edu> References: <511B6BA4-95B5-4B47-A7C9-7BD34966F113@uiuc.edu> Message-ID: <6196559356amadoz@uv.es> Hi, I have tried it and both my computer and the server give the same response: > ping www.ncbi.nih.gov PING www.ncbi.nih.gov (130.14.29.110) 56(84) bytes of data. and nothing else. I have tried other domain (ping my computer from the server) and give more lines of response like 64 bytes from 83.XX.XXX.2: icmp_seq=1 ttl=246 time=1226 ms 64 bytes from 83.XX.XXX.2: icmp_seq=2 ttl=246 time=1230 ms Thanks for your help. Alicia From mheusel at gmail.com Fri Jul 18 11:57:31 2008 From: mheusel at gmail.com (Martin Heusel) Date: Fri, 18 Jul 2008 17:57:31 +0200 Subject: [Bioperl-l] Bio_Tools_Run_RemoteBlast error: 500 Can't connect to www.ncbi.nlm.nih.gov:80 In-Reply-To: <6196559356amadoz@uv.es> References: <511B6BA4-95B5-4B47-A7C9-7BD34966F113@uiuc.edu> <6196559356amadoz@uv.es> Message-ID: <6127fc200807180857g25bc9ca0p35834ae04c2538a1@mail.gmail.com> On Fri, Jul 18, 2008 at 17:32, Alicia Amadoz wrote: >> ping www.ncbi.nih.gov > PING www.ncbi.nih.gov (130.14.29.110) 56(84) bytes of data. > > and nothing else. Right, same here, seems like this server is not configured to answer pings but the name was resolved successfully into 130.14.29.110 so DNS works. Can you ping some hosts outside of your network like ping www.google.com ? -- + Two bosons walk into a bar. The first one orders a beer. + The second one says, "I'll have what he's having." From Alicia.Amadoz at uv.es Fri Jul 18 13:52:27 2008 From: Alicia.Amadoz at uv.es (Alicia Amadoz) Date: Fri, 18 Jul 2008 19:52:27 +0200 (CEST) Subject: [Bioperl-l] Bio_Tools_Run_RemoteBlast error: 500 Can't connect to www.ncbi.nlm.nih.gov:80 In-Reply-To: <511B6BA4-95B5-4B47-A7C9-7BD34966F113@uiuc.edu> References: <511B6BA4-95B5-4B47-A7C9-7BD34966F113@uiuc.edu> Message-ID: <9554129967amadoz@uv.es> >From my server, > ping www.google.com PING www.l.google.com (74.125.39.147) 56(84) bytes of data. 64 bytes from fx-in-f147.google.com (74.125.39.147): icmp_seq=1 ttl=242 time=41.7 ms 64 bytes from fx-in-f147.google.com (74.125.39.147): icmp_seq=2 ttl=242 time=41.9 ms 64 bytes from fx-in-f147.google.com (74.125.39.147): icmp_seq=3 ttl=242 time=41.7 ms 64 bytes from fx-in-f147.google.com (74.125.39.147): icmp_seq=4 ttl=242 time=41.8 ms 64 bytes from fx-in-f147.google.com (74.125.39.147): icmp_seq=5 ttl=242 time=41.6 ms 64 bytes from fx-in-f147.google.com (74.125.39.147): icmp_seq=6 ttl=242 time=41.7 ms .. So, do you think I should change some network configuration of my server or is it a problem only related to www.ncbi.nih.gov?? I think is the later but then, how can I manage to run my script at my server? Thanks a lot. Regards, Alicia From mheusel at gmail.com Fri Jul 18 14:13:19 2008 From: mheusel at gmail.com (Martin Heusel) Date: Fri, 18 Jul 2008 20:13:19 +0200 Subject: [Bioperl-l] Bio_Tools_Run_RemoteBlast error: 500 Can't connect to www.ncbi.nlm.nih.gov:80 In-Reply-To: <9554129967amadoz@uv.es> References: <511B6BA4-95B5-4B47-A7C9-7BD34966F113@uiuc.edu> <9554129967amadoz@uv.es> Message-ID: <6127fc200807181113p5c50cf9cj3fdca4f85214f601@mail.gmail.com> On Fri, Jul 18, 2008 at 19:52, Alicia Amadoz wrote: > From my server, > >> ping www.google.com > PING www.l.google.com (74.125.39.147) 56(84) bytes of data. > 64 bytes from fx-in-f147.google.com (74.125.39.147): icmp_seq=1 ttl=242 time=41.7 ms > 64 bytes from fx-in-f147.google.com (74.125.39.147): icmp_seq=2 ttl=242 time=41.9 ms > 64 bytes from fx-in-f147.google.com (74.125.39.147): icmp_seq=3 ttl=242 time=41.7 ms > 64 bytes from fx-in-f147.google.com (74.125.39.147): icmp_seq=4 ttl=242 time=41.8 ms > 64 bytes from fx-in-f147.google.com (74.125.39.147): icmp_seq=5 ttl=242 time=41.6 ms > 64 bytes from fx-in-f147.google.com (74.125.39.147): icmp_seq=6 ttl=242 time=41.7 ms perfect > So, do you think I should change some network configuration of my server or is it a problem > only related to www.ncbi.nih.gov?? I think is the later but then, how can I manage to run my > script at my server? Your network configuration looks good. The error is 500 Can't connect to www.ncbi.nlm.nih.gov:80 (Bad hostname 'www.ncbi.nlm.nih.gov') Do you have a browser on your server? Can you reach www.ncbi.nlm.nih.gov? Or for security reasons you can test this on the console with telnet www.ncbi.nlm.nih.gov 80 If it's okay this should appear $ telnet www.ncbi.nlm.nih.gov 80 Trying 130.14.29.110... Connected to www.ncbi.nlm.nih.gov. Escape character is '^]'. If this appears www.ncbi.nlm.nih.gov is reachable and i don't know where the error comes from. I wonder myself who produces this output anyway An Error Occurred

An Error Occurred

500 Can't connect to www.ncbi.nlm.nih.gov:80 (Bad hostname 'www.ncbi.nlm.nih.gov') Is it bioperl or the ncbi server? Martin -- + Martin Heusel + Institute of Bioinformatics, Johannes Kepler University Linz, Austria + http://www.bioinf.jku.at/ + Two bosons walk into a bar. The first one orders a beer. + The second one says, "I'll have what he's having." From cjfields at uiuc.edu Fri Jul 18 14:26:52 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 18 Jul 2008 13:26:52 -0500 Subject: [Bioperl-l] Bio_Tools_Run_RemoteBlast error: 500 Can't connect to www.ncbi.nlm.nih.gov:80 In-Reply-To: <6127fc200807181113p5c50cf9cj3fdca4f85214f601@mail.gmail.com> References: <511B6BA4-95B5-4B47-A7C9-7BD34966F113@uiuc.edu> <9554129967amadoz@uv.es> <6127fc200807181113p5c50cf9cj3fdca4f85214f601@mail.gmail.com> Message-ID: <5408288A-FF5E-47C8-9D1F-D69958567B26@uiuc.edu> On Jul 18, 2008, at 1:13 PM, Martin Heusel wrote: >> ... > > Your network configuration looks good. > > The error is > > 500 Can't connect to www.ncbi.nlm.nih.gov:80 (Bad hostname > 'www.ncbi.nlm.nih.gov') > > ... > I wonder myself who produces this output anyway > > > An Error Occurred > >

An Error Occurred

> 500 Can't connect to www.ncbi.nlm.nih.gov:80 (Bad hostname > 'www.ncbi.nlm.nih.gov') > > > > Is it bioperl or the ncbi server? > > Martin It's not BioPerl. I checked RemoteBlast myself; beyond a failure in tabular BLAST parsing everything works (i.e. text parsing, XML parsing, connections, etc.). chris From Alicia.Amadoz at uv.es Fri Jul 18 14:38:26 2008 From: Alicia.Amadoz at uv.es (Alicia Amadoz) Date: Fri, 18 Jul 2008 20:38:26 +0200 (CEST) Subject: [Bioperl-l] Bio_Tools_Run_RemoteBlast error: 500 Can't connect to www.ncbi.nlm.nih.gov:80 Message-ID: <2284623158amadoz@uv.es> Hi, I have tried >telnet www.ncbi.nlm.nih.gov 80 and it gives what you said, $ telnet www.ncbi.nlm.nih.gov 80 Trying 130.14.29.110... Connected to www.ncbi.nlm.nih.gov. Escape character is '^]'. I don't know exactly who gives the output message with the error. It creates a file as my script is launched. The file is called "delete" and is like de STDERR/STDOUT of the script. I haven't programmed anything to create this file, but I can say that the message of error is given just after this line: my $submit = $remote->submit_blast($query_filepath."/".$query_filename); So, I don't know if the message is given by bioperl functions or by the ncbi. Any help at this point? Thanks a lot in advance. Regards, Alicia From cjfields at uiuc.edu Fri Jul 18 14:53:03 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 18 Jul 2008 13:53:03 -0500 Subject: [Bioperl-l] Bio_Tools_Run_RemoteBlast error: 500 Can't connect to www.ncbi.nlm.nih.gov:80 In-Reply-To: <2284623158amadoz@uv.es> References: <2284623158amadoz@uv.es> Message-ID: <9BABA21B-A59B-4EF1-B456-DED215FB1070@uiuc.edu> On Jul 18, 2008, at 1:38 PM, Alicia Amadoz wrote: > Hi, > > I have tried >telnet www.ncbi.nlm.nih.gov 80 and it gives what you > said, > > $ telnet www.ncbi.nlm.nih.gov 80 > Trying 130.14.29.110... > Connected to www.ncbi.nlm.nih.gov. > Escape character is '^]'. > > I don't know exactly who gives the output message with the error. It > creates a file as my > script is launched. The file is called "delete" and is like de > STDERR/STDOUT of the script. I > haven't programmed anything to create this file, but I can say that > the message of error is > given just after this line: > > my $submit = $remote->submit_blast($query_filepath."/". > $query_filename); From the original script you appear to be running things from a PHP environment, so maybe it has something to do with that, e.g. maybe you need to set other env. settings (like a proxy) in order to connect. You can test this; in the same script, try using another module which makes remote connections. For instance, try the following to see if you have a similar error: use Bio::DB::GenBank; my $gb = Bio::DB::GenBank->new(); my $seqio = $gb->get_Stream_by_id([qw(J00522 AF303112 2981014)]); while (my $seq = $seqio->next_seq) { print $seq->accession_number."\n"; } > So, I don't know if the message is given by bioperl functions or by > the ncbi. By LWP, actually. The BLAST request is retrieved using the RID and if there is an error flag, either due to connection issues or from a problem on their server, an exception is thrown with the proper message which the module catches and converts into the relevant display message. > Any help at this point? Thanks a lot in advance. > > Regards, > Alicia From ronnie.dejonge at gmail.com Mon Jul 21 06:13:47 2008 From: ronnie.dejonge at gmail.com (Dhr. R. de Jonge) Date: Mon, 21 Jul 2008 12:13:47 +0200 Subject: [Bioperl-l] (no subject) Message-ID: Dear all, I've recently started working with the bioperl package. However, as I wasn't trained a bioinformatician (rather molecular biologist) I'm now and then facing difficulties starting up. Though, using some books from James Tisdall and documenting the bioperl manuals I figured out much of the stuff. Still I'm facing a problem I don't seem to get fixed easily. The problem is as follows: 1) I've set-up a blastable database of cDNA/transcript sequences of a complete set of fungal genomes (and produced a protein blastable database from this one). 2) I've checked this database for a particular HMM domain using the Bio::Tools::Run::Hmmer module and some custom scripting. Using this I generated a file containing a simple fasta header and corresponding domain-sequence (protein). 3) However, from an evolutionary view I want to look at non-synonymous versus synonymous mutations (using the transcript data I started with). To perform this test I'd like to use the bioperl PAML module. Naturally; I need the 'original' cDNA sequence to test my hypotheses. (the question then is: how to obtain this cDNA sequence?). I tried to solve this issue by blasting the obtained protein sequence to the cDNA database using the tblastn package. I specified in a script the number of hits to be screened (i.e. 1), and used the trunc() method (using the blast hit sequence) to get the corresponding cDNA sequence. However, it seems not all hits are perfect matches, i.e. on some occasions not the original (corresponding) sequence object is retrieved, leaving me with false cDNA --> protein lists. Coming to the actual question: Is it possible to circumvent this whole (sort of false) procedure and use e.g. the Bio::Annotation modules? If yes, can you give some hints/feedback on setting-up a method for this? I'd like to hear your thoughts on this one. Many thanks in advance. With regards, Ronnie de Jonge MSc. Ronnie de Jonge Wageningen University Department of Plant Sciences, Laboratory of Phytopathology Binnenhaven 5, 6709 PD Wageningen Tel.: +31-317-483224 From David.Messina at sbc.su.se Mon Jul 21 08:36:04 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Mon, 21 Jul 2008 14:36:04 +0200 Subject: [Bioperl-l] (no subject) In-Reply-To: References: Message-ID: <628aabb70807210536o3949368ar8dd19ed7a6d9a490@mail.gmail.com> Hi Ronnie, I'm not sure I'm following you -- you start with a database of cDNA sequences, but you're asking how to obtain the cDNA sequence. Do you mean, once you've identified in protein space with HMMer a subset of sequences that contain a certain domain, how do you pick out the corresponding cDNA sequences from your starting database? I'm not sure this is what your mean, but you should be able to generate a lookup hash of which protein sequence identifier corresponds to which cDNA identifier. Once you've used your protein IDs to get the list of cDNA IDs, then you can extract the cDNA sequences from your original database. It would probably be possible to use Bio::Annotation to keep track of the relationship between a protein ID and a cDNA ID, but this seems like overkill to me compared to a plain old hash. If you haven't already, you may want to check out the PAML HOWTO on the BioPerl website http://www.bioperl.org/wiki/HOWTO:PAML#Running_PAML_from_within_BioPerl which shows the pairwise_kaks script. Or look directly at the script itself, included in the bioperl-live distribution under scripts/utilities. In any case, I'm not sure I've answered your question -- please follow up if I've missed the point. Dave From ronnie.dejonge at gmail.com Mon Jul 21 10:17:51 2008 From: ronnie.dejonge at gmail.com (Dhr. R. de Jonge) Date: Mon, 21 Jul 2008 16:17:51 +0200 Subject: [Bioperl-l] (no subject) In-Reply-To: <628aabb70807210536o3949368ar8dd19ed7a6d9a490@mail.gmail.com> References: <628aabb70807210536o3949368ar8dd19ed7a6d9a490@mail.gmail.com> Message-ID: Hi Dave, To be more precise, I am actually looking for the subset of the cDNA sequence that contains the sequence producing the obtained domain (for multiple HMMer hits than so to speak). Cheers Ronnie 2008/7/21, Dave Messina : > Hi Ronnie, > I'm not sure I'm following you -- you start with a database of cDNA > sequences, but you're asking how to obtain the cDNA sequence. > > Do you mean, once you've identified in protein space with HMMer a subset of > sequences that contain a certain domain, how do you pick out the > corresponding cDNA sequences from your starting database? > > I'm not sure this is what your mean, but you should be able to generate a > lookup hash of which protein sequence identifier corresponds to which cDNA > identifier. Once you've used your protein IDs to get the list of cDNA IDs, > then you can extract the cDNA sequences from your original database. It > would probably be possible to use Bio::Annotation to keep track of the > relationship between a protein ID and a cDNA ID, but this seems like > overkill to me compared to a plain old hash. > > If you haven't already, you may want to check out the PAML HOWTO on the > BioPerl website > http://www.bioperl.org/wiki/HOWTO:PAML#Running_PAML_from_within_BioPerl > > which shows the pairwise_kaks script. Or look directly at the script itself, > included in the bioperl-live distribution under scripts/utilities. > > In any case, I'm not sure I've answered your question -- please follow up if > I've missed the point. > > Dave > From David.Messina at sbc.su.se Mon Jul 21 11:04:10 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Mon, 21 Jul 2008 17:04:10 +0200 Subject: [Bioperl-l] (no subject) In-Reply-To: References: <628aabb70807210536o3949368ar8dd19ed7a6d9a490@mail.gmail.com> Message-ID: <628aabb70807210804l4d7cba0el129425e40a475a81@mail.gmail.com> Okay, let me see if I've got this straight: you want to do Ka/Ks on just the subsequences of the cDNAs that match the HMMer domain? e.g. 1) You have a cDNA sequence. Let's call it Xn. 2) Xn is 300 nucleotides in length. 3) You translate Xn into protein Xp. 4) You use HMMer to search Xp against Pfam. 5) HMMer tells you that Xp has, for example, an SH2 domain from residue 30 to residue 51. 6) Likewise, let's say two additional proteins Yp and Zp have the same SH2 domain. You want to: 7) Determine which nucleotides in Xn correspond to amino acids 30-51 in Xp. 8) Extract just those nucleotides (and also the nucleotides in Yn and Zn corresponding to their SH2 domain hits). 9) Align those nucleotide sequences. 10) Give the resulting multiple alignment to PAML and calculate the Ka/Ks ratios. Is that correct? Is it steps 7 and 8 that you are trying to solve? Dave From ronnie.dejonge at gmail.com Mon Jul 21 11:09:13 2008 From: ronnie.dejonge at gmail.com (Ronnie de Jonge) Date: Mon, 21 Jul 2008 17:09:13 +0200 Subject: [Bioperl-l] (no subject) In-Reply-To: <628aabb70807210804l4d7cba0el129425e40a475a81@mail.gmail.com> References: <628aabb70807210536o3949368ar8dd19ed7a6d9a490@mail.gmail.com> <628aabb70807210804l4d7cba0el129425e40a475a81@mail.gmail.com> Message-ID: <000601c8eb43$bc6e71b0$d250e089@wurnet.nl> Hi Dave, Exactly my problem there in step 7 and 8. As said, I tried to solve this problem by blasting the domain sequence to the cdna database, and use the first hit reference (parse by searchIO) for further truncation of the cdna hit. Though this gives false positives. ----- I'm wonder now if i could do the same, though instead of blasting the entire database just blast the hit to it's own cdna sequence (single fasta) 'on-the-fly'? (guess not possible, regarding the formatdb step?) ----- Cheers Ronnie _____ From: dave at davemessina.com [mailto:dave at davemessina.com] On Behalf Of Dave Messina Sent: maandag 21 juli 2008 17:04 To: Dhr. R. de Jonge Cc: bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] (no subject) Okay, let me see if I've got this straight: you want to do Ka/Ks on just the subsequences of the cDNAs that match the HMMer domain? e.g. 1) You have a cDNA sequence. Let's call it Xn. 2) Xn is 300 nucleotides in length. 3) You translate Xn into protein Xp. 4) You use HMMer to search Xp against Pfam. 5) HMMer tells you that Xp has, for example, an SH2 domain from residue 30 to residue 51. 6) Likewise, let's say two additional proteins Yp and Zp have the same SH2 domain. You want to: 7) Determine which nucleotides in Xn correspond to amino acids 30-51 in Xp. 8) Extract just those nucleotides (and also the nucleotides in Yn and Zn corresponding to their SH2 domain hits). 9) Align those nucleotide sequences. 10) Give the resulting multiple alignment to PAML and calculate the Ka/Ks ratios. Is that correct? Is it steps 7 and 8 that you are trying to solve? Dave From Alicia.Amadoz at uv.es Mon Jul 21 11:24:24 2008 From: Alicia.Amadoz at uv.es (Alicia Amadoz) Date: Mon, 21 Jul 2008 17:24:24 +0200 (CEST) Subject: [Bioperl-l] Bio_Tools_Run_RemoteBlast error: 500 Can't connect to www.ncbi.nlm.nih.gov:80 In-Reply-To: <9BABA21B-A59B-4EF1-B456-DED215FB1070@uiuc.edu> References: <9BABA21B-A59B-4EF1-B456-DED215FB1070@uiuc.edu> Message-ID: <1358281254amadoz@uv.es> Hi, I have tried what you suggested and what I get is another error: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: WebDBSeqI Request Error: 500 Can't connect to eutils.ncbi.nlm.nih.gov:80 (Bad hostname 'eutils.ncbi.nlm.nih.gov') Content-Type: text/plain Client-Date: Mon, 21 Jul 2008 15:07:39 GMT Client-Warning: Internal response 500 Can't connect to eutils.ncbi.nlm.nih.gov:80 (Bad hostname 'eutils.ncbi.nlm.nih.gov') STACK: Error::throw STACK: Bio::Root::Root::throw /usr/lib/perl5/vendor_perl/5.8.8/Bio/Root/Root.pm:359 STACK: Bio::DB::WebDBSeqI::_stream_request /usr/lib/perl5/vendor_perl/5.8.8/Bio/DB/WebDBSeqI.pm:758 STACK: Bio::DB::WebDBSeqI::get_seq_stream /usr/lib/perl5/vendor_perl/5.8.8/Bio/DB/WebDBSeqI.pm:454 STACK: Bio::DB::WebDBSeqI::get_Stream_by_id /usr/lib/perl5/vendor_perl/5.8.8/Bio/DB/WebDBSeqI.pm:275 STACK: /var/www/html/perl-cgi//remote_blast_ncbi.pl:48 ----------------------------------------------------------- in line 48 of my script is, my $seqio = $gb->get_Stream_by_id([qw(J00522 AF303112 2981014)]); > From the original script you appear to be running things from a PHP > environment, so maybe it has something to do with that, e.g. maybe you > need to set other env. settings (like a proxy) in order to connect. I am going to check again php.info but I have no idea what can it be. Thanks again for your help. Alicia From diriano at uni-potsdam.de Mon Jul 21 11:49:10 2008 From: diriano at uni-potsdam.de (Diego Mauricio Riano Pachon) Date: Mon, 21 Jul 2008 17:49:10 +0200 Subject: [Bioperl-l] (no subject) In-Reply-To: <000601c8eb43$bc6e71b0$d250e089@wurnet.nl> References: <628aabb70807210536o3949368ar8dd19ed7a6d9a490@mail.gmail.com> <628aabb70807210804l4d7cba0el129425e40a475a81@mail.gmail.com> <000601c8eb43$bc6e71b0$d250e089@wurnet.nl> Message-ID: <4884AFF6.2010008@uni-potsdam.de> Hi Ronnie, Ronnie de Jonge wrote: > Hi Dave, > Exactly my problem there in step 7 and 8. > As said, I tried to solve this problem by blasting the domain sequence to > the cdna database, and use the first hit reference (parse by searchIO) for > further truncation of the cdna hit. Though this gives false positives. > > ----- > I'm wonder now if i could do the same, though instead of blasting the > entire database just blast the hit to it's own cdna sequence (single fasta) > 'on-the-fly'? (guess not possible, regarding the formatdb step?) > ----- Yes, you can do this. using bl2seq (BLAST 2 sequences), something like: Assuming that: - $DNA has your Xn DNA sequence as a bioperl object, as in Dave e-mail. - $protein_subseq has the SH2 domain from residue 30 to 51 from protein Xp, as a bioperl object my $blast_factory= Bio::Tools::Run::StandAloneBlast->new(-program => 'blastx', -F => 'F', -outfile => "$blast_output"); $blast_factory->bl2seq($DNA,$protein_subseq); then you can parse the blast result using Bio::SearchIO. hope this helps, Diego > > Cheers > Ronnie > > _____ > > From: dave at davemessina.com [mailto:dave at davemessina.com] On Behalf Of Dave > Messina > Sent: maandag 21 juli 2008 17:04 > To: Dhr. R. de Jonge > Cc: bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] (no subject) > > > Okay, let me see if I've got this straight: you want to do Ka/Ks on just the > subsequences of the cDNAs that match the HMMer domain? > > > e.g. > 1) You have a cDNA sequence. Let's call it Xn. > 2) Xn is 300 nucleotides in length. > 3) You translate Xn into protein Xp. > 4) You use HMMer to search Xp against Pfam. > 5) HMMer tells you that Xp has, for example, an SH2 domain from residue 30 > to residue 51. > 6) Likewise, let's say two additional proteins Yp and Zp have the same SH2 > domain. > > You want to: > 7) Determine which nucleotides in Xn correspond to amino acids 30-51 in Xp. > 8) Extract just those nucleotides (and also the nucleotides in Yn and Zn > corresponding to their SH2 domain hits). > 9) Align those nucleotide sequences. > 10) Give the resulting multiple alignment to PAML and calculate the Ka/Ks > ratios. > > Is that correct? > Is it steps 7 and 8 that you are trying to solve? > > > > Dave > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ___________________________________ Diego Mauricio Ria?o Pach?n Biologist - PhD student AG Mueller-Roeber Institute for Biochemistry and Biology University of Potsdam Address: Karl-Liebknecht-Str. 24-25 Haus 20 14476 Golm Germany Tel: +49 331 977 2809 Fax: +49 331 977 2512 web: http://www.geocities.com/dmrp.geo From cjfields at uiuc.edu Mon Jul 21 12:24:45 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 21 Jul 2008 11:24:45 -0500 Subject: [Bioperl-l] Bio_Tools_Run_RemoteBlast error: 500 Can't connect to www.ncbi.nlm.nih.gov:80 In-Reply-To: <1358281254amadoz@uv.es> References: <9BABA21B-A59B-4EF1-B456-DED215FB1070@uiuc.edu> <1358281254amadoz@uv.es> Message-ID: <0196157D-0D2F-4DB3-AEE0-91BB56F3B82C@uiuc.edu> Okay, so it appears there are overall connection issues (i.e. this isn't just a RemoteBlast issue). The fact that you can ping from command line also makes me think it isn't a proxy issue. I'm not familiar with PHP myself, but I would think it only allows user- defined processes to access network connections, so that's my next guess. Out of curiosity, is there any particular reason you are using PHP? chris On Jul 21, 2008, at 10:24 AM, Alicia Amadoz wrote: > Hi, > > I have tried what you suggested and what I get is another error: > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: WebDBSeqI Request Error: > 500 Can't connect to eutils.ncbi.nlm.nih.gov:80 (Bad hostname > 'eutils.ncbi.nlm.nih.gov') > Content-Type: text/plain > Client-Date: Mon, 21 Jul 2008 15:07:39 GMT > Client-Warning: Internal response > > 500 Can't connect to eutils.ncbi.nlm.nih.gov:80 (Bad hostname > 'eutils.ncbi.nlm.nih.gov') > > STACK: Error::throw > STACK: Bio::Root::Root::throw /usr/lib/perl5/vendor_perl/5.8.8/Bio/ > Root/Root.pm:359 > STACK: Bio::DB::WebDBSeqI::_stream_request > /usr/lib/perl5/vendor_perl/5.8.8/Bio/DB/WebDBSeqI.pm:758 > STACK: Bio::DB::WebDBSeqI::get_seq_stream > /usr/lib/perl5/vendor_perl/5.8.8/Bio/DB/WebDBSeqI.pm:454 > STACK: Bio::DB::WebDBSeqI::get_Stream_by_id > /usr/lib/perl5/vendor_perl/5.8.8/Bio/DB/WebDBSeqI.pm:275 > STACK: /var/www/html/perl-cgi//remote_blast_ncbi.pl:48 > ----------------------------------------------------------- > > in line 48 of my script is, > > my $seqio = $gb->get_Stream_by_id([qw(J00522 AF303112 2981014)]); > >> From the original script you appear to be running things from a PHP >> environment, so maybe it has something to do with that, e.g. maybe >> you >> need to set other env. settings (like a proxy) in order to connect. > > I am going to check again php.info but I have no idea what can it be. > > Thanks again for your help. > Alicia > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Marie-Claude Hofmann College of Veterinary Medicine University of Illinois Urbana-Champaign From David.Messina at sbc.su.se Mon Jul 21 12:31:19 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Mon, 21 Jul 2008 18:31:19 +0200 Subject: [Bioperl-l] (no subject) In-Reply-To: <4884AFF6.2010008@uni-potsdam.de> References: <628aabb70807210536o3949368ar8dd19ed7a6d9a490@mail.gmail.com> <628aabb70807210804l4d7cba0el129425e40a475a81@mail.gmail.com> <000601c8eb43$bc6e71b0$d250e089@wurnet.nl> <4884AFF6.2010008@uni-potsdam.de> Message-ID: <628aabb70807210931g7744b11ax25805075a7f1413f@mail.gmail.com> You know which protein sequence corresponds to which cDNA sequence, so I think you could also: - take the start and end coordinates of the domain in the protein (from the HMMer output) - convert those into the start and end coordinates of the domain in the cDNA - use the subseq() method to extract the subsequence of the cDNA Dave From cjfields at uiuc.edu Mon Jul 21 12:42:37 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 21 Jul 2008 11:42:37 -0500 Subject: [Bioperl-l] (no subject) In-Reply-To: <628aabb70807210931g7744b11ax25805075a7f1413f@mail.gmail.com> References: <628aabb70807210536o3949368ar8dd19ed7a6d9a490@mail.gmail.com> <628aabb70807210804l4d7cba0el129425e40a475a81@mail.gmail.com> <000601c8eb43$bc6e71b0$d250e089@wurnet.nl> <4884AFF6.2010008@uni-potsdam.de> <628aabb70807210931g7744b11ax25805075a7f1413f@mail.gmail.com> Message-ID: Ya beat me to it! I agree, this is the best way to go, and it would save an extra BLAST run (though if you need it Diego's bl2seq suggestion is the way to go). chris On Jul 21, 2008, at 11:31 AM, Dave Messina wrote: > You know which protein sequence corresponds to which cDNA sequence, > so I > think you could also: > > - take the start and end coordinates of the domain in the protein > (from the > HMMer output) > - convert those into the start and end coordinates of the domain in > the cDNA > - use the subseq() method to extract the subsequence of the cDNA > > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From MEC at stowers-institute.org Mon Jul 21 17:19:57 2008 From: MEC at stowers-institute.org (Cook, Malcolm) Date: Mon, 21 Jul 2008 16:19:57 -0500 Subject: [Bioperl-l] public qblast servers? In-Reply-To: References: Message-ID: Russell, I don't think anyone but NCBI implements the qblast protocol. However, much of the sequences at wormbase for nematode are submitted to genbank. So, you simply need to figure out the appopriate combination or organism, database, and entrez query that corresponds to the dataset you want to query. Also, you should know, that Vector NTI gives you a list of ncbi databases from which to choose. But his list is incomplete. You can type into this box any database listed here: http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html and it works So, for example, to blast against c elegans refseq mrnas, you would provide refseq_mrna as the database and 'Caenorhabditis elegans' as the organism. Of course many other combinations are possible. This should work for nematode and elegans data. H contortus appears not yet released to genbank, so I think you will have to download them and build your own blast database for use with your qblast wroapper. Regarding your faked qblast, would you be willing to share this code with our non-profit research institute? I'm in a similar position and have planned to write a fake qblast wrapper but have not made the time..... I, and many researchers here, would be obliged. Malcolm Cook Stowers Institute for Medical Research - Kansas City, Missouri -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Smithies, Russell Sent: Tuesday, July 08, 2008 9:37 PM To: Bioperl-l at lists.open-bio.org Subject: [Bioperl-l] public qblast servers? Hi all, Not a BioPerl question, but does anyone know of any public qblast servers? DB's of interest would be at: Wormbase: http://www.wormbase.org/ Nematode Net: http://www.nematode.net/ H. contortus: http://www.sanger.ac.uk/Projects/H_contortus/ We have a script that fakes qblast internally so Vector NTI will work with it but some of our users would like to blast elsewhere. Thanx, Russell Smithies ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From alperyilmaz at gmail.com Mon Jul 21 18:18:55 2008 From: alperyilmaz at gmail.com (Alper Yilmaz) Date: Mon, 21 Jul 2008 18:18:55 -0400 Subject: [Bioperl-l] bio::graphics:panel track name Message-ID: Hi, I went through the manual but couldn't solve the problem. I'm trying to have track labels in a graph generated by bio::graphics::panel. I'm using -key=>'CRE' within add_track. but the output is not what I wanted. This generates a key legend on the bottom of the graph instead of putting the track name on left of the track. below is a sample track and as I said this does NOT generate a track with track name "CRE" on left. @features gets the start, end information via Bio::SeqFeature::Generic What am I doing wrong here? $panel->add_track(\@features, -glyph => 'generic', -bgcolor => 'yellow', -title => sub { my $element = shift; my $name = $element->display_name; return $name; }, -key=>'CRE', -label=> 1, -description=>0, -link => 'cis_info.html?cis_name=$name', ); Sorry for bothering you with my questions lately, but I ensure that I go through the manual and some pain, and then ask the question here. thanks, alper From lstein at cshl.edu Mon Jul 21 20:02:36 2008 From: lstein at cshl.edu (Lincoln Stein) Date: Mon, 21 Jul 2008 20:02:36 -0400 Subject: [Bioperl-l] Any volunteers for doing a Nested Containment List implementation? Message-ID: <6dce9a0b0807211702k1742884enf02ae53587a42922@mail.gmail.com> Hi Folks, This paper describes an indexing algorithm for genome feature databases called Nested Containment Lists. Apparently it is substantially faster than the indexing systems we use in BioPerl for the Bio::DB::GFF, Bio::DB::SeqFeature::Store, and Chado. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btl647v1?papetoc The concept and data structures are quite simple, and I think it would be straightforward to implement this system in MySQL tables. Would anybody be interested in taking this on as a summer project? Lincoln -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Stacey Fairfield Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 USA (516) 367-8380 Assistant: Sandra Michelsen From lincoln.stein at gmail.com Mon Jul 21 20:17:29 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Mon, 21 Jul 2008 20:17:29 -0400 Subject: [Bioperl-l] bio::graphics:panel track name In-Reply-To: References: Message-ID: <6dce9a0b0807211717j5b1c4893j9a4c0fc80f27a7ac@mail.gmail.com> Hi Alper, When you create the Bio::Graphics::Panel, pass it a *-key_style* option of "left" or "between". If you use "left" you may also need to provide a * -pad_left* option to add extra space in the image for the keys to fit, depending on which version of bioperl you are using. Lincoln On Mon, Jul 21, 2008 at 6:18 PM, Alper Yilmaz wrote: > Hi, > I went through the manual but couldn't solve the problem. I'm trying > to have track labels in a graph generated by bio::graphics::panel. I'm > using > -key=>'CRE' within add_track. > > but the output is not what I wanted. This generates a key legend on > the bottom of the graph instead of putting the track name on left of > the track. > > below is a sample track and as I said this does NOT generate a track > with track name "CRE" on left. @features gets the start, end > information via Bio::SeqFeature::Generic > What am I doing wrong here? > > $panel->add_track(\@features, -glyph => 'generic', > -bgcolor => 'yellow', > -title => sub { > my $element = shift; > my $name = $element->display_name; > return $name; > }, > -key=>'CRE', > -label=> 1, > -description=>0, > -link => 'cis_info.html?cis_name=$name', > ); > > Sorry for bothering you with my questions lately, but I ensure that I > go through the manual and some pain, and then ask the question here. > > thanks, > > alper > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Stacey Fairfield Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 USA (516) 367-8380 Assistant: Sandra Michelsen From cjfields at uiuc.edu Mon Jul 21 21:27:58 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 21 Jul 2008 20:27:58 -0500 Subject: [Bioperl-l] Any volunteers for doing a Nested Containment List implementation? In-Reply-To: <6dce9a0b0807211702k1742884enf02ae53587a42922@mail.gmail.com> References: <6dce9a0b0807211702k1742884enf02ae53587a42922@mail.gmail.com> Message-ID: <38ECEED6-4825-4634-ABFD-D07D2FBA28C7@uiuc.edu> It's definitely worth exploring. Might be nice to sort a few things out, for instance, do we want to use their C library, or role our own data structures? And would we want this to retain a similar interface to Bio::DB::SeqFeature::Store? chris On Jul 21, 2008, at 7:02 PM, Lincoln Stein wrote: > Hi Folks, > > This paper describes an indexing algorithm for genome feature > databases > called Nested Containment Lists. Apparently it is substantially > faster than > the indexing systems we use in BioPerl for the Bio::DB::GFF, > Bio::DB::SeqFeature::Store, and Chado. > > http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btl647v1?papetoc > > The concept and data structures are quite simple, and I think it > would be > straightforward to implement this system in MySQL tables. Would > anybody be > interested in taking this on as a summer project? > > Lincoln > > -- > Lincoln D. Stein > > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Stacey Fairfield > > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 USA > (516) 367-8380 > Assistant: Sandra Michelsen > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Marie-Claude Hofmann College of Veterinary Medicine University of Illinois Urbana-Champaign From khalid.ELKARKOURI at univmed.fr Thu Jul 17 10:25:24 2008 From: khalid.ELKARKOURI at univmed.fr (EL KARKOURI Khalid) Date: Thu, 17 Jul 2008 16:25:24 +0200 Subject: [Bioperl-l] Bioperl Message-ID: <5.0.2.1.2.20080717161015.00bdbfc0@imap.univmed.fr> Dear All, I am working on the Linux OpenSuse platform, and I would like some help for installing bioperl suite in this platform. Thank you very much, Khalid From potterbond007 at gmail.com Thu Jul 17 12:14:17 2008 From: potterbond007 at gmail.com (#Raul#~~ WeAtHerEd~~) Date: Thu, 17 Jul 2008 17:14:17 +0100 Subject: [Bioperl-l] PHYLIP problem. In-Reply-To: <628aabb70807170857u19300dd7md079878f6fd38e75@mail.gmail.com> References: <87ec85590807162127k56396f64j3998604ee29f1a6a@mail.gmail.com> <628aabb70807170259p6536dfa0oe70579f291c011a0@mail.gmail.com> <87ec85590807170734v2f24b5c1n962b15e22b067896@mail.gmail.com> <628aabb70807170857u19300dd7md079878f6fd38e75@mail.gmail.com> Message-ID: <87ec85590807170914u4b27746as33155c7e5d22bd41@mail.gmail.com> Dear sir, I installed PHYLIP locally and ran the input file on it and the output was given in a flash. This seems to be the miss of a package that has to be installed since it isn't working on my friend's computer too. I haven't tried the program on windows. I tried changing the folder of my input file and running the program but it still refuses to work. I will try working out the rest of the function availavle in the documentation and let you know if I am getting any further errors after skipping the protdist function. Thank you, Rahul On Thu, Jul 17, 2008 at 4:57 PM, Dave Messina wrote: > Hi Rahul, > Please keep the mailing list on the Cc so that this discussion can be > archived and others can see it. > > There's an error in your program -- you change the variable for the input > file from $inputfilename in one place to $inputfile in another. It's a > good idea to always use warnings and use strict with Perl. With warnings, > the first error shown is: > > Name "main::inputfile" used only once: possible typo at test.pl line 9. > > which indicates that there is something wrong with $inputfile. > > Here's the complete program I ran: > #!/usr/bin/perl > > > use warnings; > use strict; > use Bio::Tools::Run::Phylo::Phylip::ProtDist; > > my $inputfilename = 'align.phy'; > my $prodistfactory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(); > > my ($matrix)= $prodistfactory->run($inputfilename); > print $matrix->print_matrix; > > > Note that your perl may be in a different location than mine, so the first > line may need to be changed. Also note that I changed the location of the > input file -- it was in the same directory as my Perl script. > > The error you saw about 'protdist did not create matrix correctly' is > unfortunately vague. It simply means that, for some reason, protdist didn't > produce any output that BioPerl could see. A likely reason for this to occur > is that protdist didn't run at all. > > Have you installed PHYLIP (and specifically protdist), and have you tried > running it outside of BioPerl? > > > Dave > > > > On Thu, Jul 17, 2008 at 16:34, #Raul#~~ WeAtHerEd~~ < > potterbond007 at gmail.com> wrote: > >> Dear Dave, >> >> I added the print line and the error message that I used to receive >> changed but the program is still refusing to run. >> >> Modified program >> >> use Bio::Tools::Run::Phylo::Phylip::ProtDist; >> >> my $inputfilename = '/home/rc174/pro/align.phy'; >> #@params = ('MODEL' => 'PAM'); >> my $prodistfactory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(); >> my ($matrix)= $prodistfactory->run($inputfile); >> print $matrix->print_matrix; >> >> >> The error I receive is now >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Problems setting up for protdist. Probably bad input data in ! >> STACK: Error::throw >> STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:328 >> STACK: Bio::Tools::Run::Phylo::Phylip::ProtDist::run >> /usr/local/share/perl/5.8.8/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm:362 >> STACK: phylip2.pl:6 >> >> The error I used to receive before I inserted the line was, >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: protdist did not create matrix correctly (/tmp/S3a5QG6CCd/outfile) >> STACK: Error::throw >> STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:328 >> STACK: Bio::Tools::Run::Phylo::Phylip::ProtDist::_run >> /usr/local/share/perl/5.8.8/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm:409 >> STACK: Bio::Tools::Run::Phylo::Phylip::ProtDist::run >> /usr/local/share/perl/5.8.8/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm:366 >> STACK: phylip.pl:55 >> ----------------------------------------------------------- >> >> Is this because I have missed out any specific packages for installation. >> I use an Ubuntu Linux computer version 7.10 . I am not sure of the bioperl >> version. I am trying to learn a bit of bioperl on my own so if you could >> send me a model program for getting a tree so that I could work out the >> issues I am facing I would be grateful. >> >> Cheers, >> Rahul >> > From Nathan.Watson-Haigh at csiro.au Mon Jul 21 19:09:59 2008 From: Nathan.Watson-Haigh at csiro.au (Nathan.Watson-Haigh at csiro.au) Date: Tue, 22 Jul 2008 09:09:59 +1000 Subject: [Bioperl-l] Smaller Bioperl Modules Message-ID: <9BEB5FD4EB2BF3468A6A546A17480BC2277CED@exactn3-cbr.nexus.csiro.au> Hi all, I'm developing a web-based application and it'd be cool to use some Bioperl modules. However, I'll be providing my tool for downloaded and installation on a web server, so having to ask the sys admin to install all of bioperl where I only need a few modules is overkill and is likely to cause installation headaches. Since I've been out of the loop for quite a while now, I was wondering if any decisions had been made about whether or not Bioperl was going to be released on CPAN in smaller sets of modules with correct dependencies and possibly a Bundle::Bioperl? It'd be nice to have my application, for example, depend on Bio::SeqIO, such that only Bio::SeqIO::* and it's dependencies are installable through CPAN. Cheers, Nath ------------------------------------------------------------- Dr. Nathan S. Watson-Haigh (publish under Haigh, N.S.) OCE Post Doctoral Fellow CSIRO Livestock Industries J M Rendel Laboratory Rockhampton QLD 4701 Tel: +61 (0)7 4923 8121 Australia Fax: +61 (0)7 4923 8222 ------------------------------------------------------------- From lstein at cshl.edu Mon Jul 21 21:49:00 2008 From: lstein at cshl.edu (Lincoln Stein) Date: Mon, 21 Jul 2008 21:49:00 -0400 Subject: [Bioperl-l] Any volunteers for doing a Nested Containment List implementation? In-Reply-To: <38ECEED6-4825-4634-ABFD-D07D2FBA28C7@uiuc.edu> References: <6dce9a0b0807211702k1742884enf02ae53587a42922@mail.gmail.com> <38ECEED6-4825-4634-ABFD-D07D2FBA28C7@uiuc.edu> Message-ID: <6dce9a0b0807211849s6903097o8f22b67ab1797190@mail.gmail.com> I was thinking that the data structures could be reimplemented as MySQL tables. The main data structures are both fixed-width records. They do a binary search across the arrays, and MySQL can do the same thing with its B-tree indexing. Lincoln On Mon, Jul 21, 2008 at 9:27 PM, Chris Fields wrote: > It's definitely worth exploring. Might be nice to sort a few things out, > for instance, do we want to use their C library, or role our own data > structures? And would we want this to retain a similar interface to > Bio::DB::SeqFeature::Store? > > chris > > > On Jul 21, 2008, at 7:02 PM, Lincoln Stein wrote: > > Hi Folks, >> >> This paper describes an indexing algorithm for genome feature databases >> called Nested Containment Lists. Apparently it is substantially faster >> than >> the indexing systems we use in BioPerl for the Bio::DB::GFF, >> Bio::DB::SeqFeature::Store, and Chado. >> >> >> http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btl647v1?papetoc >> >> The concept and data structures are quite simple, and I think it would be >> straightforward to implement this system in MySQL tables. Would anybody be >> interested in taking this on as a summer project? >> >> Lincoln >> >> -- >> Lincoln D. Stein >> >> Ontario Institute for Cancer Research >> 101 College St., Suite 800 >> Toronto, ON, Canada M5G0A3 >> 416 673-8514 >> Assistant: Stacey Fairfield >> >> Cold Spring Harbor Laboratory >> 1 Bungtown Road >> Cold Spring Harbor, NY 11724 USA >> (516) 367-8380 >> Assistant: Sandra Michelsen >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Marie-Claude Hofmann > College of Veterinary Medicine > University of Illinois Urbana-Champaign > > > > > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Stacey Fairfield Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 USA (516) 367-8380 Assistant: Sandra Michelsen From cjfields at uiuc.edu Mon Jul 21 22:39:34 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 21 Jul 2008 21:39:34 -0500 Subject: [Bioperl-l] Smaller Bioperl Modules In-Reply-To: <9BEB5FD4EB2BF3468A6A546A17480BC2277CED@exactn3-cbr.nexus.csiro.au> References: <9BEB5FD4EB2BF3468A6A546A17480BC2277CED@exactn3-cbr.nexus.csiro.au> Message-ID: Hi Nat! We have discussed breaking things up but there was never a full consensus on it and I think, in the long run, it would have been too hard to convince everyone, particularly the CPAN folk, that it made sense to have tons of separately installable mini-bioperl modules. We do still intend on paring down core to the bare essentials, removing as many dependencies as possible, and having a separate tools and dev set of modules. I added a page on the wiki on my proposal for the intended split (others have added a few things here and there): http://www.bioperl.org/wiki/Proposed_1.6_core_modules It's worth reviving this discussion again; when I have more time I want to spearhead a 1.6 release. chris On Jul 21, 2008, at 6:09 PM, wrote: > Hi all, > > I'm developing a web-based application and it'd be cool to use some > Bioperl modules. However, I'll be providing my tool for downloaded and > installation on a web server, so having to ask the sys admin to > install > all of bioperl where I only need a few modules is overkill and is > likely > to cause installation headaches. > > Since I've been out of the loop for quite a while now, I was wondering > if any decisions had been made about whether or not Bioperl was > going to > be released on CPAN in smaller sets of modules with correct > dependencies > and possibly a Bundle::Bioperl? It'd be nice to have my application, > for > example, depend on Bio::SeqIO, such that only Bio::SeqIO::* and it's > dependencies are installable through CPAN. > > Cheers, > Nath > > ------------------------------------------------------------- > Dr. Nathan S. Watson-Haigh (publish under Haigh, N.S.) > OCE Post Doctoral Fellow > CSIRO Livestock Industries > J M Rendel Laboratory > Rockhampton > QLD 4701 Tel: +61 (0)7 4923 8121 > Australia Fax: +61 (0)7 4923 8222 > ------------------------------------------------------------- > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Marie-Claude Hofmann College of Veterinary Medicine University of Illinois Urbana-Champaign From ste.ghi at libero.it Tue Jul 22 07:28:24 2008 From: ste.ghi at libero.it (ste.ghi at libero.it) Date: Tue, 22 Jul 2008 13:28:24 +0200 (CEST) Subject: [Bioperl-l] fasta file parser Message-ID: <28031626.19861216726104997.JavaMail.defaultUser@defaultHost> Dear all, I'm trying to write a script wich, given a file containing a list of IDs, parses a big fasta file returning only sequences NOT listed in the list- file. To do so, I first create an array with the IDs to be excluded: [...] #Load LIST content in an array; avoids duplicates while (my $line = ) { push(@array1,$line ); foreach my $uniq ( @array1 ){ next if $seen { $uniq }++; push @unique, $uniq; } } then, process the fasta file in this way (NOT WORKING). #Fasta file processing my $newSeqFileName = Bio:: SeqIO->new(-file=> ">>INFILE", -format=>'fasta'); while (my $query = $SeqFileName->next_seq()) { foreach my $elem(@unique){ chomp $elem; if ($elem eq $query->id) { print $query->id." matched with $elem listed in $ARGV[1]: skipped!\n"; next; } elsif ($elem ne $query->id) { next if $seen2{ $query->id }++; $newSeqFileName->write_seq($query); } } } ... in this way I get only an exact copy of the input file....where am I wrong? Thanks a lot for your kind help! Stefano From bix at sendu.me.uk Tue Jul 22 08:42:31 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 22 Jul 2008 13:42:31 +0100 Subject: [Bioperl-l] fasta file parser In-Reply-To: <28031626.19861216726104997.JavaMail.defaultUser@defaultHost> References: <28031626.19861216726104997.JavaMail.defaultUser@defaultHost> Message-ID: <4885D5B7.3080103@sendu.me.uk> ste.ghi at libero.it wrote: > Dear all, > I'm trying to write a script wich, given a file containing a list of > IDs, parses a big fasta file returning only sequences NOT listed in the list- > file. > > To do so, I first create an array with the IDs to be excluded: > > [...] > > #Load LIST content in an array; avoids duplicates > while (my $line = ) { > > > push(@array1,$line ); > > foreach my $uniq ( @array1 ){ > > next if $seen > { $uniq }++; > > push @unique, $uniq; > > } > } Not sure what you're doing here (probably the cause of your problem?). But hashes are your friend: @list = ; %unique = map { chomp($_) => 1 } @list; > then, process the fasta file in > this way (NOT WORKING). > > #Fasta file processing > my $newSeqFileName = Bio:: > SeqIO->new(-file=> ">>INFILE", -format=>'fasta'); > while (my $query = > $SeqFileName->next_seq()) { if (defined $unique{$query->id}) { > print $query->id." matched > with $elem listed in $ARGV[1]: skipped!\n"; > next; > } else { > next if $seen2{ $query->id }++; > > $newSeqFileName->write_seq($query); > > } > > } From cjfields at uiuc.edu Tue Jul 22 09:00:06 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 22 Jul 2008 08:00:06 -0500 Subject: [Bioperl-l] fasta file parser In-Reply-To: <28031626.19861216726104997.JavaMail.defaultUser@defaultHost> References: <28031626.19861216726104997.JavaMail.defaultUser@defaultHost> Message-ID: <6E0CFA1A-0273-4829-91B3-1D625913859E@uiuc.edu> Use exists() directly on the %seen lookup hash for your test. Also, use chomp up front when creating %seen to get rid of newlines. # assuming you have one ID per line... while (my $line = ) { chomp $line; $seen{$line}++; # do whatever else here... } close LIST; my $newSeqFileName = Bio::SeqIO->new(-file=> ">>INFILE", - format=>'fasta'); while (my $query = $SeqFileName->next_seq()) { my $id = $query->id; if ( exists( $seen{$id} ) ) { print "$id matched with $seen{$id} listed in $ARGV[1]: skipped!\n"; next; } elsif ( $elem ne $query->id ) { if ( exists( $seen2{$id}++ ) ) {; print "$id matched with $seen2{$id}, already found: skipped!\n"; next; } $newSeqFileName->write_seq($query); } } chris On Jul 22, 2008, at 6:28 AM, ste.ghi at libero.it wrote: > Dear all, > I'm trying to write a script wich, given a file containing a list of > IDs, parses a big fasta file returning only sequences NOT listed in > the list- > file. > > To do so, I first create an array with the IDs to be excluded: > > [...] > > #Load LIST content in an array; avoids duplicates > while (my $line = ) { > > > push(@array1,$line ); > > foreach my $uniq ( @array1 ){ > > next if $seen > { $uniq }++; > > push @unique, $uniq; > > } > } > > then, process the fasta file in > this way (NOT WORKING). > > #Fasta file processing > my $newSeqFileName = Bio:: > SeqIO->new(-file=> ">>INFILE", -format=>'fasta'); > while (my $query = > $SeqFileName->next_seq()) { > foreach my $elem(@unique){ > chomp $elem; > > > if ($elem eq $query->id) { > > print $query->id." matched > with $elem listed in $ARGV[1]: skipped!\n"; > next; > } > elsif ($elem ne $query->id) { > next if $seen2{ $query->id }++; > > $newSeqFileName->write_seq($query); > > } > > } > } > > > ... > in this way I get only an exact copy of the input file....where am I > wrong? > > Thanks a lot for your kind help! > Stefano > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Marie-Claude Hofmann College of Veterinary Medicine University of Illinois Urbana-Champaign From bix at sendu.me.uk Tue Jul 22 08:49:51 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 22 Jul 2008 13:49:51 +0100 Subject: [Bioperl-l] fasta file parser In-Reply-To: <4885D5B7.3080103@sendu.me.uk> References: <28031626.19861216726104997.JavaMail.defaultUser@defaultHost> <4885D5B7.3080103@sendu.me.uk> Message-ID: <4885D76F.4080403@sendu.me.uk> Sendu Bala wrote: > ste.ghi at libero.it wrote: >> #Load LIST content in an array; avoids duplicates [snip] > @list = ; > %unique = map { chomp($_) => 1 } @list; Oops, my chomp usage is wrong. This'll work better: @list = ; chomp(@list); %unique = map { $_ => 1 } grep { /\S/ } @list; From ste.ghi at libero.it Tue Jul 22 10:17:06 2008 From: ste.ghi at libero.it (ste.ghi at libero.it) Date: Tue, 22 Jul 2008 16:17:06 +0200 (CEST) Subject: [Bioperl-l] R: Re: fasta file parser Message-ID: <22819225.29451216736226098.JavaMail.defaultUser@defaultHost> guys, thanks for your ready replies but now I'm a little confused... the first 'while' was just to avoid duplicates in the list... does your code create a cleared list? what should I write where you say "# do whatever else here..." thanks ----Messaggio originale---- Da: cjfields at uiuc.edu Data: 22/07/2008 15.00 A: "ste.ghi at libero.it" Cc: Ogg: Re: [Bioperl-l] fasta file parser Use exists() directly on the %seen lookup hash for your test. Also, use chomp up front when creating %seen to get rid of newlines. # assuming you have one ID per line...while (my $line = ) { chomp $line; $seen{$line}++; # do whatever else here...} close LIST; my $newSeqFileName = Bio::SeqIO->new(-file=> ">>INFILE", -format=>'fasta'); while (my $query = $SeqFileName->next_seq()) { my $id = $query->id; if ( exists( $seen{$id} ) ) { print "$id matched with $seen{$id} listed in $ARGV[1]: skipped!\n"; next; } elsif ( $elem ne $query->id ) { if ( exists( $seen2{$id}++ ) ) {; print "$id matched with $seen2{$id}, already found: skipped!\n"; next; } $newSeqFileName->write_seq($query); }} chris On Jul 22, 2008, at 6:28 AM, ste.ghi at libero.it wrote:Dear all, I'm trying to write a script wich, given a file containing a list of IDs, parses a big fasta file returning only sequences NOT listed in the list- file. To do so, I first create an array with the IDs to be excluded: [...] #Load LIST content in an array; avoids duplicates while (my $line = ) { push(@array1,$line ); foreach my $uniq ( @array1 ){ next if $seen { $uniq }++; push @unique, $uniq; } } then, process the fasta file in this way (NOT WORKING). #Fasta file processing my $newSeqFileName = Bio:: SeqIO->new(-file=> ">>INFILE", -format=>'fasta'); while (my $query = $SeqFileName->next_seq()) { foreach my $elem(@unique){ chomp $elem; if ($elem eq $query->id) { print $query->id." matched with $elem listed in $ARGV[1]: skipped!\n"; next; } elsif ($elem ne $query->id) { next if $seen2{ $query->id }++; $newSeqFileName->write_seq($query); } } } ... in this way I get only an exact copy of the input file....where am I wrong? Thanks a lot for your kind help! Stefano _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher FieldsPostdoctoral ResearcherLab of Dr. Marie-Claude HofmannCollege of Veterinary MedicineUniversity of Illinois Urbana-Champaign From ronnie.dejonge at gmail.com Tue Jul 22 10:36:17 2008 From: ronnie.dejonge at gmail.com (Dhr. R. de Jonge) Date: Tue, 22 Jul 2008 16:36:17 +0200 Subject: [Bioperl-l] (no subject) In-Reply-To: References: <628aabb70807210536o3949368ar8dd19ed7a6d9a490@mail.gmail.com> <628aabb70807210804l4d7cba0el129425e40a475a81@mail.gmail.com> <000601c8eb43$bc6e71b0$d250e089@wurnet.nl> <4884AFF6.2010008@uni-potsdam.de> <628aabb70807210931g7744b11ax25805075a7f1413f@mail.gmail.com> Message-ID: Hi all, Thanks for the very quick responses. I've been trying to fix it today, trying both the bl2seq method and the direct approach. Unfortunately, I'm unable to fix either of the two. At the moment I'm trying to get the direct approach working, however, I'm not able to obtain the hit_start and hit_end numbers of the domain. It seems that these methods, which are not implemented in the Bio::Search::HSP::HMMERHSP module (which I used to obtain the domain sequence). I've screened through the appropriate modules, with no luck. Is there a method to obtain these hit_start/hit_end figures by parsing? Or is there a better method? Many thanks again! Cheers Ronnie 2008/7/21, Chris Fields : > Ya beat me to it! I agree, this is the best way to go, and it would > save an extra BLAST run (though if you need it Diego's bl2seq > suggestion is the way to go). > > chris > > On Jul 21, 2008, at 11:31 AM, Dave Messina wrote: > >> You know which protein sequence corresponds to which cDNA sequence, >> so I >> think you could also: >> >> - take the start and end coordinates of the domain in the protein >> (from the >> HMMer output) >> - convert those into the start and end coordinates of the domain in >> the cDNA >> - use the subseq() method to extract the subsequence of the cDNA >> >> >> Dave >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at uiuc.edu Tue Jul 22 11:01:11 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 22 Jul 2008 10:01:11 -0500 Subject: [Bioperl-l] R: Re: fasta file parser In-Reply-To: <22819225.29451216736226098.JavaMail.defaultUser@defaultHost> References: <22819225.29451216736226098.JavaMail.defaultUser@defaultHost> Message-ID: <40DA953F-E3C8-42B3-9B22-024E0A2C17F1@uiuc.edu> On Jul 22, 2008, at 9:17 AM, ste.ghi at libero.it wrote: > guys, thanks for your ready replies > but now I'm a little confused... > > the first 'while' was just to avoid duplicates in the list... > does your code create a cleared list? what should I write where you > say "# do whatever else here..." > > thanks Up to you; you can do absolutely nothing if you prefer. The script is simply a demo of what could be done based upon what we assume you want using the code you provided. Sendu's approach is also quite applicable (remember, this is perl, so TIMTOWTDI). For instance, the way I would go about this myself: start by creating a FASTA database (flatfile or otherwise) of the sequences using the ID as the primary key (always a good practice IMHO). After the database is set up, create a lookup table by mapping the list of IDs from the database to a hash, similarly to what Sendu demonstrated; I believe all DB implementations in BioPerl allow you to retrieve all seq IDs in the database as an array. Using that you would then delete any matching IDs in the file from the lookup hash; the leftovers (i.e. those NOT found in the file) would be used to retrieve the sequences from the database. Avoids iterating over every sequence (unless you count database creation, of course, but again that could be used for other purposes as well). chris > > ----Messaggio originale---- > Da: cjfields at uiuc.edu > Data: 22/07/2008 15.00 > A: "ste.ghi at libero.it" > Cc: > Ogg: Re: [Bioperl-l] fasta file parser > > Use exists() directly on the %seen lookup hash for your test. Also, > use chomp up front when creating %seen to get rid of newlines. > > # assuming you have one ID per line... > while (my $line = ) { > chomp $line; > $seen{$line}++; > # do whatever else here... > } > > close LIST; > > my $newSeqFileName = Bio::SeqIO->new(-file=> ">>INFILE", - > format=>'fasta'); > while (my $query = $SeqFileName->next_seq()) { > my $id = $query->id; > if ( exists( $seen{$id} ) ) { > print "$id matched with $seen{$id} listed in $ARGV[1]: > skipped!\n"; > next; > } > elsif ( $elem ne $query->id ) { > if ( exists( $seen2{$id}++ ) ) {; > print "$id matched with $seen2{$id}, already found: > skipped!\n"; > next; > } > $newSeqFileName->write_seq($query); > } > } > > chris > > On Jul 22, 2008, at 6:28 AM, ste.ghi at libero.it wrote: > >> Dear all, >> I'm trying to write a script wich, given a file containing a list of >> IDs, parses a big fasta file returning only sequences NOT listed in >> the list- >> file. >> >> To do so, I first create an array with the IDs to be excluded: >> >> [...] >> >> #Load LIST content in an array; avoids duplicates >> while (my $line = ) { >> >> >> push(@array1,$line ); >> >> foreach my $uniq ( @array1 ){ >> >> next if $seen >> { $uniq }++; >> >> push @unique, $uniq; >> >> } >> } >> >> then, process the fasta file in >> this way (NOT WORKING). >> >> #Fasta file processing >> my $newSeqFileName = Bio:: >> SeqIO->new(-file=> ">>INFILE", -format=>'fasta'); >> while (my $query = >> $SeqFileName->next_seq()) { >> foreach my $elem(@unique){ >> chomp $elem; >> >> >> if ($elem eq $query->id) { >> >> print $query->id." matched >> with $elem listed in $ARGV[1]: skipped!\n"; >> next; >> } >> elsif ($elem ne $query->id) { >> next if $seen2{ $query->id }++; >> >> $newSeqFileName->write_seq($query); >> >> } >> >> } >> } >> >> >> ... >> in this way I get only an exact copy of the input file....where am >> I wrong? >> >> Thanks a lot for your kind help! >> Stefano >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Marie-Claude Hofmann > College of Veterinary Medicine > University of Illinois Urbana-Champaign > > > > > > Christopher Fields Postdoctoral Researcher Lab of Dr. Marie-Claude Hofmann College of Veterinary Medicine University of Illinois Urbana-Champaign From cjfields at uiuc.edu Tue Jul 22 11:10:30 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 22 Jul 2008 10:10:30 -0500 Subject: [Bioperl-l] (no subject) In-Reply-To: References: <628aabb70807210536o3949368ar8dd19ed7a6d9a490@mail.gmail.com> <628aabb70807210804l4d7cba0el129425e40a475a81@mail.gmail.com> <000601c8eb43$bc6e71b0$d250e089@wurnet.nl> <4884AFF6.2010008@uni-potsdam.de> <628aabb70807210931g7744b11ax25805075a7f1413f@mail.gmail.com> Message-ID: On Jul 22, 2008, at 9:36 AM, Dhr. R. de Jonge wrote: > Hi all, > Thanks for the very quick responses. I've been trying to fix it today, > trying both the bl2seq method and the direct approach. Unfortunately, > I'm unable to fix either of the two. > At the moment I'm trying to get the direct approach working, however, > I'm not able to obtain the hit_start and hit_end numbers of the > domain. It seems that these methods, which are not implemented in the > Bio::Search::HSP::HMMERHSP module (which I used to obtain the domain I believe the query is your sequence and the 'hits' are the HMMs (been a while since I used HMMER though). In this case you don't want the hit start/end, you want $hsp->start('query')/$hsp->end('query') (or $hsp->query->start/$hsp->query->end, which should be the same thing). > sequence). I've screened through the appropriate modules, with no > luck. Is there a method to obtain these hit_start/hit_end figures by > parsing? Or is there a better method? > Many thanks again! > Cheers > Ronnie See the HOWTO for SearchIO for more methods. http://www.bioperl.org/wiki/HOWTO:SearchIO Some hit/HSP methods for HMMER aren't implemented, IIRC. For an alternative faster approach you can try Sendu's hmmer_pull implementation. chris From bix at sendu.me.uk Tue Jul 22 11:05:03 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 22 Jul 2008 16:05:03 +0100 Subject: [Bioperl-l] (no subject) In-Reply-To: References: <628aabb70807210536o3949368ar8dd19ed7a6d9a490@mail.gmail.com> <628aabb70807210804l4d7cba0el129425e40a475a81@mail.gmail.com> <000601c8eb43$bc6e71b0$d250e089@wurnet.nl> <4884AFF6.2010008@uni-potsdam.de> <628aabb70807210931g7744b11ax25805075a7f1413f@mail.gmail.com> Message-ID: <4885F71F.8040801@sendu.me.uk> Dhr. R. de Jonge wrote: > Hi all, > Thanks for the very quick responses. I've been trying to fix it today, > trying both the bl2seq method and the direct approach. Unfortunately, > I'm unable to fix either of the two. > At the moment I'm trying to get the direct approach working, however, > I'm not able to obtain the hit_start and hit_end numbers of the > domain. It seems that these methods, which are not implemented in the > Bio::Search::HSP::HMMERHSP module (which I used to obtain the domain > sequence). I've screened through the appropriate modules, with no > luck. Is there a method to obtain these hit_start/hit_end figures by > parsing? The methods are called start() and end(). If $hsp->start doesn't work, try $hsp->hit->start & $hsp->query->start instead. If that's the wrong answer, try using the 'hmmer_pull' parser and $hsp->start('query') & $hsp->start('hit'). (likewise for end()) From ronnie.dejonge at gmail.com Tue Jul 22 11:27:48 2008 From: ronnie.dejonge at gmail.com (Dhr. R. de Jonge) Date: Tue, 22 Jul 2008 17:27:48 +0200 Subject: [Bioperl-l] (no subject) In-Reply-To: References: <628aabb70807210536o3949368ar8dd19ed7a6d9a490@mail.gmail.com> <628aabb70807210804l4d7cba0el129425e40a475a81@mail.gmail.com> <000601c8eb43$bc6e71b0$d250e089@wurnet.nl> <4884AFF6.2010008@uni-potsdam.de> <628aabb70807210931g7744b11ax25805075a7f1413f@mail.gmail.com> Message-ID: Thanks, I'm trying the options right now! update: Seems I get it roling now using the bl2seq directly in my hmm parser script! The results look very promising, and no false positives (by quick visual inspection!). Cheers Ronnie 2008/7/22, Chris Fields : > > On Jul 22, 2008, at 9:36 AM, Dhr. R. de Jonge wrote: > >> Hi all, >> Thanks for the very quick responses. I've been trying to fix it today, >> trying both the bl2seq method and the direct approach. Unfortunately, >> I'm unable to fix either of the two. >> At the moment I'm trying to get the direct approach working, however, >> I'm not able to obtain the hit_start and hit_end numbers of the >> domain. It seems that these methods, which are not implemented in the >> Bio::Search::HSP::HMMERHSP module (which I used to obtain the domain > > I believe the query is your sequence and the 'hits' are the HMMs (been > a while since I used HMMER though). In this case you don't want the > hit start/end, you want $hsp->start('query')/$hsp->end('query') (or > $hsp->query->start/$hsp->query->end, which should be the same thing). > >> sequence). I've screened through the appropriate modules, with no >> luck. Is there a method to obtain these hit_start/hit_end figures by >> parsing? Or is there a better method? >> Many thanks again! >> Cheers >> Ronnie > > See the HOWTO for SearchIO for more methods. > > http://www.bioperl.org/wiki/HOWTO:SearchIO > > Some hit/HSP methods for HMMER aren't implemented, IIRC. For an > alternative faster approach you can try Sendu's hmmer_pull > implementation. > > chris > From ste.ghi at libero.it Tue Jul 22 11:51:03 2008 From: ste.ghi at libero.it (ste.ghi at libero.it) Date: Tue, 22 Jul 2008 17:51:03 +0200 (CEST) Subject: [Bioperl-l] R: Re: R: Re: fasta file parser Message-ID: <1355409.35331216741863636.JavaMail.defaultUser@defaultHost> chris, your suggestion sound reasonable, but I still prefer a file parser solution. and I'd like to better understand your demo code, 'couse actually it's not working...can you just put a comment to the instructions you wrote? thanks. stefano >----Messaggio originale---- >Da: cjfields at uiuc.edu >Data: 22/07/2008 17.01 >A: "ste.ghi at libero.it" >Cc: >Ogg: Re: R: Re: [Bioperl-l] fasta file parser > > >On Jul 22, 2008, at 9:17 AM, ste.ghi at libero.it wrote: > >> guys, thanks for your ready replies >> but now I'm a little confused... >> >> the first 'while' was just to avoid duplicates in the list... >> does your code create a cleared list? what should I write where you >> say "# do whatever else here..." >> >> thanks > >Up to you; you can do absolutely nothing if you prefer. The script is >simply a demo of what could be done based upon what we assume you want >using the code you provided. > >Sendu's approach is also quite applicable (remember, this is perl, so >TIMTOWTDI). For instance, the way I would go about this myself: start >by creating a FASTA database (flatfile or otherwise) of the sequences >using the ID as the primary key (always a good practice IMHO). After >the database is set up, create a lookup table by mapping the list of >IDs from the database to a hash, similarly to what Sendu demonstrated; >I believe all DB implementations in BioPerl allow you to retrieve all >seq IDs in the database as an array. > >Using that you would then delete any matching IDs in the file from the >lookup hash; the leftovers (i.e. those NOT found in the file) would be >used to retrieve the sequences from the database. Avoids iterating >over every sequence (unless you count database creation, of course, >but again that could be used for other purposes as well). > >chris > >> >> ----Messaggio originale---- >> Da: cjfields at uiuc.edu >> Data: 22/07/2008 15.00 >> A: "ste.ghi at libero.it" >> Cc: >> Ogg: Re: [Bioperl-l] fasta file parser >> >> Use exists() directly on the %seen lookup hash for your test. Also, >> use chomp up front when creating %seen to get rid of newlines. >> >> # assuming you have one ID per line... >> while (my $line = ) { >> chomp $line; >> $seen{$line}++; >> # do whatever else here... >> } >> >> close LIST; >> >> my $newSeqFileName = Bio::SeqIO->new(- file=> ">>INFILE", - >> format=>'fasta'); >> while (my $query = $SeqFileName- >next_seq()) { >> my $id = $query->id; >> if ( exists( $seen{$id} ) ) { >> print "$id matched with $seen{$id} listed in $ARGV[1]: >> skipped! \n"; >> next; >> } >> elsif ( $elem ne $query->id ) { >> if ( exists( $seen2{$id}++ ) ) {; >> print "$id matched with $seen2 {$id}, already found: >> skipped!\n"; >> next; >> } >> $newSeqFileName->write_seq($query); >> } >> } >> >> chris >> >> On Jul 22, 2008, at 6:28 AM, ste.ghi at libero.it wrote: >> >>> Dear all, >>> I'm trying to write a script wich, given a file containing a list of >>> IDs, parses a big fasta file returning only sequences NOT listed in >>> the list- >>> file. >>> >>> To do so, I first create an array with the IDs to be excluded: >>> >>> [...] >>> >>> #Load LIST content in an array; avoids duplicates >>> while (my $line = ) { >>> >>> >>> push(@array1,$line ); >>> >>> foreach my $uniq ( @array1 ){ >>> >>> next if $seen >>> { $uniq } ++; >>> >>> push @unique, $uniq; >>> >>> } >>> } >>> >>> then, process the fasta file in >>> this way (NOT WORKING). >>> >>> #Fasta file processing >>> my $newSeqFileName = Bio:: >>> SeqIO->new(-file=> ">>INFILE", -format=>'fasta'); >>> while (my $query = >>> $SeqFileName->next_seq()) { >>> foreach my $elem(@unique){ >>> chomp $elem; >>> >>> >>> if ($elem eq $query->id) { >>> >>> print $query->id." matched >>> with $elem listed in $ARGV [1]: skipped!\n"; >>> next; >>> } >>> elsif ($elem ne $query->id) { >>> next if $seen2{ $query->id }++; >>> >>> $newSeqFileName->write_seq($query); >>> >>> } >>> >>> } >>> } >>> >>> >>> ... >>> in this way I get only an exact copy of the input file.... where am >>> I wrong? >>> >>> Thanks a lot for your kind help! >>> Stefano >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio. org/mailman/listinfo/bioperl-l >> >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Marie-Claude Hofmann >> College of Veterinary Medicine >> University of Illinois Urbana-Champaign >> >> >> >> >> >> > >Christopher Fields >Postdoctoral Researcher >Lab of Dr. Marie-Claude Hofmann >College of Veterinary Medicine >University of Illinois Urbana-Champaign > > > > > From cjfields at uiuc.edu Tue Jul 22 14:38:38 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 22 Jul 2008 13:38:38 -0500 Subject: [Bioperl-l] R: Re: R: Re: fasta file parser In-Reply-To: <1355409.35331216741863636.JavaMail.defaultUser@defaultHost> References: <1355409.35331216741863636.JavaMail.defaultUser@defaultHost> Message-ID: <60EF10F8-5D81-4850-8FA5-BA1E967DEBAC@uiuc.edu> On Jul 22, 2008, at 10:51 AM, ste.ghi at libero.it wrote: > chris, your suggestion sound reasonable, but I still prefer a file > parser > solution. > > and I'd like to better understand your demo code, 'couse actually > it's not working...can you just put a comment to the instructions > you wrote? Hadn't tested it out myself (nothing to test it on, sorry). Glad you found a solution, though. chris > > thanks. > stefano From tiarua at gmail.com Wed Jul 23 02:05:56 2008 From: tiarua at gmail.com (Eileen Heo) Date: Wed, 23 Jul 2008 02:05:56 -0400 Subject: [Bioperl-l] Installing bioperl-ext on windows Message-ID: <848865e30807222305w7382841bhd5f4975521fba8bf@mail.gmail.com> Hello, I am trying to install the latest version of bioperl-ext (Bio::Ext::Align) on Windows xp. (I already have the following packages installed up to date: bioperl core, bioperl db, bioperl gui, bioperl network, bioperl run.) In the bioperl-ext-1.5.1\Bio\Ext\Align directory, I get the following output from 'perl Makefile.PL'. C:\Perl\bioperl-ext-1.5.1\Bio\Ext\Align>perl Makefile.PL Note (probably harmless): No library found for -lm Note (probably harmless): No library found for oldnames.lib Note (probably harmless): No library found for kernel32.lib Note (probably harmless): No library found for user32.lib Note (probably harmless): No library found for gdi32.lib Note (probably harmless): No library found for winspool.lib Note (probably harmless): No library found for comdlg32.lib Note (probably harmless): No library found for advapi32.lib Note (probably harmless): No library found for shell32.lib Note (probably harmless): No library found for ole32.lib Note (probably harmless): No library found for oleaut32.lib Note (probably harmless): No library found for netapi32.lib Note (probably harmless): No library found for uuid.lib Note (probably harmless): No library found for ws2_32.lib Note (probably harmless): No library found for mpr.lib Note (probably harmless): No library found for winmm.lib Note (probably harmless): No library found for version.lib Note (probably harmless): No library found for odbc32.lib Note (probably harmless): No library found for odbccp32.lib Note (probably harmless): No library found for msvcrt.lib Writing Makefile for Bio::Ext::Align When I proceed anyways with 'nmake', I get the following errors: C:\Perl\bioperl-ext-1.5.1\Bio\Ext\Align>nmake Microsoft (R) Program Maintenance Utility Version 1.50 Copyright (c) Microsoft Corp 1988-94. All rights reserved. DEFINE='-DPOSIX -DNOERROR'; CC='cl'; CFLAGS='-nologo -GF -W3 -MD -Zi -DN DEBUG -O1 -DWIN32 -D_CONSOLE -DNO_STRICT -DHAVE_DES_FCRYPT -DNO_HASH_SEED -DUSE_ SITECUSTOMIZE -DPERL_IMPLICIT_CONTEXT -DPERL_IMPLICIT_SYS -DUSE_PERLIO -DPERL_MS VCRT_READFIX'; export DEFINE INC CC CFLAGS; cd libs && nmake CC='cl' CFLAGS='-n ologo -GF -W3 -MD -Zi -DNDEBUG -O1 -DWIN32 -D_CONSOLE -DNO_STRICT -DHAVE_DES_FCR YPT -DNO_HASH_SEED -DUSE_SITECUSTOMIZE -DPERL_IMPLICIT_CONTEXT -DPERL_IMPLICIT_S YS -DUSE_PERLIO -DPERL_MSVCRT_READFIX -DPOSIX -DNOERROR' DEFINE='-DPOSIX -DNOERR OR' libsw.lib -e 'DEFINE' is not recognized as an internal or external command, operable program or batch file. NMAKE : fatal error U1077: 'C:\WINDOWS\system32\cmd.exe' : return code '0x1' Stop. I get the same error as above when I run 'nmake test' and 'nmake install' as well. How can this problem be solved so that installing bioperl-ext is successful? Thank you in advance for any help. From Jorge.DUARTE at biogemma.com Wed Jul 23 05:08:44 2008 From: Jorge.DUARTE at biogemma.com (Jorge.DUARTE at biogemma.com) Date: Wed, 23 Jul 2008 11:08:44 +0200 Subject: [Bioperl-l] phd format parsing produces infinite memory usage Message-ID: Hello, i've been trying to use Bio::SeqIO to parse a phd-like format file. The script doesn't produce any error (nor output), but the memory usage keeps increasing until it reaches its limit (well i stoped the process at 16Gb of memory) Is the problem known ? Or is my file format wrong ? If i use only the first sequence from my file (bellow), the script works fine, maybe there is something wrong in the middle of the file... how can i print debugging info ? Thanks for any help jorge example data : BEGIN_SEQUENCE FAINC1H01EI6V4.9-204 BEGIN_COMMENT CHROMAT_FILE: sff:FAINC1H01.sff:FAINC1H01EI6V4 ABI_THUMBPRINT: none PHRED_VERSION: not called by phred CALL_METHOD: 454 QUALITY_LEVELS: 99 TIME: Thu Jul 27 12:33:48 2000 TRACE_ARRAY_MIN_INDEX: 0 TRACE_ARRAY_MAX_INDEX: 4628 CHEM: unknown DYE: unknown END_COMMENT BEGIN_DNA a 40 718 c 40 737 g 40 756 c 40 775 g 40 794 g 40 813 g 40 832 g 40 851 a 40 870 a 40 889 g 40 908 t 39 927 c 37 946 t 37 965 g 37 984 a 37 1003 a 37 1022 g 37 1041 a 38 1060 a 38 1079 a 38 1098 c 37 1117 a 37 1136 a 37 1155 t 37 1174 c 37 1193 a 37 1212 a 37 1231 c 37 1250 t 37 1269 a 37 1288 t 38 1307 t 38 1326 t 38 1345 a 37 1364 c 37 1383 c 37 1402 t 37 1421 a 37 1440 t 37 1459 g 37 1478 c 37 1497 a 37 1516 t 37 1535 a 37 1554 c 37 1573 t 37 1592 t 37 1611 c 37 1630 a 37 1649 g 37 1668 a 37 1687 t 37 1706 g 37 1725 c 37 1744 t 37 1763 t 37 1782 a 37 1801 c 37 1820 a 37 1839 a 37 1858 g 37 1877 a 37 1896 g 37 1915 a 37 1934 g 37 1953 a 37 1972 g 37 1991 g 37 2010 t 37 2029 c 37 2048 a 37 2067 c 37 2086 a 37 2105 c 37 2124 t 37 2143 g 37 2162 c 37 2181 c 37 2200 a 37 2219 c 37 2238 t 37 2257 t 37 2276 g 37 2295 a 37 2314 g 37 2333 c 37 2352 t 37 2371 g 37 2390 c 37 2409 a 37 2428 g 37 2447 c 37 2466 t 37 2485 a 37 2504 g 37 2523 c 37 2542 c 37 2561 t 37 2580 t 37 2599 g 37 2618 c 37 2637 a 37 2656 a 37 2675 t 37 2694 t 37 2713 g 37 2732 g 37 2751 a 37 2770 a 37 2789 c 37 2808 c 37 2827 c 37 2846 t 37 2865 g 37 2884 a 37 2903 a 37 2922 g 37 2941 g 37 2960 g 37 2979 t 37 2998 g 37 3017 a 37 3036 a 37 3055 c 37 3074 a 37 3093 t 37 3112 g 37 3131 a 37 3150 a 37 3169 a 37 3188 c 37 3207 a 37 3226 t 37 3245 a 37 3264 g 38 3283 t 34 3302 c 34 3321 c 34 3340 a 24 3359 a 24 3378 a 24 3397 t 34 3416 c 34 3435 c 34 3454 a 34 3473 g 38 3492 c 38 3511 t 37 3530 t 37 3549 c 37 3568 t 38 3587 g 38 3606 c 38 3625 a 38 3644 a 38 3663 a 38 3682 g 37 3701 a 37 3720 a 37 3739 c 37 3758 g 37 3777 c 37 3796 t 37 3815 a 37 3834 c 37 3853 t 37 3872 g 37 3891 a 37 3910 t 37 3929 g 37 3948 a 34 3967 a 34 3986 g 33 4005 g 33 4024 c 38 4043 t 38 4062 c 26 4081 c 26 4100 c 21 4119 c 21 4138 a 34 4157 c 34 4176 c 23 4195 g 31 4214 t 33 4233 g 36 4252 c 36 4271 t 36 4290 c 36 4309 t 36 4328 c 36 4347 c 36 4366 g 36 4385 c 36 4404 a 36 4423 t 33 4442 a 33 4461 t 33 4480 t 33 4499 c 26 4518 c 26 4537 c 26 4556 a 26 4575 END_DNA END_SEQUENCE --- Jorge Duarte Bioinformatics Research Engineer BIOGEMMA - Upstream Genomics Group Z.I. Du Br?zet 8, Rue des Fr?res Lumi?re 63028 CLERMONT FERRAND Cedex 2 FRANCE Tel : +33 (0)4 73 39 60 73 Fax : +33 (0)4 73 39 60 71 E-mail : jorge.duarte at biogemma.com ***************************************************************** Pour toute demande de support merci d'inclure BIOGEMMA_BioInfo_Service ou bioinfo at biogemma.com dans les destinataires lors du premier contact ***************************************************************** BIOGEMMA S.A.S. au capital social de 48.335.652,00 ?. 1, Rue Edouard Colonne - 75001 PARIS. RCS PARIS 412 514 366 This message and any attachments are confidential and intended solely for the use of the addressee(s) named above. The information contained in this email may also be legally privileged. If you have received this email in error, please notify us immediately by reply email or by fax and then delete it. Any use, distribution or reproduction of this message is strictly prohibited. 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From Alicia.Amadoz at uv.es Wed Jul 23 07:03:04 2008 From: Alicia.Amadoz at uv.es (Alicia Amadoz) Date: Wed, 23 Jul 2008 13:03:04 +0200 (CEST) Subject: [Bioperl-l] Bio_Tools_Run_RemoteBlast error: 500 Can't connect to www.ncbi.nlm.nih.gov:80 In-Reply-To: <0196157D-0D2F-4DB3-AEE0-91BB56F3B82C@uiuc.edu> References: <0196157D-0D2F-4DB3-AEE0-91BB56F3B82C@uiuc.edu> Message-ID: <1557668399amadoz@uv.es> Hi, Finally I've been talking with my system administrator and the error was because some security configuration of our server. Now it is already solved and works ok Thanks for your help and comments. I am using PHP because our application is developed in PHP and from this application different scripts are launched. Alicia > Okay, so it appears there are overall connection issues (i.e. this > isn't just a RemoteBlast issue). The fact that you can ping from > command line also makes me think it isn't a proxy issue. I'm not > familiar with PHP myself, but I would think it only allows user- > defined processes to access network connections, so that's my next > guess. > > Out of curiosity, is there any particular reason you are using PHP? > > chris > > On Jul 21, 2008, at 10:24 AM, Alicia Amadoz wrote: > > > Hi, > > > > I have tried what you suggested and what I get is another error: > > > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: WebDBSeqI Request Error: > > 500 Can't connect to eutils.ncbi.nlm.nih.gov:80 (Bad hostname > > 'eutils.ncbi.nlm.nih.gov') > > Content-Type: text/plain > > Client-Date: Mon, 21 Jul 2008 15:07:39 GMT > > Client-Warning: Internal response > > > > 500 Can't connect to eutils.ncbi.nlm.nih.gov:80 (Bad hostname > > 'eutils.ncbi.nlm.nih.gov') > > > > STACK: Error::throw > > STACK: Bio::Root::Root::throw /usr/lib/perl5/vendor_perl/5.8.8/Bio/ > > Root/Root.pm:359 > > STACK: Bio::DB::WebDBSeqI::_stream_request > > /usr/lib/perl5/vendor_perl/5.8.8/Bio/DB/WebDBSeqI.pm:758 > > STACK: Bio::DB::WebDBSeqI::get_seq_stream > > /usr/lib/perl5/vendor_perl/5.8.8/Bio/DB/WebDBSeqI.pm:454 > > STACK: Bio::DB::WebDBSeqI::get_Stream_by_id > > /usr/lib/perl5/vendor_perl/5.8.8/Bio/DB/WebDBSeqI.pm:275 > > STACK: /var/www/html/perl-cgi//remote_blast_ncbi.pl:48 > > ----------------------------------------------------------- > > > > in line 48 of my script is, > > > > my $seqio = $gb->get_Stream_by_id([qw(J00522 AF303112 2981014)]); > > > >> From the original script you appear to be running things from a PHP > >> environment, so maybe it has something to do with that, e.g. maybe > >> you > >> need to set other env. settings (like a proxy) in order to connect. > > > > I am going to check again php.info but I have no idea what can it be. > > > > Thanks again for your help. > > Alicia > > > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Marie-Claude Hofmann > College of Veterinary Medicine > University of Illinois Urbana-Champaign > > > > > > -- *********************************************** Alicia Amadoz Navarro Evolutionary Genetics Unit Cavanilles Institute for Biodiversity and Evolutionary Biology University of Valencia Pol?gono de la Coma s/n, 46980 Paterna (Valencia), Phone: (+34) 96 354 3687 FAX: (+34) 96 354 3733 e-mail: alicia.amadoz at uv.es http://www.uv.es/~biodiver/v/index.htm *********************************************** From ak at ebi.ac.uk Wed Jul 23 08:03:21 2008 From: ak at ebi.ac.uk (Andreas Kahari) Date: Wed, 23 Jul 2008 13:03:21 +0100 Subject: [Bioperl-l] Bio_Tools_Run_RemoteBlast error: 500 Can't connect to www.ncbi.nlm.nih.gov:80 In-Reply-To: <1557668399amadoz@uv.es> References: <0196157D-0D2F-4DB3-AEE0-91BB56F3B82C@uiuc.edu> <1557668399amadoz@uv.es> Message-ID: <20080723120321.GA10546@ebi.ac.uk> On Wed, Jul 23, 2008 at 01:03:04PM +0200, Alicia Amadoz wrote: > Hi, > > Finally I've been talking with my system administrator and the error was because some > security configuration of our server. Now it is already solved and works ok Thanks for your > help and comments. > > I am using PHP because our application is developed in PHP and from this application > different scripts are launched. > > Alicia Probably a chroot'ed httpd without the proper /etc/resolv.conf in its chroot. I hope they fixed it properly and not by un-chroot'ing it... Andreas > > > Okay, so it appears there are overall connection issues (i.e. this > > isn't just a RemoteBlast issue). The fact that you can ping from > > command line also makes me think it isn't a proxy issue. I'm not > > familiar with PHP myself, but I would think it only allows user- > > defined processes to access network connections, so that's my next > > guess. > > > > Out of curiosity, is there any particular reason you are using PHP? > > > > chris > > > > On Jul 21, 2008, at 10:24 AM, Alicia Amadoz wrote: > > > > > Hi, > > > > > > I have tried what you suggested and what I get is another error: > > > > > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > > MSG: WebDBSeqI Request Error: > > > 500 Can't connect to eutils.ncbi.nlm.nih.gov:80 (Bad hostname > > > 'eutils.ncbi.nlm.nih.gov') > > > Content-Type: text/plain > > > Client-Date: Mon, 21 Jul 2008 15:07:39 GMT > > > Client-Warning: Internal response > > > > > > 500 Can't connect to eutils.ncbi.nlm.nih.gov:80 (Bad hostname > > > 'eutils.ncbi.nlm.nih.gov') > > > > > > STACK: Error::throw > > > STACK: Bio::Root::Root::throw /usr/lib/perl5/vendor_perl/5.8.8/Bio/ > > > Root/Root.pm:359 > > > STACK: Bio::DB::WebDBSeqI::_stream_request > > > /usr/lib/perl5/vendor_perl/5.8.8/Bio/DB/WebDBSeqI.pm:758 > > > STACK: Bio::DB::WebDBSeqI::get_seq_stream > > > /usr/lib/perl5/vendor_perl/5.8.8/Bio/DB/WebDBSeqI.pm:454 > > > STACK: Bio::DB::WebDBSeqI::get_Stream_by_id > > > /usr/lib/perl5/vendor_perl/5.8.8/Bio/DB/WebDBSeqI.pm:275 > > > STACK: /var/www/html/perl-cgi//remote_blast_ncbi.pl:48 > > > ----------------------------------------------------------- > > > > > > in line 48 of my script is, > > > > > > my $seqio = $gb->get_Stream_by_id([qw(J00522 AF303112 2981014)]); > > > > > >> From the original script you appear to be running things from a PHP > > >> environment, so maybe it has something to do with that, e.g. maybe > > >> you > > >> need to set other env. settings (like a proxy) in order to connect. > > > > > > I am going to check again php.info but I have no idea what can it be. > > > > > > Thanks again for your help. > > > Alicia > > > > > > > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > Christopher Fields > > Postdoctoral Researcher > > Lab of Dr. Marie-Claude Hofmann > > College of Veterinary Medicine > > University of Illinois Urbana-Champaign > > > > > > > > > > > > > > > -- > *********************************************** > Alicia Amadoz Navarro > > Evolutionary Genetics Unit > Cavanilles Institute for Biodiversity and Evolutionary > Biology > University of Valencia > Pol?gono de la Coma s/n, > 46980 Paterna (Valencia), > Phone: (+34) 96 354 3687 > FAX: (+34) 96 354 3733 > e-mail: alicia.amadoz at uv.es > http://www.uv.es/~biodiver/v/index.htm > > *********************************************** > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Andreas K?h?ri, Ensembl Software Developer European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, United Kingdom From michael.watson at bbsrc.ac.uk Wed Jul 23 11:49:21 2008 From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C)) Date: Wed, 23 Jul 2008 16:49:21 +0100 Subject: [Bioperl-l] Parsing strand and frame for blastx results using SearchIO Message-ID: <8975119BCD0AC5419D61A9CF1A923E9506D876F8@iahce2ksrv1.iah.bbsrc.ac.uk> Hello Am currently using bioperl-1.5.2_102 and BLASTX 2.2.17 [Aug-26-2007], but this also holds true in 1.5.1 and 1.4.0. I have a results file that is pasted below, and a script that is also pasted below - just wondering how searchIO thinks the strand is 0 and the frame is 2? Result: BLASTX 2.2.17 [Aug-26-2007] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= lcl|chr2 42223489 - 44537930 (2,314,442 letters) Database: ../chemokine_receptors_aa.txt 15 sequences; 5543 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value chCCRc 727 0.0 >chCCRc Length = 377 Score = 727 bits (1877), Expect = 0.0 Identities = 362/377 (96%), Positives = 362/377 (96%) Frame = -3 Query: 496563 MEQRKKLTGRHTRALYLWFFPSQESKMNPTDLFLSTTEYDYGYDENTAPCNEGNSFPRFK 496384 MEQRKKLTGRHTRALYLWFFPSQESKMNPTDLFLSTTEYDYGYDENTAPCNEGNSFPRFK Sbjct: 1 MEQRKKLTGRHTRALYLWFFPSQESKMNPTDLFLSTTEYDYGYDENTAPCNEGNSFPRFK 60 Query: 496383 SLFLPILYCLVFVFCLLGNSLVLWILLTRKRLMTMTDICLLNLAASDLLFIVPLPFQAYY 496204 SLFLPILYCLVFVFCLLGNSLVLWILLTRKRLMTMTDICLLNLAASDLLFIVPLPFQAYY Sbjct: 61 SLFLPILYCLVFVFCLLGNSLVLWILLTRKRLMTMTDICLLNLAASDLLFIVPLPFQAYY 120 Query: 496203 ASDQWVFGNALCKIMGGIYYTGFYSSIFFITLMSIDRYIAIVHAVYAMKIRTASCGTMIS 496024 ASDQWVFGNALCKIMGGIYYTGFYSSIFFITLMSIDRYIAIVHAVYAMKIRTASCGTMIS Sbjct: 121 ASDQWVFGNALCKIMGGIYYTGFYSSIFFITLMSIDRYIAIVHAVYAMKIRTASCGTMIS 180 Query: 496023 LVLWLVAGLASVPNIVFNQQLEIEQSVQCVPVYPPGNNIWKVTTQFAANILGLLIPFSIL 495844 LVLWLVAGLASVPNIVFNQQLEIEQSVQCVPVYPPGNNIWKVTTQFAANILGLLIPFSIL Sbjct: 181 LVLWLVAGLASVPNIVFNQQLEIEQSVQCVPVYPPGNNIWKVTTQFAANILGLLIPFSIL 240 Query: 495843 IHCYAQILRNLRKCKNQNXXXXXXXXXXXXXXXFLFWTPFNVVLFLDSLQSLLIIDNCQA 495664 IHCYAQILRNLRKCKNQN FLFWTPFNVVLFLDSLQSLLIIDNCQA Sbjct: 241 IHCYAQILRNLRKCKNQNKIKAIKMIFIIVIVFFLFWTPFNVVLFLDSLQSLLIIDNCQA 300 Query: 495663 SSQITLALQLTETISFIHCCLNPVIYAFAGVTFKAHLKRLLQPCARILWSPTRGSGVTQS 495484 SSQITLALQLTETISFIHCCLNPVIYAFAGVTFKAHLKRLLQPCARILWSPTRGSGVTQS Sbjct: 301 SSQITLALQLTETISFIHCCLNPVIYAFAGVTFKAHLKRLLQPCARILWSPTRGSGVTQS 360 Query: 495483 SLVLSQISGCSDSAGVL 495433 SLVLSQISGCSDSAGVL Sbjct: 361 SLVLSQISGCSDSAGVL 377 Database: ../chemokine_receptors_aa.txt Posted date: Jul 23, 2008 2:43 PM Number of letters in database: 5543 Number of sequences in database: 15 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 15 Number of Hits to DB: 28,029,184 Number of extensions: 721812 Number of successful extensions: 2651 Number of sequences better than 1.0e-05: 15 Number of HSP's gapped: 2358 Number of HSP's successfully gapped: 148 Length of query: 771480 Length of database: 5543 Length adjustment: 102 Effective length of query: 771378 Effective length of database: 4013 Effective search space: 3095539914 Effective search space used: 3095539914 Neighboring words threshold: 12 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 33 (17.3 bits) Script: #!/usr/bin/perl use lib "/usr/local/bioperl-1.5.2_102"; use Bio::SearchIO; my $searchio = Bio::SearchIO->new(-format => 'blast', -file => "test.blast"); while (my($result) = $searchio->next_result()) { unless (defined $result) { # there is an undefined result at the end of SearchIO objects last; } while(my $hit = $result->next_hit) { while (my $hsp = $hit->next_hsp) { print $hit->name, "\t"; print $hsp->strand('hit'), "\t"; print $hsp->frame, "\n"; } } } Output: -bash-3.00$ perl parse_test_blast.pl chCCRc 0 2 Head of Informatics Institute for Animal Health Compton Berks RG20 7NN 01635 578411 http://www.iah.ac.uk/research/bioinformatics/bioinf.shtml The information contained in this message may be confidential or legally privileged and is intended solely for the addressee. 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From roy.chaudhuri at gmail.com Wed Jul 23 12:13:41 2008 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Wed, 23 Jul 2008 17:13:41 +0100 Subject: [Bioperl-l] Parsing strand and frame for blastx results using SearchIO In-Reply-To: <8975119BCD0AC5419D61A9CF1A923E9506D876F8@iahce2ksrv1.iah.bbsrc.ac.uk> References: <8975119BCD0AC5419D61A9CF1A923E9506D876F8@iahce2ksrv1.iah.bbsrc.ac.uk> Message-ID: <488758B5.1050104@gmail.com> There's an explanation in the BioPerl FAQ: http://www.bioperl.org/wiki/FAQ#How_do_I_get_the_frame_for_a_translated_search.3F The problem with the strand being reported as 0 is because you are asking for the strand of the hit (protein) rather than the query (DNA). Roy. -- Dr. Roy Chaudhuri Department of Veterinary Medicine University of Cambridge, U.K. michael watson (IAH-C) wrote: > Hello > > Am currently using bioperl-1.5.2_102 and BLASTX 2.2.17 [Aug-26-2007], > but this also holds true in 1.5.1 and 1.4.0. > > I have a results file that is pasted below, and a script that is also > pasted below - just wondering how searchIO thinks the strand is 0 and > the frame is 2? > > Result: > BLASTX 2.2.17 [Aug-26-2007] > > > Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. > Schaffer, > Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), > "Gapped BLAST and PSI-BLAST: a new generation of protein database search > programs", Nucleic Acids Res. 25:3389-3402. > > Query= lcl|chr2 42223489 - 44537930 > (2,314,442 letters) > > Database: ../chemokine_receptors_aa.txt > 15 sequences; 5543 total letters > > Searching..................................................done > > > > Score > E > Sequences producing significant alignments: (bits) > Value > > chCCRc > 727 0.0 > >> chCCRc > Length = 377 > > Score = 727 bits (1877), Expect = 0.0 > Identities = 362/377 (96%), Positives = 362/377 (96%) > Frame = -3 > > Query: 496563 > MEQRKKLTGRHTRALYLWFFPSQESKMNPTDLFLSTTEYDYGYDENTAPCNEGNSFPRFK 496384 > > MEQRKKLTGRHTRALYLWFFPSQESKMNPTDLFLSTTEYDYGYDENTAPCNEGNSFPRFK > Sbjct: 1 > MEQRKKLTGRHTRALYLWFFPSQESKMNPTDLFLSTTEYDYGYDENTAPCNEGNSFPRFK 60 > > Query: 496383 > SLFLPILYCLVFVFCLLGNSLVLWILLTRKRLMTMTDICLLNLAASDLLFIVPLPFQAYY 496204 > > SLFLPILYCLVFVFCLLGNSLVLWILLTRKRLMTMTDICLLNLAASDLLFIVPLPFQAYY > Sbjct: 61 > SLFLPILYCLVFVFCLLGNSLVLWILLTRKRLMTMTDICLLNLAASDLLFIVPLPFQAYY 120 > > Query: 496203 > ASDQWVFGNALCKIMGGIYYTGFYSSIFFITLMSIDRYIAIVHAVYAMKIRTASCGTMIS 496024 > > ASDQWVFGNALCKIMGGIYYTGFYSSIFFITLMSIDRYIAIVHAVYAMKIRTASCGTMIS > Sbjct: 121 > ASDQWVFGNALCKIMGGIYYTGFYSSIFFITLMSIDRYIAIVHAVYAMKIRTASCGTMIS 180 > > Query: 496023 > LVLWLVAGLASVPNIVFNQQLEIEQSVQCVPVYPPGNNIWKVTTQFAANILGLLIPFSIL 495844 > > LVLWLVAGLASVPNIVFNQQLEIEQSVQCVPVYPPGNNIWKVTTQFAANILGLLIPFSIL > Sbjct: 181 > LVLWLVAGLASVPNIVFNQQLEIEQSVQCVPVYPPGNNIWKVTTQFAANILGLLIPFSIL 240 > > Query: 495843 > IHCYAQILRNLRKCKNQNXXXXXXXXXXXXXXXFLFWTPFNVVLFLDSLQSLLIIDNCQA 495664 > IHCYAQILRNLRKCKNQN > FLFWTPFNVVLFLDSLQSLLIIDNCQA > Sbjct: 241 > IHCYAQILRNLRKCKNQNKIKAIKMIFIIVIVFFLFWTPFNVVLFLDSLQSLLIIDNCQA 300 > > Query: 495663 > SSQITLALQLTETISFIHCCLNPVIYAFAGVTFKAHLKRLLQPCARILWSPTRGSGVTQS 495484 > > SSQITLALQLTETISFIHCCLNPVIYAFAGVTFKAHLKRLLQPCARILWSPTRGSGVTQS > Sbjct: 301 > SSQITLALQLTETISFIHCCLNPVIYAFAGVTFKAHLKRLLQPCARILWSPTRGSGVTQS 360 > > Query: 495483 SLVLSQISGCSDSAGVL 495433 > SLVLSQISGCSDSAGVL > Sbjct: 361 SLVLSQISGCSDSAGVL 377 > > > Database: ../chemokine_receptors_aa.txt > Posted date: Jul 23, 2008 2:43 PM > Number of letters in database: 5543 > Number of sequences in database: 15 > > Lambda K H > 0.318 0.134 0.401 > > Gapped > Lambda K H > 0.267 0.0410 0.140 > > > Matrix: BLOSUM62 > Gap Penalties: Existence: 11, Extension: 1 > Number of Sequences: 15 > Number of Hits to DB: 28,029,184 > Number of extensions: 721812 > Number of successful extensions: 2651 > Number of sequences better than 1.0e-05: 15 > Number of HSP's gapped: 2358 > Number of HSP's successfully gapped: 148 > Length of query: 771480 > Length of database: 5543 > Length adjustment: 102 > Effective length of query: 771378 > Effective length of database: 4013 > Effective search space: 3095539914 > Effective search space used: 3095539914 > Neighboring words threshold: 12 > Window for multiple hits: 40 > X1: 16 ( 7.3 bits) > X2: 38 (14.6 bits) > X3: 64 (24.7 bits) > S1: 41 (21.7 bits) > S2: 33 (17.3 bits) > > > Script: > #!/usr/bin/perl > > use lib "/usr/local/bioperl-1.5.2_102"; > use Bio::SearchIO; > > my $searchio = Bio::SearchIO->new(-format => 'blast', -file => > "test.blast"); > > while (my($result) = $searchio->next_result()) { > unless (defined $result) { > # there is an undefined result at the end of SearchIO > objects > last; > } > > while(my $hit = $result->next_hit) { > while (my $hsp = $hit->next_hsp) { > > print $hit->name, "\t"; > print $hsp->strand('hit'), "\t"; > print $hsp->frame, "\n"; > } > } > } > > Output: > -bash-3.00$ perl parse_test_blast.pl > chCCRc 0 2 > > > Head of Informatics > Institute for Animal Health > Compton > Berks > RG20 7NN > 01635 578411 > > http://www.iah.ac.uk/research/bioinformatics/bioinf.shtml > > The information contained in this message may be confidential or legally > privileged and is intended solely for the addressee. > If you have received this message in error please delete it & notify the > originator immediately. > Unauthorised use, disclosure, copying or alteration of this message is > forbidden & may be unlawful. > The contents of this e-mail are the views of the sender and do not > necessarily represent the views of the Institute. > This email and associated attachments has been checked locally for > viruses but we can accept no responsibility once it has left our > systems. > Communications on Institute computers are monitored to secure the > effective operation of the systems and for other lawful purposes. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From jason.stajich at gmail.com Wed Jul 23 12:40:24 2008 From: jason.stajich at gmail.com (Jason Stajich) Date: Wed, 23 Jul 2008 09:40:24 -0700 Subject: [Bioperl-l] amino acid composition In-Reply-To: <5.0.2.1.2.20080723145044.00be8fd0@pop.univ-montp2.fr> References: <5.0.2.1.2.20080723145044.00be8fd0@pop.univ-montp2.fr> Message-ID: <8A751791-317D-4175-B212-8569FFFE370C@gmail.com> List is best place to ask. On Jul 23, 2008, at 5:53 AM, Laurent Manchon wrote: > Hello, > > > have you another version of your program aacomp.pl to compute > amino acid composition in a multi-fasta protein file to obtain a > simple output like > that: > > >ID_sequence_1: composition ... > >ID_sequence_2: composition ... > >ID_sequence_n: composition ... > > thank you, > Laurent. > > > > +---------------------------------------------+ > Laurent Manchon > Email: lmanchon at univ-montp2.fr > +---------------------------------------------+ From yee.leon at gmail.com Thu Jul 24 07:41:42 2008 From: yee.leon at gmail.com (Leon Yee) Date: Thu, 24 Jul 2008 19:41:42 +0800 Subject: [Bioperl-l] MSA2PSSM? Message-ID: <48886A76.5060203@gmail.com> Hi all, Given a multiple sequence alignment produced by clustalW or POA or Tcoffee, how can I calculate the corresponding position-specific scoring matrix (like Psi-blast checkpoint file) using Bioperl? Thank you very much! Best wishes, Leon Yee From hlapp at gmx.net Wed Jul 23 21:02:19 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 23 Jul 2008 21:02:19 -0400 Subject: [Bioperl-l] Smaller Bioperl Modules In-Reply-To: <9BEB5FD4EB2BF3468A6A546A17480BC2277CED@exactn3-cbr.nexus.csiro.au> References: <9BEB5FD4EB2BF3468A6A546A17480BC2277CED@exactn3-cbr.nexus.csiro.au> Message-ID: What would be really nice to have for such purposes is a build option that, given a list of modules, creates a tar (or whatever else that's suitable for distribution) with those modules and all other modules they depend on, recursively of course. Presumably this is what you would be looking for? It'd be great if someone would like to take this on (perhaps yourself?), though we should also keep in mind that in reality this is going to be a rather rare need. Still, as you describe, for those that do have the need it might help a lot. I should also note that in my observation it is not uncommon for sysadmins in biology or other department to have had to install bioperl already for faculty or students, so having to do this may not be such an extraordinary task for many out there. -hilmar On Jul 21, 2008, at 7:09 PM, wrote: > Hi all, > > I'm developing a web-based application and it'd be cool to use some > Bioperl modules. However, I'll be providing my tool for downloaded and > installation on a web server, so having to ask the sys admin to > install > all of bioperl where I only need a few modules is overkill and is > likely > to cause installation headaches. > > Since I've been out of the loop for quite a while now, I was wondering > if any decisions had been made about whether or not Bioperl was > going to > be released on CPAN in smaller sets of modules with correct > dependencies > and possibly a Bundle::Bioperl? It'd be nice to have my application, > for > example, depend on Bio::SeqIO, such that only Bio::SeqIO::* and it's > dependencies are installable through CPAN. > > Cheers, > Nath > > ------------------------------------------------------------- > Dr. Nathan S. Watson-Haigh (publish under Haigh, N.S.) > OCE Post Doctoral Fellow > CSIRO Livestock Industries > J M Rendel Laboratory > Rockhampton > QLD 4701 Tel: +61 (0)7 4923 8121 > Australia Fax: +61 (0)7 4923 8222 > ------------------------------------------------------------- > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From lmanchon at univ-montp2.fr Thu Jul 24 10:01:32 2008 From: lmanchon at univ-montp2.fr (Laurent Manchon) Date: Thu, 24 Jul 2008 16:01:32 +0200 Subject: [Bioperl-l] retrieve ensembl sequence using bioperl Message-ID: <5.0.2.1.2.20080724155739.00be0b58@pop.univ-montp2.fr> Hi, I try to download sequence from ensembl database submiting the ID via the perl code below. For swiss or genbank ID submission it works fine but for ensembl it fails and i don't know why. Tell me if you have an idea . thank you. #!/usr/bin/perl -w use Bio::Perl; if ($#ARGV < 0) { print "Usage: $0 databaseID\n"; exit; } #database availables 'swiss','genbank','genpept','embl','refseq' $seq_object = get_sequence('embl',$ARGV[0]); write_sequence(">${ARGV[0]}.fasta",'fasta',$seq_object); +---------------------------------------------+ Laurent Manchon Email: lmanchon at univ-montp2.fr +---------------------------------------------+ From cjfields at uiuc.edu Thu Jul 24 11:09:39 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 24 Jul 2008 10:09:39 -0500 Subject: [Bioperl-l] Smaller Bioperl Modules In-Reply-To: References: <9BEB5FD4EB2BF3468A6A546A17480BC2277CED@exactn3-cbr.nexus.csiro.au> Message-ID: On Jul 23, 2008, at 8:02 PM, Hilmar Lapp wrote: > What would be really nice to have for such purposes is a build > option that, given a list of modules, creates a tar (or whatever > else that's suitable for distribution) with those modules and all > other modules they depend on, recursively of course. > > Presumably this is what you would be looking for? It'd be great if > someone would like to take this on (perhaps yourself?), though we > should also keep in mind that in reality this is going to be a > rather rare need. Still, as you describe, for those that do have the > need it might help a lot. I think that's a really good idea, and obviates the need to split everything up. We need to come up with a scheme to tie together the various dependencies and tests with their modules, though, but I think it's doable. Just needs someone with the time to try it out on a branch *cough*Nathan*cough* > I should also note that in my observation it is not uncommon for > sysadmins in biology or other department to have had to install > bioperl already for faculty or students, so having to do this may > not be such an extraordinary task for many out there. > > -hilmar Agreed, though many sysadmins are adverse to installing bioperl-live over (say) an RPM or off CPAN, so the latest one could get in that case would be 1.5.2. Actually, some don't even consider 1.5.2 'stable' due to our designation of the 1.5 series as 'developer'; maybe something we need to rethink down the road (and the reason I proposed the core-tools-dev split). chris From pmiguel at purdue.edu Thu Jul 24 11:09:08 2008 From: pmiguel at purdue.edu (Phillip San Miguel) Date: Thu, 24 Jul 2008 11:09:08 -0400 Subject: [Bioperl-l] How to input fasta and qual into Bio::Seq::Quality? Message-ID: <48889B14.1000909@purdue.edu> I usually use both sequence and quality data. See below[1] if you don't know what I mean. As I mentioned int a previous thread, Bio::Seq::Quality seems great for this sort of work. But, near as I can tell, Bio::SeqIO does not directly create these objects. Specifically, what I would like is for someone to tell me that my way of creating a Bio::Seq::Quality object is unnecessarily brute force. I would like this to be possible: my $BSQ_in_obj =Bio::SeqIO ->new( -file =>$seq_infile, -qfile =>$qual_infile ); such that $BSQ_in_obj->next_seq would create a Bio::Seq::Quality object. But I don't have a good overall sense of the guts of bioperl, so I'm not sure if this would create other problems. It might not be clear what my problem is. So I've pasted code to show how I currently create a Bio::Seq::Quality object. The code and data files are here: http://www.genomics.purdue.edu/~pmiguel/programs/BSQ_simple_trial.perl http://www.genomics.purdue.edu/~pmiguel/programs/HEX1057J19scaffold.fasta http://www.genomics.purdue.edu/~pmiguel/programs/HEX1057J19scaffold.fasta.qual Or just the text: #!/usr/bin/perl use warnings; use strict; use Bio::SeqIO; use Bio::Seq::Quality; my ($seq_infile,$qual_infile) =(scalar @ARGV == 1) ?($ARGV[0] ,"$ARGV[0].qual") :@ARGV; #Create input objects for both a seq (fasta) and qual file my $in_seq_obj =Bio::SeqIO ->new( -file =>$seq_infile, -format =>'fasta', ); my $in_qual_obj =Bio::SeqIO ->new( -file =>$qual_infile, -format =>'qual', ); while (1){ #create actual objects for both a seq and its associated qual my $seq_obj =$in_seq_obj->next_seq() || last; my $qual_obj=$in_qual_obj->next_seq(); #use seq and qual object methods feed info for new BSQ object my $bsq_obj =Bio::Seq::Quality->new ( -seq => $seq_obj->seq(), -qual=> $qual_obj->qual(), ); #Do something with BSQ object to show off its powers print $bsq_obj ->subseq(10,100) ,"\n" ,$bsq_obj ->subqual_text(10,100) ,"\n"; } It seems unwieldy though. Is there a better way? Phillip [1] With finished sequence, quality should be uniformly high. But frequently we work with single pass, or other types of unfinished sequences. These type of sequences will have variable quality. That is, the SNP you just found may really be a sequencing ("measurement") error--a miscall. Pairing a fasta sequence file with a quality file, like the phred/phrap/consed package does, is now a common way to handle sequence data of variable quality. All modern sequencers (that I know of) will generate quality scores for each base called. From Frigerio at pierroton.inra.fr Thu Jul 24 12:15:22 2008 From: Frigerio at pierroton.inra.fr (Jean-Marc FRIGERIO) Date: Thu, 24 Jul 2008 18:15:22 +0200 Subject: [Bioperl-l] phd format parsing produces infinite memory usage Message-ID: <200807241815.22749.Frigerio@pierroton.inra.fr> > Date: Wed, 23 Jul 2008 11:08:44 +0200 > From: Jorge.DUARTE at biogemma.com > Subject: [Bioperl-l] phd format parsing produces infinite memory usage > To: bioperl-l at lists.open-bio.org > Message-ID: > > > > Content-Type: text/plain; charset="ISO-8859-1" > > Hello, > > i've been trying to use Bio::SeqIO to parse a phd-like format file. > > The script doesn't produce any error (nor output), but the memory usage > keeps increasing until it reaches its limit (well i stoped the process at > 16Gb of memory) > > Is the problem known ? Or is my file format wrong ? > > If i use only the first sequence from my file (bellow), the script works > fine, maybe there is something wrong in the middle of the file... how can > i print debugging info ? > > Thanks for any help > > jorge Hi, > If i use only the first sequence from my file (bellow), the script works > fine Huuh !! phd files should contain only one sequence !! The following code works well on your file. #!/usr/bin/env perl # vim: filetype=perl fdm=marker fdl=0 fdc=2 fmr=#/*,#*\ use strict; use warnings; use Bio::SeqIO; my $seqqio = Bio::SeqIO->new('-file' => 'phd_test', '-format' => 'phd'); my $seqout = Bio::SeqIO->new('-fh' => \*STDOUT, '-format' => 'phd'); while(my $seq = $seqqio->next_seq) { print $seq->id,"\n",$seq->seq,"\n"; $seqout->write_seq($seq); } From johnsonm at gmail.com Thu Jul 24 15:35:00 2008 From: johnsonm at gmail.com (Mark Johnson) Date: Thu, 24 Jul 2008 14:35:00 -0500 Subject: [Bioperl-l] How to input fasta and qual into Bio::Seq::Quality? In-Reply-To: <48889B14.1000909@purdue.edu> References: <48889B14.1000909@purdue.edu> Message-ID: On Thu, Jul 24, 2008 at 10:09 AM, Phillip San Miguel wrote: > Specifically, what I would like is for someone to tell me that my way of > creating a Bio::Seq::Quality object is unnecessarily brute force. I would > like this to be possible: > > my $BSQ_in_obj =Bio::SeqIO > ->new( -file =>$seq_infile, > -qfile =>$qual_infile > ); > such that $BSQ_in_obj->next_seq would create a Bio::Seq::Quality object. I'm no design pattern ninja, but I think what you're looking for is something like a Facade for Bio::SeqIO::fasta and Bio::SeqIO::qual: my $seqio = Bio::SeqIO::SomeCleverName->new(-seq => $seq_file, -qual => $qual_file); # $bsq is a Bio::Seq::Quality while (my $bsq = $seqio->next_seq()) { # Do Stuff } I don't think this is implemented anywhere in Bioperl, though I have not done an exhaustive search. > But I don't have a good overall sense of the guts of bioperl, so I'm not > sure if this would create other problems. A wrapper would have just should have zero impact. There seems to be some sort of precedent for this sort of thing (see Bio::SeqIO::MultiFile). You could code this up and start using it yourself immediately. If you were so inclined, you could contribute it back to Bioperl (no guarantees it would be accepted, at least as is, but talking about it on the list first helps grease the tracks, so to speak). > while (1){ > #create actual objects for both a seq and its associated qual > my $seq_obj =$in_seq_obj->next_seq() || last; > my $qual_obj=$in_qual_obj->next_seq(); Your code assumes that the files are in the same order. That is, that the Nth fasta sequence in the seq file goes with the Nth fasta quality sequence in the qual file. I suppose that's a safe assumption if you generated the files, but if you were to code this up as a wrapper for Bio::SeqIO::fasta and Bio::SeqIO::qual you'd want some sort of sanity check that would throw an exception if the identifiers didn't match. I suppose another option would be to convert your seq/qual files to fastq format (See Bio::SeqIO::fastq). From johnsonm at gmail.com Thu Jul 24 15:45:59 2008 From: johnsonm at gmail.com (Mark Johnson) Date: Thu, 24 Jul 2008 14:45:59 -0500 Subject: [Bioperl-l] retrieve ensembl sequence using bioperl In-Reply-To: <5.0.2.1.2.20080724155739.00be0b58@pop.univ-montp2.fr> References: <5.0.2.1.2.20080724155739.00be0b58@pop.univ-montp2.fr> Message-ID: On Thu, Jul 24, 2008 at 9:01 AM, Laurent Manchon wrote: > #!/usr/bin/perl -w > use Bio::Perl; Ah. Ye Olde Functional Interace. > if ($#ARGV < 0) { > print "Usage: $0 databaseID\n"; > exit; > } > #database availables 'swiss','genbank','genpept','embl','refseq' > $seq_object = get_sequence('embl',$ARGV[0]); > write_sequence(">${ARGV[0]}.fasta",'fasta',$seq_object); Can you give us an example of an accession / identifier / whatever that does not work? Are you sure your queries are valid EMBL accessions? If you go here: http://www.ebi.ac.uk/ebisearch/ and plug in your input, do you get any sequences returned? From cjfields at uiuc.edu Thu Jul 24 15:55:27 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 24 Jul 2008 14:55:27 -0500 Subject: [Bioperl-l] retrieve ensembl sequence using bioperl In-Reply-To: References: <5.0.2.1.2.20080724155739.00be0b58@pop.univ-montp2.fr> Message-ID: <60ADE80E-4680-4AD3-9342-13475D2B5F08@uiuc.edu> Note that you can't retrieve ***Ensembl*** seqs from bioperl, but you can get seqs from ***EMBL*** (two different beasts; the example code below is for EMBL retrieval). You can use the ensembl perl API to retrieve seqs from ensembl, though. chris On Jul 24, 2008, at 2:45 PM, Mark Johnson wrote: > On Thu, Jul 24, 2008 at 9:01 AM, Laurent Manchon > wrote: > >> #!/usr/bin/perl -w >> use Bio::Perl; > > Ah. Ye Olde Functional Interace. > >> if ($#ARGV < 0) { >> print "Usage: $0 databaseID\n"; >> exit; >> } >> #database availables 'swiss','genbank','genpept','embl','refseq' >> $seq_object = get_sequence('embl',$ARGV[0]); >> write_sequence(">${ARGV[0]}.fasta",'fasta',$seq_object); > > Can you give us an example of an accession / identifier / whatever > that does not work? Are you sure your queries are valid EMBL > accessions? If you go here: > > http://www.ebi.ac.uk/ebisearch/ > > and plug in your input, do you get any sequences returned? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Marie-Claude Hofmann College of Veterinary Medicine University of Illinois Urbana-Champaign From Nathan.Watson-Haigh at csiro.au Thu Jul 24 02:26:42 2008 From: Nathan.Watson-Haigh at csiro.au (Nathan.Watson-Haigh at csiro.au) Date: Thu, 24 Jul 2008 16:26:42 +1000 Subject: [Bioperl-l] Smaller Bioperl Modules References: <9BEB5FD4EB2BF3468A6A546A17480BC2277CED@exactn3-cbr.nexus.csiro.au> Message-ID: <9BEB5FD4EB2BF3468A6A546A17480BC2334B5B@exactn3-cbr.nexus.csiro.au> Hi Chris, It seems that the issue of having "tons of separately installable mini-bioperl modules" is not an issue at all for anyone at CPAN, not a problem for end users (as long as dependencies between modules are done correctly) but maybe/is an issue for dev maintainance: http://www.perlmonks.org/?node_id=699449 Anyway, I thought it might be interesting to visualise the network of dependencies within Bioperl to see if any tight clusters of heavy connected modules that would be candidates for a separate "mini-modules". To this end, I'm trying to use Module::ScanDeps in conjunction with File::Find and GraphViz in order to produce a directed graph showing the dependencies within a set of modules. This seems to be working nicely (for a small set of modules e.g. Bio::AlignIO::*) but I seem to be getting some dependencies that I didn't expect. So I'm hoping someone might be able to shed light on why these dependencies might be coming up, or if it's something wrong with Module::ScanDeps. In particular I'm looking at the dependencies of Bio::AlignIO::* modules. One of the modules (Bio::AlignIO::largemultifasta) is connected to lots of Bio::SeqIO::* modules and I'm not sure why/how these dependencies have come about. You can see the dependency graph at http://www.watsonhaigh.net/img/Bio_AlignIO_deps_graph.png The Bio::AlignIO::largemultifasta node is towards the right and is the centre of the radial fan. Below is my script, in case it helps. Cheers, Nath -- start script -- use strict; use File::Find; use Module::ScanDeps; use GraphViz; use Data::Dumper; my @module_paths; my $g = GraphViz->new( layout => 'neato', overlap => 'scale', ); my $dir = $ARGV[0]; print STDERR "Finding module files ... "; find(\&wanted, $dir); print STDERR "DONE\n"; sub wanted { next unless /\.pm$/; push @module_paths, $File::Find::name; } print STDERR "Scanning dependencies ... "; my $rv = scan_deps( files => \@module_paths, recurse => 0, ); print STDERR "DONE\n"; foreach my $module ( keys %{$rv} ) { delete $rv->{$module} unless $module =~ /^Bio/; } print STDERR "Building dependency graph ... "; foreach my $module ( keys %{$rv} ) { if ( exists$rv->{$module}{'uses'} ) { foreach my $uses ( @{$rv->{$module}{'uses'}} ) { next unless $uses =~ /^Bio/; $g->add_edge($module => $uses); } } } print STDERR "Printing dependency graph ... "; print $g->as_png; print STDERR "DONE\n"; -- end script -- -----Original Message----- From: Chris Fields [mailto:cjfields at uiuc.edu] Sent: Tuesday, 22 July 2008 12:40 PM To: Watson-Haigh, Nathan (LI, Rock. Rendel) Cc: bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] Smaller Bioperl Modules Hi Nat! We have discussed breaking things up but there was never a full consensus on it and I think, in the long run, it would have been too hard to convince everyone, particularly the CPAN folk, that it made sense to have tons of separately installable mini-bioperl modules. We do still intend on paring down core to the bare essentials, removing as many dependencies as possible, and having a separate tools and dev set of modules. I added a page on the wiki on my proposal for the intended split (others have added a few things here and there): http://www.bioperl.org/wiki/Proposed_1.6_core_modules It's worth reviving this discussion again; when I have more time I want to spearhead a 1.6 release. chris On Jul 21, 2008, at 6:09 PM, wrote: > Hi all, > > I'm developing a web-based application and it'd be cool to use some > Bioperl modules. However, I'll be providing my tool for downloaded and > installation on a web server, so having to ask the sys admin to > install > all of bioperl where I only need a few modules is overkill and is > likely > to cause installation headaches. > > Since I've been out of the loop for quite a while now, I was wondering > if any decisions had been made about whether or not Bioperl was > going to > be released on CPAN in smaller sets of modules with correct > dependencies > and possibly a Bundle::Bioperl? It'd be nice to have my application, > for > example, depend on Bio::SeqIO, such that only Bio::SeqIO::* and it's > dependencies are installable through CPAN. > > Cheers, > Nath > > ------------------------------------------------------------- > Dr. Nathan S. Watson-Haigh (publish under Haigh, N.S.) > OCE Post Doctoral Fellow > CSIRO Livestock Industries > J M Rendel Laboratory > Rockhampton > QLD 4701 Tel: +61 (0)7 4923 8121 > Australia Fax: +61 (0)7 4923 8222 > ------------------------------------------------------------- > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Marie-Claude Hofmann College of Veterinary Medicine University of Illinois Urbana-Champaign From johnsonm at gmail.com Thu Jul 24 17:38:35 2008 From: johnsonm at gmail.com (Mark Johnson) Date: Thu, 24 Jul 2008 16:38:35 -0500 Subject: [Bioperl-l] retrieve ensembl sequence using bioperl In-Reply-To: <4888E60C.1040501@univ-montp2.fr> References: <5.0.2.1.2.20080724155739.00be0b58@pop.univ-montp2.fr> <4888E60C.1040501@univ-montp2.fr> Message-ID: On Thu, Jul 24, 2008 at 3:29 PM, Laurent Manchon wrote: > > try this: ENSTRUP00000005947 That's an Ensembl Peptide ID. As Chris pointed out (I missed the reference to Ensembl at the top of your original message), Ensembl != EMBL. This is what I end up with: use Bio::Perl; my $seq = get_sequence('embl', 'ENSTRUP00000005947'); ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: EMBL stream with no ID. Not embl in my book STACK: Error::throw STACK: Bio::Root::Root::throw /gsc/lib/perl5/site_perl/5.8.7/Bio/Root/Root.pm:359 STACK: Bio::SeqIO::embl::next_seq /gsc/lib/perl5/site_perl/5.8.7/Bio/SeqIO/embl.pm:189 STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc /gsc/lib/perl5/site_perl/5.8.7/Bio/DB/WebDBSeqI.pm:180 STACK: Bio::Perl::get_sequence /gsc/lib/perl5/site_perl/5.8.7/Bio/Perl.pm:507 STACK: -:3 ----------------------------------------------------------- The response to a GET to this URL http://www.ebi.ac.uk/cgi-bin/dbfetch?db=embl&style=raw&format=embl&id=ENSTRUP00000005947 is 'No entries found.' Which Bio::SeqIO::embl of course does not consider valid EMBL format. You can query Ensembl via the Ensembl Perl API. You can find documentation for that here: http://www.ensembl.org/info/using/api/index.html Here are a couple tutorials I found via a quick Google search http://www.bioperl.org/wiki/Getting_Genomic_Sequences#Using_the_Perl_API_at_ENSEMBL http://www.ebi.ac.uk/2can/pdf/ensembl_tutorial.pdf Good luck! From pmiguel at purdue.edu Thu Jul 24 17:38:33 2008 From: pmiguel at purdue.edu (Phillip San Miguel) Date: Thu, 24 Jul 2008 17:38:33 -0400 Subject: [Bioperl-l] phd format parsing produces infinite memory usage In-Reply-To: <200807241815.22749.Frigerio@pierroton.inra.fr> References: <200807241815.22749.Frigerio@pierroton.inra.fr> Message-ID: <4888F659.4020900@purdue.edu> Jean-Marc FRIGERIO wrote: > > Huuh !! phd files should contain only one sequence !! > > > This is no longer necessarily true. Consed allows concatenated phd files now. From pmiguel at purdue.edu Thu Jul 24 18:00:25 2008 From: pmiguel at purdue.edu (Phillip San Miguel) Date: Thu, 24 Jul 2008 18:00:25 -0400 Subject: [Bioperl-l] How to input fasta and qual into Bio::Seq::Quality? In-Reply-To: References: <48889B14.1000909@purdue.edu> Message-ID: <4888FB79.60006@purdue.edu> Mark Johnson wrote: > I suppose another option would be to convert your seq/qual files to > fastq format (See Bio::SeqIO::fastq). > > Or, with prompting from another thread, I now see that Bio::SeqIO::phd creates Bio::Seq::Quality objects. Thanks, Phillip From cjfields at uiuc.edu Thu Jul 24 18:18:50 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 24 Jul 2008 17:18:50 -0500 Subject: [Bioperl-l] How to input fasta and qual into Bio::Seq::Quality? In-Reply-To: <4888FB79.60006@purdue.edu> References: <48889B14.1000909@purdue.edu> <4888FB79.60006@purdue.edu> Message-ID: On Jul 24, 2008, at 5:00 PM, Phillip San Miguel wrote: > Mark Johnson wrote: >> I suppose another option would be to convert your seq/qual files to >> fastq format (See Bio::SeqIO::fastq). >> >> > Or, with prompting from another thread, I now see that > Bio::SeqIO::phd creates Bio::Seq::Quality objects. > > Thanks, > Phillip There are a few SeqIO modules which create Bio::Seq::Quality (phd, scf, ctf, etc). It all depends on which format you want/specify. chris From bix at sendu.me.uk Thu Jul 24 19:15:08 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 25 Jul 2008 00:15:08 +0100 Subject: [Bioperl-l] Smaller Bioperl Modules In-Reply-To: <9BEB5FD4EB2BF3468A6A546A17480BC2334B5B@exactn3-cbr.nexus.csiro.au> References: <9BEB5FD4EB2BF3468A6A546A17480BC2277CED@exactn3-cbr.nexus.csiro.au> <9BEB5FD4EB2BF3468A6A546A17480BC2334B5B@exactn3-cbr.nexus.csiro.au> Message-ID: <48890CFC.6050808@sendu.me.uk> Nathan.Watson-Haigh at csiro.au wrote: > It seems that the issue of having "tons of separately installable > mini-bioperl modules" is not an issue at all for anyone at CPAN, not a > problem for end users (as long as dependencies between modules are done > correctly) but maybe/is an issue for dev maintainance: > http://www.perlmonks.org/?node_id=699449 I asked on the perl mailing list. It was very strongly discouraged, with good reasons. http://www.nntp.perl.org/group/perl.modules/2007/07/msg55160.html (especially Adam Kennedy's postings of 4/07) Please remind yourself of the past discussion before pressing forward: http://thread.gmane.org/gmane.comp.lang.perl.bio.general/15506/ > Anyway, I thought it might be interesting to visualise the network of > dependencies within Bioperl to see if any tight clusters of heavy > connected modules that would be candidates for a separate > "mini-modules". I've already done something along these lines. Check out 'module_usage.pl' in the maintenance directory. From hiekeen at gmail.com Fri Jul 25 04:52:51 2008 From: hiekeen at gmail.com (Jinyan Huang) Date: Fri, 25 Jul 2008 01:52:51 -0700 Subject: [Bioperl-l] How to get gene offical symbol by geneid and acc number? Message-ID: How to get gene offical symbol by geneid and acc number? From bernd.web at gmail.com Fri Jul 25 05:00:46 2008 From: bernd.web at gmail.com (Bernd Web) Date: Fri, 25 Jul 2008 11:00:46 +0200 Subject: [Bioperl-l] Smaller Bioperl Modules In-Reply-To: <9BEB5FD4EB2BF3468A6A546A17480BC2277CED@exactn3-cbr.nexus.csiro.au> References: <9BEB5FD4EB2BF3468A6A546A17480BC2277CED@exactn3-cbr.nexus.csiro.au> Message-ID: <716af09c0807250200q43e9d6aer8b29f129e83c24a2@mail.gmail.com> Hi, We often just copied the Bio directory into a Perl library dir. This worked great as we only used Perl-only modules (AlignIO, SearchIO etc.). Persons doing short projects even copied Bioperl (w/o installing etc) directly on their USB stick. Their scripts just worked fine on all computers with "use lib", of course). This is not an alternative for smaller modules clearly, but made people get into BioPerl quick. Regards, Bernd On Tue, Jul 22, 2008 at 1:09 AM, wrote: > Hi all, > > I'm developing a web-based application and it'd be cool to use some > Bioperl modules. However, I'll be providing my tool for downloaded and > installation on a web server, so having to ask the sys admin to install > all of bioperl where I only need a few modules is overkill and is likely > to cause installation headaches. > > Since I've been out of the loop for quite a while now, I was wondering > if any decisions had been made about whether or not Bioperl was going to > be released on CPAN in smaller sets of modules with correct dependencies > and possibly a Bundle::Bioperl? It'd be nice to have my application, for > example, depend on Bio::SeqIO, such that only Bio::SeqIO::* and it's > dependencies are installable through CPAN. > > Cheers, > Nath > > ------------------------------------------------------------- > Dr. Nathan S. Watson-Haigh (publish under Haigh, N.S.) > OCE Post Doctoral Fellow > CSIRO Livestock Industries > J M Rendel Laboratory > Rockhampton > QLD 4701 Tel: +61 (0)7 4923 8121 > Australia Fax: +61 (0)7 4923 8222 > ------------------------------------------------------------- > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From alexl at users.sourceforge.net Fri Jul 25 10:50:04 2008 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Fri, 25 Jul 2008 07:50:04 -0700 Subject: [Bioperl-l] Smaller Bioperl Modules In-Reply-To: <48890CFC.6050808@sendu.me.uk> (Sendu Bala's message of "Fri\, 25 Jul 2008 00\:15\:08 +0100") References: <9BEB5FD4EB2BF3468A6A546A17480BC2277CED@exactn3-cbr.nexus.csiro.au> <9BEB5FD4EB2BF3468A6A546A17480BC2334B5B@exactn3-cbr.nexus.csiro.au> <48890CFC.6050808@sendu.me.uk> Message-ID: >>>>> "SB" == Sendu Bala writes: SB> Nathan.Watson-Haigh at csiro.au wrote: >> It seems that the issue of having "tons of separately installable >> mini-bioperl modules" is not an issue at all for anyone at CPAN, >> not a problem for end users (as long as dependencies between >> modules are done correctly) but maybe/is an issue for dev >> maintainance: http://www.perlmonks.org/?node_id=699449 SB> I asked on the perl mailing list. It was very strongly SB> discouraged, with good SB> reasons. http://www.nntp.perl.org/group/perl.modules/2007/07/msg55160.html SB> (especially Adam Kennedy's postings of 4/07) SB> Please remind yourself of the past discussion before pressing SB> forward: SB> http://thread.gmane.org/gmane.comp.lang.perl.bio.general/15506/ I concur. It's definitely a major issue for package maintainers. If you split up bioperl into too many little CPAN modules, it will make packaging bioperl via RPMs in Fedora (or other distros, I suspect) a real pain. In Fedora that would mean that we might have to individually review/build each package separately which would add a lot of overhead. Some split up along the lines previously discussed seems sensible (into a "core" and "dev", i.e. not more that 3-4 separate modules), but please not 900 CPAN packages... ;) Alex From aaron.j.mackey at gsk.com Fri Jul 25 10:59:27 2008 From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com) Date: Fri, 25 Jul 2008 10:59:27 -0400 Subject: [Bioperl-l] Any volunteers for doing a Nested Containment List implementation? In-Reply-To: <6dce9a0b0807211702k1742884enf02ae53587a42922@mail.gmail.com> Message-ID: FYI, there's also (native) support for RTREE-based spatial indices in MySQL 5.1 and beyond ... http://dev.mysql.com/doc/refman/5.1/en/optimizing-spatial-analysis.html I once took a day to try to implement this NCL algorithm as a MySQL UDF (i.e. written entirely in C), but got bogged down and discouraged. The PostgreSQL implementation is available from the authors, if I remember correctly. -Aaron bioperl-l-bounces at lists.open-bio.org wrote on 07/21/2008 08:02:36 PM: > Hi Folks, > > This paper describes an indexing algorithm for genome feature databases > called Nested Containment Lists. Apparently it is substantially faster than > the indexing systems we use in BioPerl for the Bio::DB::GFF, > Bio::DB::SeqFeature::Store, and Chado. > > http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btl647v1?papetoc > > The concept and data structures are quite simple, and I think it would be > straightforward to implement this system in MySQL tables. Would anybody be > interested in taking this on as a summer project? > > Lincoln > > -- > Lincoln D. Stein > > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Stacey Fairfield > > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 USA > (516) 367-8380 > Assistant: Sandra Michelsen > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at uiuc.edu Sat Jul 26 20:08:37 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Sat, 26 Jul 2008 19:08:37 -0500 Subject: [Bioperl-l] Smaller Bioperl Modules In-Reply-To: References: <9BEB5FD4EB2BF3468A6A546A17480BC2277CED@exactn3-cbr.nexus.csiro.au> <9BEB5FD4EB2BF3468A6A546A17480BC2334B5B@exactn3-cbr.nexus.csiro.au> <48890CFC.6050808@sendu.me.uk> Message-ID: <15BFEFB1-64A4-4A0C-9618-3B7369AC4095@uiuc.edu> On Jul 25, 2008, at 9:50 AM, Alex Lancaster wrote: >>>>>> ... > I concur. It's definitely a major issue for package maintainers. If > you split up bioperl into too many little CPAN modules, it will make > packaging bioperl via RPMs in Fedora (or other distros, I suspect) a > real pain. In Fedora that would mean that we might have to > individually review/build each package separately which would add a > lot of overhead. > > Some split up along the lines previously discussed seems sensible > (into a "core" and "dev", i.e. not more that 3-4 separate modules), > but please not 900 CPAN packages... ;) > > Alex So something like what we indicate in the below link would be okay? http://www.bioperl.org/wiki/Proposed_1.6_core_modules chris From Jorge.DUARTE at biogemma.com Mon Jul 28 04:11:17 2008 From: Jorge.DUARTE at biogemma.com (Jorge.DUARTE at biogemma.com) Date: Mon, 28 Jul 2008 10:11:17 +0200 Subject: [Bioperl-l] phd format parsing produces infinite memory usage In-Reply-To: <4888F659.4020900@purdue.edu> Message-ID: bioperl-l-bounces at lists.open-bio.org a ?crit sur 24/07/2008 23:38:33 : > Jean-Marc FRIGERIO wrote: > > > > Huuh !! phd files should contain only one sequence !! > > > > > > > This is no longer necessarily true. Consed allows concatenated phd files > now. > Alright, thank you for your answers. In case it can help others until the parser is updated, if i modify the phd.pm code this way, it seems to work fine for my file : if ($entry =~ /^END_SEQUENCE/) { $entry = $self->_readline(); last; } I'm not sure this is the best way to do it though, as i'm not a perl expert. Thanks for your help, Jorge. From ewijaya at gmail.com Mon Jul 28 04:40:46 2008 From: ewijaya at gmail.com (Edward Wijaya) Date: Mon, 28 Jul 2008 17:40:46 +0900 Subject: [Bioperl-l] Obtain GO/Gene Names from GNF Probe Names Message-ID: <3521d3670807280140vd618557jc0f3a98c10e70a9a@mail.gmail.com> Dear all, I have the following probe names selected from a dataset (GDS592), taken from GEO (SOFT format). gnf1m29878_a_at gnf1m13556_at gnf1m09610_a_at gnf1m11352_a_at gnf1m26036_at ...more... And I want to get the GO term and Official Gene Name from these probe names. After conversion we only want to compute the over-represented GO term from this selected genes. Is there a way to do it with BioPerl? - E.W. From alexl at users.sourceforge.net Mon Jul 28 07:06:23 2008 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Mon, 28 Jul 2008 04:06:23 -0700 Subject: [Bioperl-l] Smaller Bioperl Modules In-Reply-To: <15BFEFB1-64A4-4A0C-9618-3B7369AC4095@uiuc.edu> (Chris Fields's message of "Sat\, 26 Jul 2008 19\:08\:37 -0500") References: <9BEB5FD4EB2BF3468A6A546A17480BC2277CED@exactn3-cbr.nexus.csiro.au> <9BEB5FD4EB2BF3468A6A546A17480BC2334B5B@exactn3-cbr.nexus.csiro.au> <48890CFC.6050808@sendu.me.uk> <15BFEFB1-64A4-4A0C-9618-3B7369AC4095@uiuc.edu> Message-ID: >>>>> "CF" == Chris Fields writes: CF> On Jul 25, 2008, at 9:50 AM, Alex Lancaster wrote: >>>>>> ... >> I concur. It's definitely a major issue for package maintainers. >> If you split up bioperl into too many little CPAN modules, it will >> make packaging bioperl via RPMs in Fedora (or other distros, I >> suspect) a real pain. In Fedora that would mean that we might have >> to individually review/build each package separately which would >> add a lot of overhead. >> >> Some split up along the lines previously discussed seems sensible >> (into a "core" and "dev", i.e. not more that 3-4 separate modules), >> but please not 900 CPAN packages... ;) >> >> Alex CF> So something like what we indicate in the below link would be CF> okay? CF> http://www.bioperl.org/wiki/Proposed_1.6_core_modules Yep, that was what I was referring to as the "previously discussed" plan, assuming that you end up with 3 tarballs: bioperl{-core} (?), bioperl-tools, bioperl-dev. In Fedora-land they would be named: perl-bioperl (the core package probably doesn't a qualified name as it is the base package), perl-bioperl-tools, perl-bioperl-dev That's quite manageable and there is a precendent on most Linux distros with gstreamer's (Linux's media library) split up of audio plugins into gstreamer-plugins-{good,bad,ugly}: http://gstreamer.net/ based on quality (and to some extent on the basis of license, but that shouldn't apply to bioperl). One question: how would bioperl-run (and the other modules) factor into this scheme? Would you just keep those together at the moment? Would bioperl-run depend only on "core" or would it also need bioperl-tools or bioperl-dev? Also could each of these separate packages be updated independently (i.e have different version numbers in principle)? Alex From cjfields at uiuc.edu Mon Jul 28 11:23:58 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 28 Jul 2008 10:23:58 -0500 Subject: [Bioperl-l] Smaller Bioperl Modules In-Reply-To: References: <9BEB5FD4EB2BF3468A6A546A17480BC2277CED@exactn3-cbr.nexus.csiro.au> <9BEB5FD4EB2BF3468A6A546A17480BC2334B5B@exactn3-cbr.nexus.csiro.au> <48890CFC.6050808@sendu.me.uk> <15BFEFB1-64A4-4A0C-9618-3B7369AC4095@uiuc.edu> Message-ID: On Jul 28, 2008, at 6:06 AM, Alex Lancaster wrote: > ... > CF> So something like what we indicate in the below link would be > CF> okay? > > CF> http://www.bioperl.org/wiki/Proposed_1.6_core_modules > > Yep, that was what I was referring to as the "previously discussed" > plan, assuming that you end up with 3 tarballs: bioperl{-core} (?), > bioperl-tools, bioperl-dev. > > In Fedora-land they would be named: > > perl-bioperl (the core package probably doesn't a qualified name as it > is the base package), perl-bioperl-tools, perl-bioperl-dev > > That's quite manageable and there is a precendent on most Linux > distros with gstreamer's (Linux's media library) split up of audio > plugins into gstreamer-plugins-{good,bad,ugly}: http://gstreamer.net/ > based on quality (and to some extent on the basis of license, but that > shouldn't apply to bioperl). Exactly. > One question: how would bioperl-run (and the other modules) factor > into this scheme? Would you just keep those together at the moment? > Would bioperl-run depend only on "core" or would it also need > bioperl-tools or bioperl-dev? bioperl-run is (in general) a collection of 'wrapper' modules for running outside programs, such as EMBOSS, HMMER, FASTA, etc. I think it would be best to keep those as-us as an independent distribution; it would depend on core. With bioperl-db, bioperl-pedigree, and bioperl-network, we can keep those separate or incorporate them in depending on how Hilmar/Jason/ Brian feel about it. As for the other distributions, I think we can set an active deadline (soonish) for someone to step up and maintain them, otherwise we should salvage what we need from them and deprecate usage for the rest. For instance, functionality for the bioperl-ext modules probably should be replaced with code from the BioLib initiative (http://biolib.open-bio.org/wiki/Main_Page). bioperl- microarray can best be replaced with perl-based interaction with BioConductor/R (or use pure-perl-based solutions such as CPAN's Microarray). > Also could each of these separate packages be updated independently > (i.e have different version numbers in principle)? > > Alex We should have the same major release numbering (1.6, 1.7) for all of them, but each could have separate minor releases (1.6.1, 1.6.2, etc) based on bug fixes or small non-API-related changes. If we maintain a dependency chain (dev and tools relies-on core), we can increment the version requirement for each as needed. chris From cjfields at uiuc.edu Mon Jul 28 11:59:57 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 28 Jul 2008 10:59:57 -0500 Subject: [Bioperl-l] phd format parsing produces infinite memory usage In-Reply-To: References: Message-ID: <767D37C5-D9C5-4227-8FF7-049023543535@uiuc.edu> On Jul 28, 2008, at 3:11 AM, Jorge.DUARTE at biogemma.com wrote: > bioperl-l-bounces at lists.open-bio.org a ?crit sur 24/07/2008 23:38:33 : > >> Jean-Marc FRIGERIO wrote: >>> >>> Huuh !! phd files should contain only one sequence !! >>> >>> >>> >> This is no longer necessarily true. Consed allows concatenated phd >> files > >> now. >> > > Alright, > > thank you for your answers. > > In case it can help others until the parser is updated, > if i modify the phd.pm code this way, it seems to work fine for my > file : > > if ($entry =~ /^END_SEQUENCE/) { > $entry = $self->_readline(); > last; > } > > I'm not sure this is the best way to do it though, as i'm not a perl > expert. > > Thanks for your help, > Jorge. We can add this in. I'll add a few tests for multiple phd files to make sure it returns two Bio::Seq objects. chris From ocar1987 at hotmail.com Mon Jul 28 16:36:09 2008 From: ocar1987 at hotmail.com (ocar campos) Date: Mon, 28 Jul 2008 22:36:09 +0200 Subject: [Bioperl-l] Methods to GenBank Message-ID: Hello: I'm building a script to get information from GenBank according to some Accession Id, I've looked for a method to retrieve the organism lines from the GenBank, but i haven't found any specific for this. Does anyone know what is the method for this? For example i got this GenBank File: LOCUS SLLCP 1058 bp ss-RNA linear VRL 16-AUG-1994 DEFINITION Satellite tobacco mosaic virus coat protein RNA, complete cds. ACCESSION M25782 VERSION M25782.1 GI:530201 KEYWORDS coat protein. SOURCE Tobacco necrosis satellite virus ORGANISM Tobacco necrosis satellite virus Viruses; Satellites; Satellite Viruses. REFERENCE 1 (bases 1 to 1058) AUTHORS Mirkov,T.E., Mathews,D.M., Du Plessis,D.H. and Dodds,J.A. TITLE Nucleotide sequence and translation of satellite tobacco mosaic virus RNA And I want to get the Organism part in my script. Regards O'car Campos C. Estudiante Ingenier?a en Bioinform?tica Universidad de Talca. _________________________________________________________________ News, entertainment and everything you care about at Live.com. Get it now! http://www.live.com/getstarted.aspx From jason at bioperl.org Mon Jul 28 16:45:42 2008 From: jason at bioperl.org (Jason Stajich) Date: Mon, 28 Jul 2008 13:45:42 -0700 Subject: [Bioperl-l] Methods to GenBank In-Reply-To: References: Message-ID: <6F860CBD-8F00-46B5-A8E2-3B0479F71ED9@bioperl.org> you want the species method. see the Seq HowTo on the bioperl wiki -> bioperl.org/wiki for more detailed info on how to get all the fields out from a seq object. -jason On Jul 28, 2008, at 1:36 PM, ocar campos wrote: > > Hello: > I'm building a script to get information from GenBank > according to some Accession Id, I've looked for a method to > retrieve the organism lines from the GenBank, but i haven't found > any specific for this. Does anyone know what is the method for this? > > For example i got this GenBank File: > > LOCUS SLLCP 1058 bp ss-RNA linear > VRL 16-AUG-1994 > DEFINITION Satellite tobacco mosaic virus coat protein RNA, > complete cds. > ACCESSION M25782 > VERSION M25782.1 GI:530201 > KEYWORDS coat protein. > SOURCE Tobacco necrosis satellite virus > ORGANISM Tobacco necrosis satellite virus > Viruses; Satellites; Satellite Viruses. > REFERENCE 1 (bases 1 to 1058) > AUTHORS Mirkov,T.E., Mathews,D.M., Du Plessis,D.H. and Dodds,J.A. > TITLE Nucleotide sequence and translation of satellite > tobacco mosaic > virus RNA > > And I want to get the Organism part in my script. > > > > Regards > > O'car Campos C. > Estudiante Ingenier?a en Bioinform?tica > Universidad de Talca. > > _________________________________________________________________ > News, entertainment and everything you care about at Live.com. Get > it now! > http://www.live.com/getstarted.aspx > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From manchunjohn-ma at uiowa.edu Mon Jul 28 16:45:57 2008 From: manchunjohn-ma at uiowa.edu (John M.C. Ma) Date: Mon, 28 Jul 2008 15:45:57 -0500 Subject: [Bioperl-l] Issues on Bio::Tools::Primer3->next_primer Message-ID: <5486b2980807281345p3fd2c511u16ba6f4392a882c5@mail.gmail.com> Hi, I am trying a generic script to parse outputs for Primer3 results from Bio::Tools::Run::Primer3: use Bio::Tools::Run::Primer3; use Bio::Tools::Primer3; use Bio::Seq::PrimedSeq; [...] my $primer3_handle=Bio::Tools::Run::Primer3->new(-path=>'foobar'); [...] my $primer3_results=$primer3_handle->run(); my $primer_test=$primer3_results->next_primer; [...] Which is similar to what was on the docs, but when Perl gives the following error at running next_primer: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: No target sequence STACK: Error::throw STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.10.0/Bio/Root/Root.pm:359 STACK: Bio::Tools::Primer3::next_primer /usr/lib/perl5/site_perl/5.10.0/Bio/Tools/Primer3.pm:306 STACK: /home/johnma/workspace/NCBI-test/NCBI-test.pl:208 ----------------------------------------------------------- Whereas line 208 is the line that contained the next_primer. I tried to access the results manually by primer_results() and hard-calling fields, but the output of primer_results() is a hash and not very convenient for further processing. Is there a way that I can go back to next_primer...? Cheers, John From jason at bioperl.org Mon Jul 28 17:16:22 2008 From: jason at bioperl.org (Jason Stajich) Date: Mon, 28 Jul 2008 14:16:22 -0700 Subject: [Bioperl-l] Fwd: Methods to GenBank References: Message-ID: <29DD3343-5B88-48E9-974E-A518AE2F163D@bioperl.org> Please respond to the list with any queries. It is a Bio::Species object You might try and "Search" for species on the wiki and you'll find a lot of already written info... http://bioperl.org/wiki/HOWTO:Feature-Annotation#The_Species_Object Also see the perldoc for Bio::Species or the web Pdoc will tell you how to unroll it. http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/ Species.html Try something like this: my @classification = $species->classification(); print join("\t", @classification), "\n"; -jason Begin forwarded message: > From: ocar campos > Date: July 28, 2008 2:05:46 PM PDT > To: Jason Stajich > Subject: RE: [Bioperl-l] Methods to GenBank > > > I've been looking in the Seq How To but I haven't found it.... this > is what i got. > > use Bio::DB::GenBank; > use Bio::SeqIO; > > $gb = new Bio::DB::GenBank(); > $seq = $gb->get_Seq_by_version('M25782.1'); # Get sequence by > Accession.version > > print $seq->species, "\n"; > > Regards > > O'car Campos > > > ---------------------------------------- >> From: jason at bioperl.org >> Date: Mon, 28 Jul 2008 13:45:42 -0700 >> To: ocar1987 at hotmail.com >> CC: bioperl-l at lists.open-bio.org >> Subject: Re: [Bioperl-l] Methods to GenBank >> >> you want the species method. >> see the Seq HowTo on the bioperl wiki -> bioperl.org/wiki for more >> detailed info on how to get all the fields out from a seq object. >> >> -jason >> On Jul 28, 2008, at 1:36 PM, ocar campos wrote: >> >>> >>> Hello: >>> I'm building a script to get information from GenBank >>> according to some Accession Id, I've looked for a method to >>> retrieve the organism lines from the GenBank, but i haven't found >>> any specific for this. Does anyone know what is the method for this? >>> >>> For example i got this GenBank File: >>> >>> LOCUS SLLCP 1058 bp ss-RNA linear >>> VRL 16-AUG-1994 >>> DEFINITION Satellite tobacco mosaic virus coat protein RNA, >>> complete cds. >>> ACCESSION M25782 >>> VERSION M25782.1 GI:530201 >>> KEYWORDS coat protein. >>> SOURCE Tobacco necrosis satellite virus >>> ORGANISM Tobacco necrosis satellite virus >>> Viruses; Satellites; Satellite Viruses. >>> REFERENCE 1 (bases 1 to 1058) >>> AUTHORS Mirkov,T.E., Mathews,D.M., Du Plessis,D.H. and >>> Dodds,J.A. >>> TITLE Nucleotide sequence and translation of satellite >>> tobacco mosaic >>> virus RNA >>> >>> And I want to get the Organism part in my script. >>> >>> >>> >>> Regards >>> >>> O'car Campos C. >>> Estudiante Ingenier?a en Bioinform?tica >>> Universidad de Talca. >>> >>> _________________________________________________________________ >>> News, entertainment and everything you care about at Live.com. Get >>> it now! >>> http://www.live.com/getstarted.aspx >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _________________________________________________________________ > Explore the seven wonders of the world > http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en- > US&form=QBRE From ocar1987 at hotmail.com Mon Jul 28 17:39:35 2008 From: ocar1987 at hotmail.com (ocar campos) Date: Mon, 28 Jul 2008 23:39:35 +0200 Subject: [Bioperl-l] Fwd: Methods to GenBank In-Reply-To: <29DD3343-5B88-48E9-974E-A518AE2F163D@bioperl.org> References: <29DD3343-5B88-48E9-974E-A518AE2F163D@bioperl.org> Message-ID: Thanks for the help, got what i wanted. $gb = new Bio::DB::GenBank(); $seq = $gb->get_Seq_by_version('M25782.1'); $species=$seq->species; print $species->common_name, "\n"; print $species->species, "\n"; print $species->genus, "\n"; print $species->sub_species, "\n"; print $species->binomial, "\n"; print $species->ncbi_taxid, "\n"; O'car ---------------------------------------- > From: jason at bioperl.org > Date: Mon, 28 Jul 2008 14:16:22 -0700 > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] Fwd: Methods to GenBank > > Please respond to the list with any queries. > > > It is a Bio::Species object > > You might try and "Search" for species on the wiki and you'll find a > lot of already written info... > http://bioperl.org/wiki/HOWTO:Feature-Annotation#The_Species_Object > > Also see the perldoc for Bio::Species or the web Pdoc will tell you > how to unroll it. > http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/ > Species.html > > Try something like this: > my @classification = $species->classification(); > print join("\t", @classification), "\n"; > > > -jason > > Begin forwarded message: > >> From: ocar campos >> Date: July 28, 2008 2:05:46 PM PDT >> To: Jason Stajich >> Subject: RE: [Bioperl-l] Methods to GenBank >> >> >> I've been looking in the Seq How To but I haven't found it.... this >> is what i got. >> >> use Bio::DB::GenBank; >> use Bio::SeqIO; >> >> $gb = new Bio::DB::GenBank(); >> $seq = $gb->get_Seq_by_version('M25782.1'); # Get sequence by >> Accession.version >> >> print $seq->species, "\n"; >> >> Regards >> >> O'car Campos >> >> >> ---------------------------------------- >>> From: jason at bioperl.org >>> Date: Mon, 28 Jul 2008 13:45:42 -0700 >>> To: ocar1987 at hotmail.com >>> CC: bioperl-l at lists.open-bio.org >>> Subject: Re: [Bioperl-l] Methods to GenBank >>> >>> you want the species method. >>> see the Seq HowTo on the bioperl wiki -> bioperl.org/wiki for more >>> detailed info on how to get all the fields out from a seq object. >>> >>> -jason >>> On Jul 28, 2008, at 1:36 PM, ocar campos wrote: >>> >>>> >>>> Hello: >>>> I'm building a script to get information from GenBank >>>> according to some Accession Id, I've looked for a method to >>>> retrieve the organism lines from the GenBank, but i haven't found >>>> any specific for this. Does anyone know what is the method for this? >>>> >>>> For example i got this GenBank File: >>>> >>>> LOCUS SLLCP 1058 bp ss-RNA linear >>>> VRL 16-AUG-1994 >>>> DEFINITION Satellite tobacco mosaic virus coat protein RNA, >>>> complete cds. >>>> ACCESSION M25782 >>>> VERSION M25782.1 GI:530201 >>>> KEYWORDS coat protein. >>>> SOURCE Tobacco necrosis satellite virus >>>> ORGANISM Tobacco necrosis satellite virus >>>> Viruses; Satellites; Satellite Viruses. >>>> REFERENCE 1 (bases 1 to 1058) >>>> AUTHORS Mirkov,T.E., Mathews,D.M., Du Plessis,D.H. and >>>> Dodds,J.A. >>>> TITLE Nucleotide sequence and translation of satellite >>>> tobacco mosaic >>>> virus RNA >>>> >>>> And I want to get the Organism part in my script. >>>> >>>> >>>> >>>> Regards >>>> >>>> O'car Campos C. >>>> Estudiante Ingenier?a en Bioinform?tica >>>> Universidad de Talca. >>>> >>>> _________________________________________________________________ >>>> News, entertainment and everything you care about at Live.com. Get >>>> it now! >>>> http://www.live.com/getstarted.aspx >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> _________________________________________________________________ >> Explore the seven wonders of the world >> http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en- >> US&form=QBRE > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l _________________________________________________________________ News, entertainment and everything you care about at Live.com. Get it now! http://www.live.com/getstarted.aspx From cjfields at uiuc.edu Mon Jul 28 19:13:32 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 28 Jul 2008 18:13:32 -0500 Subject: [Bioperl-l] Issues on Bio::Tools::Primer3->next_primer In-Reply-To: <5486b2980807281345p3fd2c511u16ba6f4392a882c5@mail.gmail.com> References: <5486b2980807281345p3fd2c511u16ba6f4392a882c5@mail.gmail.com> Message-ID: You should send this in as a bug report, attaching an example script. I'll be using Primer3 soon so I'll try taking a look at it once it's filed. chris On Jul 28, 2008, at 3:45 PM, John M.C. Ma wrote: > Hi, > > I am trying a generic script to parse outputs for Primer3 results from > Bio::Tools::Run::Primer3: > > use Bio::Tools::Run::Primer3; > use Bio::Tools::Primer3; > use Bio::Seq::PrimedSeq; > [...] > my $primer3_handle=Bio::Tools::Run::Primer3->new(-path=>'foobar'); > [...] > my $primer3_results=$primer3_handle->run(); > my $primer_test=$primer3_results->next_primer; > [...] > > Which is similar to what was on the docs, but when Perl gives the > following > error at running next_primer: > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: No target sequence > STACK: Error::throw > STACK: Bio::Root::Root::throw > /usr/lib/perl5/site_perl/5.10.0/Bio/Root/Root.pm:359 > STACK: Bio::Tools::Primer3::next_primer > /usr/lib/perl5/site_perl/5.10.0/Bio/Tools/Primer3.pm:306 > STACK: /home/johnma/workspace/NCBI-test/NCBI-test.pl:208 > ----------------------------------------------------------- > > Whereas line 208 is the line that contained the next_primer. > > I tried to access the results manually by primer_results() and hard- > calling > fields, but the output of primer_results() is a hash and not very > convenient > for further processing. Is there a way that I can go back to > next_primer...? > > Cheers, > > John > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Marie-Claude Hofmann College of Veterinary Medicine University of Illinois Urbana-Champaign From roy.chaudhuri at gmail.com Tue Jul 29 06:26:34 2008 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Tue, 29 Jul 2008 11:26:34 +0100 Subject: [Bioperl-l] Issues on Bio::Tools::Primer3->next_primer In-Reply-To: <5486b2980807281345p3fd2c511u16ba6f4392a882c5@mail.gmail.com> References: <5486b2980807281345p3fd2c511u16ba6f4392a882c5@mail.gmail.com> Message-ID: <488EF05A.6030601@gmail.com> Hi John, I'm not sure if you want to run Primer3 using BioPerl, or just use BioPerl to parse an existing Primer3 output file. For the former you need to specify a target using the -seq argument when you create your Bio::Tools::Run::Primer3 object (the argument value should be a Bio::Seq object). It's also possible to add the sequence between the new() and run() methods using add_targets(), but you snipped out that section so I can't tell if you did that and there is some other problem. The run() method does not seem to check if a target sequence is present, hence you only get an error when you call next_primer() on the returned Bio::Tools::Primer3 object. If you just want to parse an existing Primer3 output file then you need to use Bio::Tools::Primer3, specifying the path to the ouput file using the -file argument to new(). The documentation to Bio::Tools::Run::Primer3: http://search.cpan.org/~sendu/bioperl-run/Bio/Tools/Run/Primer3.pm#new() suggests that you can also provide a -file argument in that module, but there doesn't seem to be any evidence of that in the code. Hope this helps. Roy. -- Dr. Roy Chaudhuri Department of Veterinary Medicine University of Cambridge, U.K. > I am trying a generic script to parse outputs for Primer3 results from > Bio::Tools::Run::Primer3: > > use Bio::Tools::Run::Primer3; > use Bio::Tools::Primer3; > use Bio::Seq::PrimedSeq; > [...] > my $primer3_handle=Bio::Tools::Run::Primer3->new(-path=>'foobar'); > [...] > my $primer3_results=$primer3_handle->run(); > my $primer_test=$primer3_results->next_primer; > [...] > > Which is similar to what was on the docs, but when Perl gives the following > error at running next_primer: > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: No target sequence > STACK: Error::throw > STACK: Bio::Root::Root::throw > /usr/lib/perl5/site_perl/5.10.0/Bio/Root/Root.pm:359 > STACK: Bio::Tools::Primer3::next_primer > /usr/lib/perl5/site_perl/5.10.0/Bio/Tools/Primer3.pm:306 > STACK: /home/johnma/workspace/NCBI-test/NCBI-test.pl:208 > ----------------------------------------------------------- > > Whereas line 208 is the line that contained the next_primer. > > I tried to access the results manually by primer_results() and hard-calling > fields, but the output of primer_results() is a hash and not very convenient > for further processing. Is there a way that I can go back to next_primer...? > > Cheers, > > John > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From mirhan at indiana.edu Tue Jul 29 12:20:33 2008 From: mirhan at indiana.edu (Han, Mira) Date: Tue, 29 Jul 2008 12:20:33 -0400 Subject: [Bioperl-l] Phyloxml Message-ID: Hi, Sorry for bombarding the list Thought this would be better on a separate thread. Phyloxml documents have s. But also s. What would be the standard approach for parsing, I guess TreeIO->next_tree shouldn't take care of the alignments. Would I need to make a AlignIO->next_aln for the phyloxml document as well? Mira From mirhan at indiana.edu Tue Jul 29 12:13:50 2008 From: mirhan at indiana.edu (Han, Mira) Date: Tue, 29 Jul 2008 12:13:50 -0400 Subject: [Bioperl-l] Phyloxml SeqI without actual sequence Message-ID: Another phyloxml parsing question. We have tags that sometimes have actual molecular sequences and sometimes don't. I decided to create a SeqI object and link it to AnnotatableNode. But when it doesn't have actual sequence It gives warning that the sequence is empty. I don't think it's a big problem, And I'd prefer having consistency than having two different solutions for the same tag. But I'd like to hear people's opinion on this as well. Thank you Mira Han From mirhan at indiana.edu Tue Jul 29 12:10:31 2008 From: mirhan at indiana.edu (Han, Mira) Date: Tue, 29 Jul 2008 12:10:31 -0400 Subject: [Bioperl-l] Phyloxml parsing Message-ID: Hi, I'd like to get some opinions on how to design the phyloxml parsing. There are a couple of tags in phyloxml that doesn't have obvious bioperl implementations. 1. This is for expressing network structures on the tree. Will mean that c and b is connected even though they are not direct parent-daughters of each other. 2. Homology relationship between sequences. These tags are both used by the . Right now I'm just saving the information in the tree as simple text by tags. So that if the user wants to follow the information he can look up the nodes by its id_src id by parsing the text. I was wondering if you would have any other ideas. From jason at bioperl.org Tue Jul 29 12:45:06 2008 From: jason at bioperl.org (Jason Stajich) Date: Tue, 29 Jul 2008 09:45:06 -0700 Subject: [Bioperl-l] Phyloxml In-Reply-To: References: Message-ID: Mira - I've not thought too clearly about how this should go, certainly Bio::AlignIO should be reused for the parsing aspect, although I'm not clear what format the alignment is in? At some point this is might need to be unified with the NEXUS-type objects that the Bio::NEXUS group has worked on. We may have to work with them to define the proper object here that holds both tree and alignment data and allows slicing out either from the object. So a super-object is probably going to have to be created to marshall out the trees and alignment data. I didn't realize the spec was going as far as to encapsulate all of the alignment data as well. We may need to think about whether we can support all of the aspects of the spec at this time as well. I hope other people have input here as well. -jason On Jul 29, 2008, at 9:20 AM, Han, Mira wrote: > > Hi, > Sorry for bombarding the list > Thought this would be better on a separate thread. > Phyloxml documents have s. > But also s. > What would be the standard approach for parsing, > I guess TreeIO->next_tree > shouldn't take care of the alignments. > Would I need to make a AlignIO->next_aln for the phyloxml document > as well? > > Mira > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From jason at bioperl.org Tue Jul 29 12:51:07 2008 From: jason at bioperl.org (Jason Stajich) Date: Tue, 29 Jul 2008 09:51:07 -0700 Subject: [Bioperl-l] Phyloxml SeqI without actual sequence In-Reply-To: References: Message-ID: So why would you create the sequence in the first place when it is empty? Shouldn't you just not create a sequence if there isn't one? Can you provide sample data so we understand better - maybe there is sequence name but no data? Maybe we can specify an option to not warn when creating a sequence if a specific flag is provided to the Seq initialization routine. -jason On Jul 29, 2008, at 9:13 AM, Han, Mira wrote: > > Another phyloxml parsing question. > We have tags that sometimes have actual molecular > sequences and > sometimes don't. > I decided to create a SeqI object and link it to AnnotatableNode. > But when it doesn't have actual sequence > It gives warning that the sequence is empty. > I don't think it's a big problem, > And I'd prefer having consistency than having two different > solutions for > the same tag. > But I'd like to hear people's opinion on this as well. > Thank you > > Mira Han > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From xyuany at mail2.sysu.edu.cn Wed Jul 30 02:47:31 2008 From: xyuany at mail2.sysu.edu.cn (melody) Date: Tue, 29 Jul 2008 23:47:31 -0700 Subject: [Bioperl-l] get_Seq_by_id: CONTIG found Message-ID: <000301c8f210$247cdb20$6d769160$@sysu.edu.cn> I'm trying to download a bunch of sequences from GenBank using the gi ,when I run the code,I got The message like this : -------------------- WARNING --------------------- MSG: CONTIG found. GenBank get_Stream_by_acc about to run. --------------------------------------------------- Warning: unable to close filehandle FETCH properly. What can I do if I want this code work. Thanks a lot, Melody xiong use Bio::DB::GenBank; my $db_obj = new Bio::DB::GenBank; $db_obj->proxy(['http','ftp'],'http://proxy2.sysu.edu.cn:3128/'); my $seq_obj=$db_obj->get_Seq_by_gi("42537818"); my $seqio_obj=Bio::SeqIO->new(-file => ">temp2.txt", -format => "fasta" ); $seqio_obj->write_seq($seq_obj); From manchunjohn-ma at uiowa.edu Tue Jul 29 13:22:09 2008 From: manchunjohn-ma at uiowa.edu (John M.C. Ma) Date: Tue, 29 Jul 2008 12:22:09 -0500 Subject: [Bioperl-l] Issues on Bio::Tools::Primer3->next_primer In-Reply-To: <488EF05A.6030601@gmail.com> References: <5486b2980807281345p3fd2c511u16ba6f4392a882c5@mail.gmail.com> <488EF05A.6030601@gmail.com> Message-ID: <5486b2980807291022h2effc94cn9ab2bdedace2e102@mail.gmail.com> Hi Roy, Hi Roy, Maybe I wasn't clear with my script fragment, I used Bioperl to run Primer3. The following is as much Primer3-related as I can get: use Bio::Tools::Run::Primer3; use Bio::Tools::Primer3; [snips other use declarations and Ensembl scripts] my $primer3_handle=Bio::Tools::Run::Primer3->new(-path=>'[Primer3 path]'); /*%gene_info is a hash that stores sequence information*/ $primer3_handle->add_targets('SEQUENCE'=>$gene_info{src_seq}, 'PRIMER_SEQUENCE_ID'=>$gene_info{name}, 'TARGET'=>$gene_info{exon_boundaries}, [snips other options] ) my $primer3_results=$primer3_handle->run(); $primer_test=$primer3_results->next_primer; Hope this helps. John On Tue, Jul 29, 2008 at 5:26 AM, Roy Chaudhuri wrote: > Hi John, > > I'm not sure if you want to run Primer3 using BioPerl, or just use BioPerl > to parse an existing Primer3 output file. > > For the former you need to specify a target using the -seq argument when > you create your Bio::Tools::Run::Primer3 object (the argument value should > be a Bio::Seq object). It's also possible to add the sequence between the > new() and run() methods using add_targets(), but you snipped out that > section so I can't tell if you did that and there is some other problem. The > run() method does not seem to check if a target sequence is present, hence > you only get an error when you call next_primer() on the returned > Bio::Tools::Primer3 object. > > If you just want to parse an existing Primer3 output file then you need to > use Bio::Tools::Primer3, specifying the path to the ouput file using the > -file argument to new(). The documentation to Bio::Tools::Run::Primer3: > http://search.cpan.org/~sendu/bioperl-run/Bio/Tools/Run/Primer3.pm#new() > suggests that you can also provide a -file argument in that module, but > there doesn't seem to be any evidence of that in the code. > > > Hope this helps. > Roy. > -- > Dr. Roy Chaudhuri > Department of Veterinary Medicine > University of Cambridge, U.K. > > I am trying a generic script to parse outputs for Primer3 results from >> Bio::Tools::Run::Primer3: >> >> use Bio::Tools::Run::Primer3; >> use Bio::Tools::Primer3; >> use Bio::Seq::PrimedSeq; >> [...] >> my $primer3_handle=Bio::Tools::Run::Primer3->new(-path=>'foobar'); >> [...] >> my $primer3_results=$primer3_handle->run(); >> my $primer_test=$primer3_results->next_primer; >> [...] >> >> Which is similar to what was on the docs, but when Perl gives the >> following >> error at running next_primer: >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: No target sequence >> STACK: Error::throw >> STACK: Bio::Root::Root::throw >> /usr/lib/perl5/site_perl/5.10.0/Bio/Root/Root.pm:359 >> STACK: Bio::Tools::Primer3::next_primer >> /usr/lib/perl5/site_perl/5.10.0/Bio/Tools/Primer3.pm:306 >> STACK: /home/johnma/workspace/NCBI-test/NCBI-test.pl:208 >> ----------------------------------------------------------- >> >> Whereas line 208 is the line that contained the next_primer. >> >> I tried to access the results manually by primer_results() and >> hard-calling >> fields, but the output of primer_results() is a hash and not very >> convenient >> for further processing. Is there a way that I can go back to >> next_primer...? >> >> Cheers, >> >> John >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > From miraceti at gmail.com Tue Jul 29 13:31:57 2008 From: miraceti at gmail.com (miraceti) Date: Tue, 29 Jul 2008 13:31:57 -0400 Subject: [Bioperl-l] Phyloxml SeqI without actual sequence In-Reply-To: References: Message-ID: sometimes the clade looks like. alcohol dehydrogenase 0.99 sometimes the clade looks like. ADHX P81431 Alcohol dehydrogenase class-3 TDATGKPIKCMAAIAWEAKKPLSIEEVEVAPPKSGEVRIKILHSGVCHTD Do you think it's better not to create the SeqI in the first case?. On Tue, Jul 29, 2008 at 12:51 PM, Jason Stajich wrote: > So why would you create the sequence in the first place when it is empty? > Shouldn't you just not create a sequence if there isn't one? Can you provide > sample data so we understand better - maybe there is sequence name but no > data? Maybe we can specify an option to not warn when creating a sequence > if a specific flag is provided to the Seq initialization routine. > > -jason > > > On Jul 29, 2008, at 9:13 AM, Han, Mira wrote: > > >> Another phyloxml parsing question. >> We have tags that sometimes have actual molecular sequences and >> sometimes don't. >> I decided to create a SeqI object and link it to AnnotatableNode. >> But when it doesn't have actual sequence >> It gives warning that the sequence is empty. >> I don't think it's a big problem, >> And I'd prefer having consistency than having two different solutions for >> the same tag. >> But I'd like to hear people's opinion on this as well. >> Thank you >> >> Mira Han >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From roy.chaudhuri at gmail.com Tue Jul 29 13:51:37 2008 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Tue, 29 Jul 2008 18:51:37 +0100 Subject: [Bioperl-l] Issues on Bio::Tools::Primer3->next_primer In-Reply-To: <5486b2980807290842i41e85149g13ca374c7eb7713@mail.gmail.com> References: <5486b2980807281345p3fd2c511u16ba6f4392a882c5@mail.gmail.com> <488EF05A.6030601@gmail.com> <5486b2980807290842i41e85149g13ca374c7eb7713@mail.gmail.com> Message-ID: <488F58A9.9030306@gmail.com> Hi John. There is a bug in there, sorry for misunderstanding your earlier post (although for future reference it is helpful if you can include a minimal runnable script that illustrates the problem). Bio::Tools::Run::Primer3 assumes the existence of a wrapped Bio::Seq object, which it copies to the returned Bio::Tools::Primer3 object. If you specify your sequence by means of add_target(SEQUENCE=>$seq), rather than by providing a Bio::Seq object, then the wrapped Bio::Seq object is undefined, leading to an error since next_primer checks for its existence. I've noted the bug in Bugzilla. I tried to upload a patch for Bio::Tools::Run::Primer3 but there seems to be a problem with the system (reported to support at open-bio.org). The patch (probably mangled by e-mail line wrapping) is: 379a380,383 > elsif (uc($key) eq "SEQUENCE") { > # Add seqobject if not present, since it is checked for by Bio::Tools::Primer3->next_primer() > $self->{'seqobject'}=Bio::Seq->new(-seq=>$args{$key}) if not defined($self->{'seqobject'}); > } Roy. -- Dr. Roy Chaudhuri Department of Veterinary Medicine University of Cambridge, U.K. John M.C. Ma wrote: > Hi Roy, > > Maybe I wasn't clear with my script fragment, I used Bioperl to run > Primer3. The following is as much Primer3-related as I can get: > > use Bio::Tools::Run::Primer3; > use Bio::Tools::Primer3; > [snips other use declarations and Ensembl scripts] > my $primer3_handle=Bio::Tools::Run::Primer3->new(-path=>'[Primer3 path]'); > /*%gene_info is a hash that stores sequence information*/ > $primer3_handle->add_targets('SEQUENCE'=>$gene_info{src_seq}, > 'PRIMER_SEQUENCE_ID'=>$gene_info{name}, > 'TARGET'=>$gene_info{exon_boundaries}, > [snips other options] ) > my $primer3_results=$primer3_handle->run(); > $primer_test=$primer3_results->next_primer; > > On Tue, Jul 29, 2008 at 5:26 AM, Roy Chaudhuri > wrote: > > Hi John, > > I'm not sure if you want to run Primer3 using BioPerl, or just use > BioPerl to parse an existing Primer3 output file. > > For the former you need to specify a target using the -seq argument > when you create your Bio::Tools::Run::Primer3 object (the argument > value should be a Bio::Seq object). It's also possible to add the > sequence between the new() and run() methods using add_targets(), > but you snipped out that section so I can't tell if you did that and > there is some other problem. The run() method does not seem to check > if a target sequence is present, hence you only get an error when > you call next_primer() on the returned Bio::Tools::Primer3 object. > > If you just want to parse an existing Primer3 output file then you > need to use Bio::Tools::Primer3, specifying the path to the ouput > file using the -file argument to new(). The documentation to > Bio::Tools::Run::Primer3: > http://search.cpan.org/~sendu/bioperl-run/Bio/Tools/Run/Primer3.pm#new() > > suggests that you can also provide a -file argument in that module, > but there doesn't seem to be any evidence of that in the code. > > > Hope this helps. > Roy. > -- > Dr. Roy Chaudhuri > Department of Veterinary Medicine > University of Cambridge, U.K. > > I am trying a generic script to parse outputs for Primer3 > results from > Bio::Tools::Run::Primer3: > > use Bio::Tools::Run::Primer3; > use Bio::Tools::Primer3; > use Bio::Seq::PrimedSeq; > [...] > my $primer3_handle=Bio::Tools::Run::Primer3->new(-path=>'foobar'); > [...] > my $primer3_results=$primer3_handle->run(); > my $primer_test=$primer3_results->next_primer; > [...] > > Which is similar to what was on the docs, but when Perl gives > the following > error at running next_primer: > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: No target sequence > STACK: Error::throw > STACK: Bio::Root::Root::throw > /usr/lib/perl5/site_perl/5.10.0/Bio/Root/Root.pm:359 > STACK: Bio::Tools::Primer3::next_primer > /usr/lib/perl5/site_perl/5.10.0/Bio/Tools/Primer3.pm:306 > STACK: /home/johnma/workspace/NCBI-test/NCBI-test.pl:208 > ----------------------------------------------------------- > > Whereas line 208 is the line that contained the next_primer. > > I tried to access the results manually by primer_results() and > hard-calling > fields, but the output of primer_results() is a hash and not > very convenient > for further processing. Is there a way that I can go back to > next_primer...? > > Cheers, > > John > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > From aaron.j.mackey at gsk.com Tue Jul 29 12:46:28 2008 From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com) Date: Tue, 29 Jul 2008 12:46:28 -0400 Subject: [Bioperl-l] Phyloxml parsing In-Reply-To: Message-ID: use Annotations, and author a new Bio::Annotation::Tree::Node::Relationship::Pairwise (or somesuch) for typing the relationship. -Aaron, a fan of AnnotatableI bioperl-l-bounces at lists.open-bio.org wrote on 07/29/2008 12:10:31 PM: > > Hi, > I'd like to get some opinions on how to design the phyloxml parsing. > There are a couple of tags in phyloxml that doesn't have obvious bioperl > implementations. > > 1. > This is for expressing network structures on the tree. > > Will mean that c and b is connected even though they are not direct > parent-daughters of each other. > > 2. > Homology relationship between sequences. > > > > These tags are both used by the . > Right now I'm just saving the information in the tree as simple text by > tags. > So that if the user wants to follow the information he can look up the nodes > by its id_src id by parsing the text. > I was wondering if you would have any other ideas. > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at uiuc.edu Tue Jul 29 13:58:43 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 29 Jul 2008 12:58:43 -0500 Subject: [Bioperl-l] Phyloxml SeqI without actual sequence In-Reply-To: References: Message-ID: <983F986E-8E05-46FD-970F-1DEDCA6C2792@uiuc.edu> On Jul 29, 2008, at 11:13 AM, Han, Mira wrote: > > Another phyloxml parsing question. > We have tags that sometimes have actual molecular > sequences and > sometimes don't. > I decided to create a SeqI object and link it to AnnotatableNode. > But when it doesn't have actual sequence > It gives warning that the sequence is empty. > I don't think it's a big problem, > And I'd prefer having consistency than having two different > solutions for > the same tag. > But I'd like to hear people's opinion on this as well. > Thank you > > Mira Han Feasibly, you could have the same AnnotationCollection be used for both the AnnotatableNode and the Seq (if present), e.g. if you called $node->annotation or $node->seq->annotation you would get the same collection. Under circumstances where no seq data is present you wouldn't need to create a blank Seq object; have $node->seq return without a Seq and (possibly) issue a warning. Following through with this line of thought, it might be advantageous to set up has_* methods in AnnotatableNode, similar to SeqFeatureI::has_tag() for simple boolean tests, where you could do: if ($node->has_Seq) { # do Seq-related things } if ($node->has_Align) { # do SimpleAlign-related things } chris From hlapp at gmx.net Tue Jul 29 13:59:24 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 29 Jul 2008 13:59:24 -0400 Subject: [Bioperl-l] Phyloxml SeqI without actual sequence In-Reply-To: References: Message-ID: On Jul 29, 2008, at 1:31 PM, miraceti wrote: > sometimes the clade looks like. > > > > alcohol dehydrogenase > 0.99 > > > > sometimes the clade looks like. > > > ADHX > P81431 > Alcohol dehydrogenase class-3 > > TDATGKPIKCMAAIAWEAKKPLSIEEVEVAPPKSGEVRIKILHSGVCHTD > > > > > Do you think it's better not to create the SeqI in the first case?. It's an option but to me it threatens to lose the fact that the annotation properties pertain to a sequence, not to something else (such as the tree node, for example). So, if you don't attach the annotation to a sequence object you create, what would you attach it to then? In the absence of a good answer creating the sequence object may the only way. I thought I'd recall some kind of Bio::Seq::EmptySeq object for exactly this kind of case, but apparently there isn't one there, so maybe I was just dreaming this up. However, a sequence object that is optimized for this case may be useful to have, though thinking about it, I'm not exactly sure what overhead the sequence slot really adds to all the other overhead added by feature and annotation slots. The only thing that really comes to mind is that a sequence object with a zero length sequence won't allow you to add features. Sorry for this random stream of thoughts here, I hope I'm not totally wasting everyone's time here. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From jason at bioperl.org Tue Jul 29 14:00:09 2008 From: jason at bioperl.org (Jason Stajich) Date: Tue, 29 Jul 2008 11:00:09 -0700 Subject: [Bioperl-l] Phyloxml SeqI without actual sequence In-Reply-To: References: Message-ID: I guess making a sequence is fine - maybe we can add a flag like - nowarnonempty => 1 to not warn when the sequence is empty (in Bio::PrimarySeq new() code ? -jason On Jul 29, 2008, at 10:31 AM, miraceti wrote: > sometimes the clade looks like. > > > > alcohol dehydrogenase > 0.99 > > > > sometimes the clade looks like. > > > ADHX > P81431 > Alcohol dehydrogenase class-3 > > TDATGKPIKCMAAIAWEAKKPLSIEEVEVAPPKSGEVRIKILHSGVCHTD > > > > > Do you think it's better not to create the SeqI in the first case?. > > > On Tue, Jul 29, 2008 at 12:51 PM, Jason Stajich > wrote: > >> So why would you create the sequence in the first place when it is >> empty? >> Shouldn't you just not create a sequence if there isn't one? Can >> you provide >> sample data so we understand better - maybe there is sequence name >> but no >> data? Maybe we can specify an option to not warn when creating a >> sequence >> if a specific flag is provided to the Seq initialization routine. >> >> -jason >> >> >> On Jul 29, 2008, at 9:13 AM, Han, Mira wrote: >> >> >>> Another phyloxml parsing question. >>> We have tags that sometimes have actual molecular >>> sequences and >>> sometimes don't. >>> I decided to create a SeqI object and link it to AnnotatableNode. >>> But when it doesn't have actual sequence >>> It gives warning that the sequence is empty. >>> I don't think it's a big problem, >>> And I'd prefer having consistency than having two different >>> solutions for >>> the same tag. >>> But I'd like to hear people's opinion on this as well. >>> Thank you >>> >>> Mira Han >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> From mirhan at indiana.edu Tue Jul 29 14:09:26 2008 From: mirhan at indiana.edu (Han, Mira) Date: Tue, 29 Jul 2008 14:09:26 -0400 Subject: [Bioperl-l] Phyloxml - made-up 'align' xml-language In-Reply-To: <230811.53116.qm@web50510.mail.re2.yahoo.com> Message-ID: Oh, I see, It was my misunderstanding. One less thing on my to-do list. :) Mira On 7/29/08 2:07 PM, "Christian Zmasek" wrote: Hi, Mira: I am so sorry for being not more clear in my examples. The "" data was intended as an example of how xml data from other namespaces (in this case "align") could reside inside phyloxml documents. There is absolutely no need to parse and store these data from other namespaces/xml-languages by your parser/objects. Christian PS: To be clear "align", is the name of a _fictional_ xml language which looks like it can store alignments. ----- Original Message ---- From: Jason Stajich To: "Han, Mira" Cc: bioperl list ; Christian Zmasek Sent: Tuesday, July 29, 2008 9:45:06 AM Subject: Re: [Bioperl-l] Phyloxml Mira - I've not thought too clearly about how this should go, certainly Bio::AlignIO should be reused for the parsing aspect, although I'm not clear what format the alignment is in? At some point this is might need to be unified with the NEXUS-type objects that the Bio::NEXUS group has worked on. We may have to work with them to define the proper object here that holds both tree and alignment data and allows slicing out either from the object. So a super-object is probably going to have to be created to marshall out the trees and alignment data. I didn't realize the spec was going as far as to encapsulate all of the alignment data as well. We may need to think about whether we can support all of the aspects of the spec at this time as well. I hope other people have input here as well. -jason On Jul 29, 2008, at 9:20 AM, Han, Mira wrote: > > Hi, > Sorry for bombarding the list > Thought this would be better on a separate thread. > Phyloxml documents have s. > But also s. > What would be the standard approach for parsing, > I guess TreeIO->next_tree > shouldn't take care of the alignments. > Would I need to make a AlignIO->next_aln for the phyloxml document > as well? > > Mira > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at uiuc.edu Tue Jul 29 14:26:55 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 29 Jul 2008 13:26:55 -0500 Subject: [Bioperl-l] Phyloxml parsing In-Reply-To: References: Message-ID: +1 on Aaron's suggestion; though maybe with a shorter namespace ;> Though is it possible to have more than two nodes in a relationship, or is it just pairwise? chris On Jul 29, 2008, at 11:10 AM, Han, Mira wrote: > > Hi, > I'd like to get some opinions on how to design the phyloxml parsing. > There are a couple of tags in phyloxml that doesn't have obvious > bioperl > implementations. > > 1. > This is for expressing network structures on the tree. > > Will mean that c and b is connected even though they are not direct > parent-daughters of each other. > > 2. > Homology relationship between sequences. > > > > These tags are both used by the . > Right now I'm just saving the information in the tree as simple text > by > tags. > So that if the user wants to follow the information he can look up > the nodes > by its id_src id by parsing the text. > I was wondering if you would have any other ideas. > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Marie-Claude Hofmann College of Veterinary Medicine University of Illinois Urbana-Champaign From cmzmasek at yahoo.com Tue Jul 29 14:07:24 2008 From: cmzmasek at yahoo.com (Christian Zmasek) Date: Tue, 29 Jul 2008 11:07:24 -0700 (PDT) Subject: [Bioperl-l] Phyloxml - made-up 'align' xml-language Message-ID: <230811.53116.qm@web50510.mail.re2.yahoo.com> Hi, Mira: I am so sorry for being not more clear in my examples. The "" data was intended as an example of how xml data from other namespaces (in this case "align") could reside inside phyloxml documents. There is absolutely no need to parse and store these data from other namespaces/xml-languages by your parser/objects. Christian PS: To be clear "align", is the name of a _fictional_ xml language which looks like it can store alignments. ----- Original Message ---- From: Jason Stajich To: "Han, Mira" Cc: bioperl list ; Christian Zmasek Sent: Tuesday, July 29, 2008 9:45:06 AM Subject: Re: [Bioperl-l] Phyloxml Mira - I've not thought too clearly about how this should go, certainly Bio::AlignIO should be reused for the parsing aspect, although I'm not clear what format the alignment is in? At some point this is might need to be unified with the NEXUS-type objects that the Bio::NEXUS group has worked on. We may have to work with them to define the proper object here that holds both tree and alignment data and allows slicing out either from the object. So a super-object is probably going to have to be created to marshall out the trees and alignment data. I didn't realize the spec was going as far as to encapsulate all of the alignment data as well. We may need to think about whether we can support all of the aspects of the spec at this time as well. I hope other people have input here as well. -jason On Jul 29, 2008, at 9:20 AM, Han, Mira wrote: > > Hi, > Sorry for bombarding the list > Thought this would be better on a separate thread. > Phyloxml documents have s. > But also s. > What would be the standard approach for parsing, > I guess TreeIO->next_tree > shouldn't take care of the alignments. > Would I need to make a AlignIO->next_aln for the phyloxml document > as well? > > Mira > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From ocar1987 at hotmail.com Tue Jul 29 14:07:58 2008 From: ocar1987 at hotmail.com (ocar campos) Date: Tue, 29 Jul 2008 20:07:58 +0200 Subject: [Bioperl-l] get_Seq_by_id: CONTIG found In-Reply-To: <000301c8f210$247cdb20$6d769160$@sysu.edu.cn> References: <000301c8f210$247cdb20$6d769160$@sysu.edu.cn> Message-ID: I got a very similar message when trying to access with a Version Number, but saying that the sequence is not in the db, and when I check via web, the sequence is there, and then the script works. regards O'car ---------------------------------------- > From: xyuany at mail2.sysu.edu.cn > To: bioperl-l at portal.open-bio.org > Date: Tue, 29 Jul 2008 23:47:31 -0700 > Subject: [Bioperl-l] get_Seq_by_id: CONTIG found > > I'm trying to download a bunch of sequences from GenBank using the gi ,when > I run the code,I got The message like this : > > -------------------- WARNING --------------------- > MSG: CONTIG found. GenBank get_Stream_by_acc about to run. > --------------------------------------------------- > Warning: unable to close filehandle FETCH properly. > > What can I do if I want this code work. > Thanks a lot, > Melody xiong > > > use Bio::DB::GenBank; > my $db_obj = new Bio::DB::GenBank; > $db_obj->proxy(['http','ftp'],'http://proxy2.sysu.edu.cn:3128/'); > my $seq_obj=$db_obj->get_Seq_by_gi("42537818"); > my $seqio_obj=Bio::SeqIO->new(-file => ">temp2.txt", -format => > "fasta" ); > $seqio_obj->write_seq($seq_obj); > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l _________________________________________________________________ Invite your mail contacts to join your friends list with Windows Live Spaces. It's easy! http://spaces.live.com/spacesapi.aspx?wx_action=create&wx_url=/friends.aspx&mkt=en-us From cmzmasek at yahoo.com Tue Jul 29 14:09:46 2008 From: cmzmasek at yahoo.com (Christian Zmasek) Date: Tue, 29 Jul 2008 11:09:46 -0700 (PDT) Subject: [Bioperl-l] Phyloxml - made-up 'align' xml-language 2 Message-ID: <156130.59343.qm@web50511.mail.re2.yahoo.com> I forgot: What the parser should do if it encounters data from other namespaces (or simply unknown (new?) phyloxml elements) is to simply ignore them, without breaking. ----- Original Message ---- From: Christian Zmasek To: Jason Stajich ; "Han, Mira" Cc: bioperl list Sent: Tuesday, July 29, 2008 11:07:24 AM Subject: Re: [Bioperl-l] Phyloxml - made-up 'align' xml-language Hi, Mira: I am so sorry for being not more clear in my examples. The "" data was intended as an example of how xml data from other namespaces (in this case "align") could reside inside phyloxml documents. There is absolutely no need to parse and store these data from other namespaces/xml-languages by your parser/objects. Christian PS: To be clear "align", is the name of a _fictional_ xml language which looks like it can store alignments. ----- Original Message ---- From: Jason Stajich To: "Han, Mira" Cc: bioperl list ; Christian Zmasek Sent: Tuesday, July 29, 2008 9:45:06 AM Subject: Re: [Bioperl-l] Phyloxml Mira - I've not thought too clearly about how this should go, certainly Bio::AlignIO should be reused for the parsing aspect, although I'm not clear what format the alignment is in? At some point this is might need to be unified with the NEXUS-type objects that the Bio::NEXUS group has worked on. We may have to work with them to define the proper object here that holds both tree and alignment data and allows slicing out either from the object. So a super-object is probably going to have to be created to marshall out the trees and alignment data. I didn't realize the spec was going as far as to encapsulate all of the alignment data as well. We may need to think about whether we can support all of the aspects of the spec at this time as well. I hope other people have input here as well. -jason On Jul 29, 2008, at 9:20 AM, Han, Mira wrote: > > Hi, > Sorry for bombarding the list > Thought this would be better on a separate thread. > Phyloxml documents have s. > But also s. > What would be the standard approach for parsing, > I guess TreeIO->next_tree > shouldn't take care of the alignments. > Would I need to make a AlignIO->next_aln for the phyloxml document > as well? > > Mira > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From aaron.j.mackey at gsk.com Tue Jul 29 12:59:59 2008 From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com) Date: Tue, 29 Jul 2008 12:59:59 -0400 Subject: [Bioperl-l] Phyloxml In-Reply-To: Message-ID: The "super-object" approach is hard, based on the experience of the NEXUS working group. I recommend the "dumber" approach of linking things together with "has-a" annotation relationships (tree is an annotation of an alignment, and vice versa), without worrying about coordinated slicing or other "joint" manipulations. We already do similar things with sequences and features (i.e. manipulation of the sequence does not affect the features, or vice versa). -Aaron bioperl-l-bounces at lists.open-bio.org wrote on 07/29/2008 12:45:06 PM: > Mira - > > I've not thought too clearly about how this should go, certainly > Bio::AlignIO should be reused for the parsing aspect, although I'm > not clear what format the alignment is in? > > At some point this is might need to be unified with the NEXUS-type > objects that the Bio::NEXUS group has worked on. We may have to work > with them to define the proper object here that holds both tree and > alignment data and allows slicing out either from the object. > > So a super-object is probably going to have to be created to marshall > out the trees and alignment data. I didn't realize the spec was > going as far as to encapsulate all of the alignment data as well. We > may need to think about whether we can support all of the aspects of > the spec at this time as well. > > I hope other people have input here as well. > > -jason > > On Jul 29, 2008, at 9:20 AM, Han, Mira wrote: > > > > > Hi, > > Sorry for bombarding the list > > Thought this would be better on a separate thread. > > Phyloxml documents have s. > > But also s. > > What would be the standard approach for parsing, > > I guess TreeIO->next_tree > > shouldn't take care of the alignments. > > Would I need to make a AlignIO->next_aln for the phyloxml document > > as well? > > > > Mira > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From hlapp at gmx.net Tue Jul 29 14:58:33 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 29 Jul 2008 14:58:33 -0400 Subject: [Bioperl-l] Phyloxml SeqI without actual sequence In-Reply-To: References: Message-ID: <2BDBE6AE-8F40-4C7F-B32C-A2FF8E093FAA@gmx.net> I think that would be good. -hilmar On Jul 29, 2008, at 2:00 PM, Jason Stajich wrote: > I guess making a sequence is fine - maybe we can add a flag like - > nowarnonempty => 1 to not warn when the sequence is empty (in > Bio::PrimarySeq new() code ? > > -jason > On Jul 29, 2008, at 10:31 AM, miraceti wrote: > >> sometimes the clade looks like. >> >> >> >> alcohol dehydrogenase >> 0.99 >> >> >> >> sometimes the clade looks like. >> >> >> ADHX >> P81431 >> Alcohol dehydrogenase class-3 >> >> TDATGKPIKCMAAIAWEAKKPLSIEEVEVAPPKSGEVRIKILHSGVCHTD >> >> >> >> >> Do you think it's better not to create the SeqI in the first case?. >> >> >> On Tue, Jul 29, 2008 at 12:51 PM, Jason Stajich >> wrote: >> >>> So why would you create the sequence in the first place when it is >>> empty? >>> Shouldn't you just not create a sequence if there isn't one? Can >>> you provide >>> sample data so we understand better - maybe there is sequence name >>> but no >>> data? Maybe we can specify an option to not warn when creating a >>> sequence >>> if a specific flag is provided to the Seq initialization routine. >>> >>> -jason >>> >>> >>> On Jul 29, 2008, at 9:13 AM, Han, Mira wrote: >>> >>> >>>> Another phyloxml parsing question. >>>> We have tags that sometimes have actual molecular >>>> sequences and >>>> sometimes don't. >>>> I decided to create a SeqI object and link it to AnnotatableNode. >>>> But when it doesn't have actual sequence >>>> It gives warning that the sequence is empty. >>>> I don't think it's a big problem, >>>> And I'd prefer having consistency than having two different >>>> solutions for >>>> the same tag. >>>> But I'd like to hear people's opinion on this as well. >>>> Thank you >>>> >>>> Mira Han >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From aaron.j.mackey at gsk.com Tue Jul 29 12:43:02 2008 From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com) Date: Tue, 29 Jul 2008 12:43:02 -0400 Subject: [Bioperl-l] Phyloxml In-Reply-To: Message-ID: Personally, I'd like to see TreeIO::phyloxml provide trees that have alignments (if present) as annotations of the Tree (Bio::Tree's are AnnotatableI). Weigang Qiu and I made a little progress on this for the Nexus parser, so all the bits and bobs are already in place for this to work. Whether a corresponding AlignIO::phyloxml would do the reverse (provide alignments with Tree's as annotations) would just be icing on the cake, but not very important, in my opinion (in fact, it seems like an AlignIO::phyloxml would just delegate the parsing to TreeIO::phyloxml, and then muck around with the objects to get the inside-out structure). -Aaron bioperl-l-bounces at lists.open-bio.org wrote on 07/29/2008 12:20:33 PM: > > Hi, > Sorry for bombarding the list > Thought this would be better on a separate thread. > Phyloxml documents have s. > But also s. > What would be the standard approach for parsing, > I guess TreeIO->next_tree > shouldn't take care of the alignments. > Would I need to make a AlignIO->next_aln for the phyloxml document as well? > > Mira > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From Kevin.M.Brown at asu.edu Tue Jul 29 15:44:48 2008 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Tue, 29 Jul 2008 12:44:48 -0700 Subject: [Bioperl-l] get_Seq_by_id: CONTIG found In-Reply-To: References: <000301c8f210$247cdb20$6d769160$@sysu.edu.cn> Message-ID: <1A4207F8295607498283FE9E93B775B40522CB7D@EX02.asurite.ad.asu.edu> Might be a proxy server issue as I notice the code snippet uses one. > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of ocar campos > Sent: Tuesday, July 29, 2008 11:08 AM > To: melody; bioperl-l at portal.open-bio.org > Subject: Re: [Bioperl-l] get_Seq_by_id: CONTIG found > > > I got a very similar message when trying to access with a > Version Number, but saying that the sequence is not in the > db, and when I check via web, the sequence is there, and then > the script works. > > regards > > O'car > > ---------------------------------------- > > From: xyuany at mail2.sysu.edu.cn > > To: bioperl-l at portal.open-bio.org > > Date: Tue, 29 Jul 2008 23:47:31 -0700 > > Subject: [Bioperl-l] get_Seq_by_id: CONTIG found > > > > I'm trying to download a bunch of sequences from GenBank > using the gi ,when > > I run the code,I got The message like this : > > > > -------------------- WARNING --------------------- > > MSG: CONTIG found. GenBank get_Stream_by_acc about to run. > > --------------------------------------------------- > > Warning: unable to close filehandle FETCH properly. > > > > What can I do if I want this code work. > > Thanks a lot, > > Melody xiong > > > > > > use Bio::DB::GenBank; > > my $db_obj = new Bio::DB::GenBank; > > $db_obj->proxy(['http','ftp'],'http://proxy2.sysu.edu.cn:3128/'); > > my $seq_obj=$db_obj->get_Seq_by_gi("42537818"); > > my $seqio_obj=Bio::SeqIO->new(-file => > ">temp2.txt", -format => > > "fasta" ); > > $seqio_obj->write_seq($seq_obj); > > > > > > > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _________________________________________________________________ > Invite your mail contacts to join your friends list with > Windows Live Spaces. It's easy! > http://spaces.live.com/spacesapi.aspx?wx_action=create&wx_url= > /friends.aspx&mkt=en-us > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at uiuc.edu Tue Jul 29 16:00:54 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 29 Jul 2008 15:00:54 -0500 Subject: [Bioperl-l] Phyloxml SeqI without actual sequence In-Reply-To: References: Message-ID: <9AE907EC-E3B2-40EC-85F2-39D4BDB2B11F@uiuc.edu> On Jul 29, 2008, at 12:59 PM, Hilmar Lapp wrote: > On Jul 29, 2008, at 1:31 PM, miraceti wrote: > >> sometimes the clade looks like. >> >> >> >> alcohol dehydrogenase >> 0.99 >> >> >> >> sometimes the clade looks like. >> >> >> ADHX >> P81431 >> Alcohol dehydrogenase class-3 >> >> TDATGKPIKCMAAIAWEAKKPLSIEEVEVAPPKSGEVRIKILHSGVCHTD >> >> >> >> >> Do you think it's better not to create the SeqI in the first case?. > > It's an option but to me it threatens to lose the fact that the > annotation properties pertain to a sequence, not to something else > (such as the tree node, for example). So, if you don't attach the > annotation to a sequence object you create, what would you attach it > to then? In the absence of a good answer creating the sequence > object may the only way. This is something we had discussed on IRC fairly recently (annotation that could be considered specific to the Tree, Node, Sequence, or combinations thereof). From the documentation the only thing designated specifically with 'annotation' is the sequence, but there are several complex types which don't easily fit within a set AnnotationI implementation (such as / ) or within class data. Mira, are there some examples where Trees/Nodes/Seqs could reasonably be expected to have separate annotation? > I thought I'd recall some kind of Bio::Seq::EmptySeq object for > exactly this kind of case, but apparently there isn't one there, so > maybe I was just dreaming this up. However, a sequence object that > is optimized for this case may be useful to have, though thinking > about it, I'm not exactly sure what overhead the sequence slot > really adds to all the other overhead added by feature and > annotation slots. The only thing that really comes to mind is that a > sequence object with a zero length sequence won't allow you to add > features. I like Jason's suggestion of using a flag (maybe specifically calling for -emptyseq => 1 to prevent warnings). > Sorry for this random stream of thoughts here, I hope I'm not > totally wasting everyone's time here. > > -hilmar Not at all. That's what this is all about! chris From aaron.j.mackey at gsk.com Tue Jul 29 15:05:30 2008 From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com) Date: Tue, 29 Jul 2008 15:05:30 -0400 Subject: [Bioperl-l] Phyloxml - made-up 'align' xml-language 2 In-Reply-To: <156130.59343.qm@web50511.mail.re2.yahoo.com> Message-ID: Although it would be nicer to not ignore those blocks, but stuff them (verbatim) into a tag/annotation of the enclosing element. This would provide round-tripping, and would also allow further processing of the tree objects to "unpack" those blocks foreign to phyloxml, but possibly quite relevant to the problem at hand. -Aaron bioperl-l-bounces at lists.open-bio.org wrote on 07/29/2008 02:09:46 PM: > I forgot: What the parser should do if it encounters data from other > namespaces (or simply unknown (new?) phyloxml elements) is to simply > ignore them, without breaking. > > > > > ----- Original Message ---- > From: Christian Zmasek > To: Jason Stajich ; "Han, Mira" > Cc: bioperl list > Sent: Tuesday, July 29, 2008 11:07:24 AM > Subject: Re: [Bioperl-l] Phyloxml - made-up 'align' xml-language > > Hi, Mira: > > I am so sorry for being not more clear in my examples. > The "" data was intended as an > example of how xml data from other namespaces (in this case > "align") could reside inside phyloxml documents. > There is absolutely no need to parse and store these data from other > namespaces/xml-languages by your parser/objects. > > Christian > > PS: To be clear "align", is the name of a _fictional_ xml language > which looks like it can store alignments. > > > > > > ----- Original Message ---- > From: Jason Stajich > To: "Han, Mira" > Cc: bioperl list ; Christian Zmasek > > Sent: Tuesday, July 29, 2008 9:45:06 AM > Subject: Re: [Bioperl-l] Phyloxml > > Mira - > > I've not thought too clearly about how this should go, certainly > Bio::AlignIO should be reused for the parsing aspect, although I'm > not clear what format the alignment is in? > > At some point this is might need to be unified with the NEXUS-type > objects that the Bio::NEXUS group has worked on. We may have to work > with them to define the proper object here that holds both tree and > alignment data and allows slicing out either from the object. > > So a super-object is probably going to have to be created to marshall > out the trees and alignment data. I didn't realize the spec was > going as far as to encapsulate all of the alignment data as well. We > may need to think about whether we can support all of the aspects of > the spec at this time as well. > > I hope other people have input here as well. > > -jason > > On Jul 29, 2008, at 9:20 AM, Han, Mira wrote: > > > > > Hi, > > Sorry for bombarding the list > > Thought this would be better on a separate thread. > > Phyloxml documents have s. > > But also s. > > What would be the standard approach for parsing, > > I guess TreeIO->next_tree > > shouldn't take care of the alignments. > > Would I need to make a AlignIO->next_aln for the phyloxml document > > as well? > > > > Mira > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at uiuc.edu Tue Jul 29 17:06:24 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 29 Jul 2008 16:06:24 -0500 Subject: [Bioperl-l] get_Seq_by_id: CONTIG found In-Reply-To: <1A4207F8295607498283FE9E93B775B40522CB7D@EX02.asurite.ad.asu.edu> References: <000301c8f210$247cdb20$6d769160$@sysu.edu.cn> <1A4207F8295607498283FE9E93B775B40522CB7D@EX02.asurite.ad.asu.edu> Message-ID: It could also be a versioning issue. Checking back through bioperl- live and the release branches, 'CONTIG found. GenBank get_Stream_by_acc about to run' is only in bioperl 1.4. I suggest an update to 1.5.2 or bioperl-live. chris On Jul 29, 2008, at 2:44 PM, Kevin Brown wrote: > Might be a proxy server issue as I notice the code snippet uses one. > >> -----Original Message----- >> From: bioperl-l-bounces at lists.open-bio.org >> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of ocar >> campos >> Sent: Tuesday, July 29, 2008 11:08 AM >> To: melody; bioperl-l at portal.open-bio.org >> Subject: Re: [Bioperl-l] get_Seq_by_id: CONTIG found >> >> >> I got a very similar message when trying to access with a >> Version Number, but saying that the sequence is not in the >> db, and when I check via web, the sequence is there, and then >> the script works. >> >> regards >> >> O'car >> >> ---------------------------------------- >>> From: xyuany at mail2.sysu.edu.cn >>> To: bioperl-l at portal.open-bio.org >>> Date: Tue, 29 Jul 2008 23:47:31 -0700 >>> Subject: [Bioperl-l] get_Seq_by_id: CONTIG found >>> >>> I'm trying to download a bunch of sequences from GenBank >> using the gi ,when >>> I run the code,I got The message like this : >>> >>> -------------------- WARNING --------------------- >>> MSG: CONTIG found. GenBank get_Stream_by_acc about to run. >>> --------------------------------------------------- >>> Warning: unable to close filehandle FETCH properly. >>> >>> What can I do if I want this code work. >>> Thanks a lot, >>> Melody xiong >>> >>> >>> use Bio::DB::GenBank; >>> my $db_obj = new Bio::DB::GenBank; >>> $db_obj->proxy(['http','ftp'],'http://proxy2.sysu.edu.cn:3128/'); >>> my $seq_obj=$db_obj->get_Seq_by_gi("42537818"); >>> my $seqio_obj=Bio::SeqIO->new(-file => >> ">temp2.txt", -format => >>> "fasta" ); >>> $seqio_obj->write_seq($seq_obj); >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> _________________________________________________________________ >> Invite your mail contacts to join your friends list with >> Windows Live Spaces. It's easy! >> http://spaces.live.com/spacesapi.aspx?wx_action=create&wx_url= >> /friends.aspx&mkt=en-us >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Marie-Claude Hofmann College of Veterinary Medicine University of Illinois Urbana-Champaign From Russell.Smithies at agresearch.co.nz Tue Jul 29 18:17:33 2008 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Wed, 30 Jul 2008 10:17:33 +1200 Subject: [Bioperl-l] get_Seq_by_id: CONTIG found In-Reply-To: References: <000301c8f210$247cdb20$6d769160$@sysu.edu.cn> Message-ID: Hi O'car, Your code works for me with the proxy stuff (on our proxy) so I suggest looking there. Are you using the right proxy port? Do you need to authenticate? use Bio::DB::GenBank; my $db_obj = new Bio::DB::GenBank; $db_obj->proxy(['http','ftp'], 'http://webgate.agresearch.co.nz:8080' ); $db_obj->authentication($user,$pass); my $seq_obj=$db_obj->get_Seq_by_gi("42537818"); my $seqio_obj=Bio::SeqIO->new(-file => ">temp.txt", -format=> "fasta" ); $seqio_obj->write_seq($seq_obj); Russell > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open- > bio.org] On Behalf Of ocar campos > Sent: Wednesday, 30 July 2008 6:08 a.m. > To: melody; bioperl-l at portal.open-bio.org > Subject: Re: [Bioperl-l] get_Seq_by_id: CONTIG found > > > I got a very similar message when trying to access with a Version Number, but > saying that the sequence is not in the db, and when I check via web, the sequence > is there, and then the script works. > > regards > > O'car > > ---------------------------------------- > > From: xyuany at mail2.sysu.edu.cn > > To: bioperl-l at portal.open-bio.org > > Date: Tue, 29 Jul 2008 23:47:31 -0700 > > Subject: [Bioperl-l] get_Seq_by_id: CONTIG found > > > > I'm trying to download a bunch of sequences from GenBank using the gi ,when > > I run the code,I got The message like this : > > > > -------------------- WARNING --------------------- > > MSG: CONTIG found. GenBank get_Stream_by_acc about to run. > > --------------------------------------------------- > > Warning: unable to close filehandle FETCH properly. > > > > What can I do if I want this code work. > > Thanks a lot, > > Melody xiong > > > > > > use Bio::DB::GenBank; > > my $db_obj = new Bio::DB::GenBank; > > $db_obj->proxy(['http','ftp'],'http://proxy2.sysu.edu.cn:3128/'); > > my $seq_obj=$db_obj->get_Seq_by_gi("42537818"); > > my $seqio_obj=Bio::SeqIO->new(-file => ">temp2.txt", -format => > > "fasta" ); > > $seqio_obj->write_seq($seq_obj); > > > > > > > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _________________________________________________________________ > Invite your mail contacts to join your friends list with Windows Live Spaces. It's > easy! > http://spaces.live.com/spacesapi.aspx?wx_action=create&wx_url=/friends.a spx&m > kt=en-us > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From arlin.stoltzfus at nist.gov Wed Jul 30 09:58:09 2008 From: arlin.stoltzfus at nist.gov (Arlin Stoltzfus) Date: Wed, 30 Jul 2008 09:58:09 -0400 Subject: [Bioperl-l] Phyloxml In-Reply-To: References: Message-ID: <672E04DC-9AE9-4DC0-B106-BC4C1510D0D8@nist.gov> Jason, et al-- In regard to the Bio::NEXUS objects, we (Bio::NEXUS team) have the aspiration to integrate with BioPerl objects via some coordinated CDAT (character-data-and-trees object) super-object that would allow coordinated operations like slicing OTUs X, Y and Z out of both the tree and the alignment. But it hasn't really happened. Aaron suggests that there might be a lesson here, and maybe its about the folly of designing one great object ("One Thing to rule them all; One Thing to find them; One Thing to gather all, and in the darkness, bind them"). Anyway, Aaron suggests we should opt for a "dumber" (his words) approach such as treating an alignment as an "annotation" of a tree. He and Weigang have done some of that. Yet, I think Rutger might have worked out a smarter approach in Bio::Phylo, which (as I understand it) *does* have bindings to BioPerl objects. It might be worth having a summit meeting to work out some strategy to solve this problem. We might be able to get support for a meeting or hackathon via NESCent if we write a White Paper that lays out a plan aimed at 1) object bindings between Bio::Phylo, BioPerl and Bio::NEXUS and 2) some coordinated operations, with or without a super-object. The purpose would be to expand the power of these Perl libraries to facilitate evolutionary analyses. Any takers? Arlin On Jul 29, 2008, at 12:45 PM, Jason Stajich wrote: > Mira - > > I've not thought too clearly about how this should go, certainly > Bio::AlignIO should be reused for the parsing aspect, although I'm > not clear what format the alignment is in? > > At some point this is might need to be unified with the NEXUS-type > objects that the Bio::NEXUS group has worked on. We may have to > work with them to define the proper object here that holds both > tree and alignment data and allows slicing out either from the object. > > So a super-object is probably going to have to be created to > marshall out the trees and alignment data. I didn't realize the > spec was going as far as to encapsulate all of the alignment data > as well. We may need to think about whether we can support all of > the aspects of the spec at this time as well. > > I hope other people have input here as well. > > -jason > > On Jul 29, 2008, at 9:20 AM, Han, Mira wrote: > >> >> Hi, >> Sorry for bombarding the list >> Thought this would be better on a separate thread. >> Phyloxml documents have s. >> But also s. >> What would be the standard approach for parsing, >> I guess TreeIO->next_tree >> shouldn't take care of the alignments. >> Would I need to make a AlignIO->next_aln for the phyloxml document >> as well? >> >> Mira >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l ------------ Arlin Stoltzfus (arlin.stoltzfus at nist.gov), Research Biologist, NIST Fellow, CARB, 9600 Gudelsky Drive, Rockville, Maryland 20850 tel 240 314 6208, fax 240 314 6255, www.molevol.org/camel From cjfields at uiuc.edu Wed Jul 30 11:44:16 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 30 Jul 2008 10:44:16 -0500 Subject: [Bioperl-l] Phyloxml In-Reply-To: <672E04DC-9AE9-4DC0-B106-BC4C1510D0D8@nist.gov> References: <672E04DC-9AE9-4DC0-B106-BC4C1510D0D8@nist.gov> Message-ID: <0F8894E4-06DD-4688-B5CE-1A06BF111889@uiuc.edu> On Jul 30, 2008, at 8:58 AM, Arlin Stoltzfus wrote: > Jason, et al-- > > In regard to the Bio::NEXUS objects, we (Bio::NEXUS team) have the > aspiration to integrate with BioPerl objects via some coordinated > CDAT (character-data-and-trees object) super-object that would allow > coordinated operations like slicing OTUs X, Y and Z out of both the > tree and the alignment. > > But it hasn't really happened. Aaron suggests that there might be a > lesson here, and maybe its about the folly of designing one great > object ("One Thing to rule them all; One Thing to find them; One > Thing to gather all, and in the darkness, bind them"). Anyway, > Aaron suggests we should opt for a "dumber" (his words) approach > such as treating an alignment as an "annotation" of a tree. He and > Weigang have done some of that. > > Yet, I think Rutger might have worked out a smarter approach in > Bio::Phylo, which (as I understand it) *does* have bindings to > BioPerl objects. > > It might be worth having a summit meeting to work out some strategy > to solve this problem. We might be able to get support for a > meeting or hackathon via NESCent if we write a White Paper that lays > out a plan aimed at 1) object bindings between Bio::Phylo, BioPerl > and Bio::NEXUS and 2) some coordinated operations, with or without a > super-object. The purpose would be to expand the power of these > Perl libraries to facilitate evolutionary analyses. > > Any takers? > > Arlin A hackathon sounds like a good idea. Would NESCent be up for hosting this? chris From cjfields at bioperl.org Wed Jul 30 11:32:16 2008 From: cjfields at bioperl.org (Chris Fields) Date: Wed, 30 Jul 2008 15:32:16 +0000 (UTC) Subject: [Bioperl-l] =?utf-8?q?Issues_on_Bio=3A=3ATools=3A=3APrimer3-=3Ene?= =?utf-8?q?xt=5Fprimer?= References: <5486b2980807281345p3fd2c511u16ba6f4392a882c5@mail.gmail.com> <488EF05A.6030601@gmail.com> <5486b2980807290842i41e85149g13ca374c7eb7713@mail.gmail.com> <488F58A9.9030306@gmail.com> Message-ID: Roy Chaudhuri gmail.com> writes: > > Hi John. > > There is a bug in there, sorry for misunderstanding your earlier post ... Roy, John, This is now fixed in bioperl-live thanks to Roy's patch (which seemed to post to bugzilla just fine). chris From roy.chaudhuri at gmail.com Wed Jul 30 13:16:15 2008 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Wed, 30 Jul 2008 18:16:15 +0100 Subject: [Bioperl-l] Issues on Bio::Tools::Primer3->next_primer In-Reply-To: References: <5486b2980807281345p3fd2c511u16ba6f4392a882c5@mail.gmail.com> <488EF05A.6030601@gmail.com> <5486b2980807290842i41e85149g13ca374c7eb7713@mail.gmail.com> <488F58A9.9030306@gmail.com> Message-ID: <4890A1DF.9060800@gmail.com> > This is now fixed in bioperl-live thanks to Roy's patch > (which seemed to post to bugzilla just fine). Thanks for adding in the patch. The bugzilla problems were an issue with cookies using Firefox, it worked when I resorted to Internet Explorer. John- I should have mentioned in my previous post, if you have any problems installing the patch (or upgrading from bioperl-live) then creating a Bio::Seq object from your raw sequence and supplying that to the -seq argument of new() is a suitable workaround. Roy. -- Dr. Roy Chaudhuri Department of Veterinary Medicine University of Cambridge, U.K. From manchunjohn-ma at uiowa.edu Wed Jul 30 14:33:09 2008 From: manchunjohn-ma at uiowa.edu (John M.C. Ma) Date: Wed, 30 Jul 2008 13:33:09 -0500 Subject: [Bioperl-l] Issues on Bio::Tools::Primer3->next_primer In-Reply-To: <4890A1DF.9060800@gmail.com> References: <5486b2980807281345p3fd2c511u16ba6f4392a882c5@mail.gmail.com> <488EF05A.6030601@gmail.com> <5486b2980807290842i41e85149g13ca374c7eb7713@mail.gmail.com> <488F58A9.9030306@gmail.com> <4890A1DF.9060800@gmail.com> Message-ID: <5486b2980807301133t387c9d53t3ea4c365bc95edef@mail.gmail.com> Hi Roy, I have checked out this from svn. However, there was a compile-time error for primer3.pm: syntax error at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 380, near "elsif" Global symbol "%args" requires explicit package name at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 382. Global symbol "$key" requires explicit package name at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 382. Global symbol "$self" requires explicit package name at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 382. Can't use global $1 in "my" at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 389, near "=$1" Global symbol "$maxlocation" requires explicit package name at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 390. Global symbol "$maxlocation" requires explicit package name at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 390. Global symbol "$location" requires explicit package name at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 393. Global symbol "$location" requires explicit package name at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394. Global symbol "$maxlocation" requires explicit package name at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394. Global symbol "$maxlocation" requires explicit package name at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394. Global symbol "$location" requires explicit package name at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394. Global symbol "$location" requires explicit package name at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 396. Global symbol "%results" requires explicit package name at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 399. Global symbol "$location" requires explicit package name at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 399. Global symbol "$self" requires explicit package name at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 399. syntax error at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 400, near "}" /home/johnma/bioperl-live/Bio/Tools/Primer3.pm has too many errors. Compilation failed in require at /usr/lib/perl5/site_perl/5.10.0/Bio/Tools/Run/Primer3.pm line 145. BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.10.0/Bio/Tools/Run/Primer3.pm line 145. Compilation failed in require at /home/johnma/workspace/NCBI-test/NCBI-test.pl line 9. BEGIN failed--compilation aborted at /home/johnma/workspace/NCBI-test/NCBI-test.pl line 9. Best regards, John On Wed, Jul 30, 2008 at 12:16 PM, Roy Chaudhuri wrote: > This is now fixed in bioperl-live thanks to Roy's patch (which seemed to >> post to bugzilla just fine). >> > > Thanks for adding in the patch. The bugzilla problems were an issue with > cookies using Firefox, it worked when I resorted to Internet Explorer. > > John- I should have mentioned in my previous post, if you have any problems > installing the patch (or upgrading from bioperl-live) then creating a > Bio::Seq object from your raw sequence and supplying that to the -seq > argument of new() is a suitable workaround. > > > Roy. > -- > Dr. Roy Chaudhuri > Department of Veterinary Medicine > University of Cambridge, U.K. > From jason at bioperl.org Wed Jul 30 14:40:39 2008 From: jason at bioperl.org (Jason Stajich) Date: Wed, 30 Jul 2008 11:40:39 -0700 Subject: [Bioperl-l] Issues on Bio::Tools::Primer3->next_primer In-Reply-To: <5486b2980807301133t387c9d53t3ea4c365bc95edef@mail.gmail.com> References: <5486b2980807281345p3fd2c511u16ba6f4392a882c5@mail.gmail.com> <488EF05A.6030601@gmail.com> <5486b2980807290842i41e85149g13ca374c7eb7713@mail.gmail.com> <488F58A9.9030306@gmail.com> <4890A1DF.9060800@gmail.com> <5486b2980807301133t387c9d53t3ea4c365bc95edef@mail.gmail.com> Message-ID: <4D57BD4C-3F0D-4D4D-9F5C-FC85C49F1E75@bioperl.org> yeah I don't know that the patch went in correctly, not sure if it was applied against the same version? Roy can you double check how this should look. -jason On Jul 30, 2008, at 11:33 AM, John M.C. Ma wrote: > Hi Roy, > > I have checked out this from svn. However, there was a compile-time > error > for primer3.pm: > > syntax error at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line > 380, > near "elsif" > Global symbol "%args" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 382. > Global symbol "$key" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 382. > Global symbol "$self" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 382. > Can't use global $1 in "my" at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 389, near "=$1" > Global symbol "$maxlocation" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 390. > Global symbol "$maxlocation" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 390. > Global symbol "$location" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 393. > Global symbol "$location" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394. > Global symbol "$maxlocation" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394. > Global symbol "$maxlocation" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394. > Global symbol "$location" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394. > Global symbol "$location" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 396. > Global symbol "%results" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 399. > Global symbol "$location" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 399. > Global symbol "$self" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 399. > syntax error at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line > 400, > near "}" > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm has too many errors. > Compilation failed in require at > /usr/lib/perl5/site_perl/5.10.0/Bio/Tools/Run/Primer3.pm line 145. > BEGIN failed--compilation aborted at > /usr/lib/perl5/site_perl/5.10.0/Bio/Tools/Run/Primer3.pm line 145. > Compilation failed in require at > /home/johnma/workspace/NCBI-test/NCBI-test.pl line 9. > BEGIN failed--compilation aborted at > /home/johnma/workspace/NCBI-test/NCBI-test.pl line 9. > > Best regards, > > John > > On Wed, Jul 30, 2008 at 12:16 PM, Roy Chaudhuri > wrote: > >> This is now fixed in bioperl-live thanks to Roy's patch (which >> seemed to >>> post to bugzilla just fine). >>> >> >> Thanks for adding in the patch. The bugzilla problems were an >> issue with >> cookies using Firefox, it worked when I resorted to Internet >> Explorer. >> >> John- I should have mentioned in my previous post, if you have any >> problems >> installing the patch (or upgrading from bioperl-live) then creating a >> Bio::Seq object from your raw sequence and supplying that to the -seq >> argument of new() is a suitable workaround. >> >> >> Roy. >> -- >> Dr. Roy Chaudhuri >> Department of Veterinary Medicine >> University of Cambridge, U.K. >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at uiuc.edu Wed Jul 30 15:08:14 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 30 Jul 2008 14:08:14 -0500 Subject: [Bioperl-l] bioperl 1.6 Message-ID: I am initiating the process towards getting a bioperl 1.6 released. However, we unfortunately have a ton of bugs which need to be fixed. What I would like is some help in categorizing bugs into ones that are blocking (i.e. represents an issue or problem which needs to be addressed, thus preventing a release) vs. non-blocking (can be fixed on the main trunk and in a stable point release). Also, for the non- blocking ones it would be nice to know which should be placed at the top of the to-fix pile. If needed we can add tickets to the queue for issues that need to be addressed; test coverage and similar issues come to mind. Speaking of, I would like to get test coverage running; should this be set up on portal? I may have my hands full with the bug fixes, so if anyone would like to step up and take care of that it would be a tremendous help. chris From cjfields1 at gmail.com Wed Jul 30 14:44:47 2008 From: cjfields1 at gmail.com (Chris Fields) Date: Wed, 30 Jul 2008 13:44:47 -0500 Subject: [Bioperl-l] Issues on Bio::Tools::Primer3->next_primer In-Reply-To: <5486b2980807301133t387c9d53t3ea4c365bc95edef@mail.gmail.com> References: <5486b2980807281345p3fd2c511u16ba6f4392a882c5@mail.gmail.com> <488EF05A.6030601@gmail.com> <5486b2980807290842i41e85149g13ca374c7eb7713@mail.gmail.com> <488F58A9.9030306@gmail.com> <4890A1DF.9060800@gmail.com> <5486b2980807301133t387c9d53t3ea4c365bc95edef@mail.gmail.com> Message-ID: <2D7916E0-9324-443B-A3F1-63B0FA0F3B54@gmail.com> D'oh! My bad, looks like the patch was off. I should have run tests. Roy, any idea where this fits in? chris On Jul 30, 2008, at 1:33 PM, John M.C. Ma wrote: > Hi Roy, > > I have checked out this from svn. However, there was a compile-time > error > for primer3.pm: > > syntax error at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line > 380, > near "elsif" > Global symbol "%args" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 382. > Global symbol "$key" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 382. > Global symbol "$self" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 382. > Can't use global $1 in "my" at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 389, near "=$1" > Global symbol "$maxlocation" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 390. > Global symbol "$maxlocation" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 390. > Global symbol "$location" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 393. > Global symbol "$location" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394. > Global symbol "$maxlocation" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394. > Global symbol "$maxlocation" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394. > Global symbol "$location" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394. > Global symbol "$location" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 396. > Global symbol "%results" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 399. > Global symbol "$location" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 399. > Global symbol "$self" requires explicit package name at > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 399. > syntax error at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line > 400, > near "}" > /home/johnma/bioperl-live/Bio/Tools/Primer3.pm has too many errors. > Compilation failed in require at > /usr/lib/perl5/site_perl/5.10.0/Bio/Tools/Run/Primer3.pm line 145. > BEGIN failed--compilation aborted at > /usr/lib/perl5/site_perl/5.10.0/Bio/Tools/Run/Primer3.pm line 145. > Compilation failed in require at > /home/johnma/workspace/NCBI-test/NCBI-test.pl line 9. > BEGIN failed--compilation aborted at > /home/johnma/workspace/NCBI-test/NCBI-test.pl line 9. > > Best regards, > > John > > On Wed, Jul 30, 2008 at 12:16 PM, Roy Chaudhuri >wrote: > >> This is now fixed in bioperl-live thanks to Roy's patch (which >> seemed to >>> post to bugzilla just fine). >>> >> >> Thanks for adding in the patch. The bugzilla problems were an issue >> with >> cookies using Firefox, it worked when I resorted to Internet >> Explorer. >> >> John- I should have mentioned in my previous post, if you have any >> problems >> installing the patch (or upgrading from bioperl-live) then creating a >> Bio::Seq object from your raw sequence and supplying that to the -seq >> argument of new() is a suitable workaround. >> >> >> Roy. >> -- >> Dr. Roy Chaudhuri >> Department of Veterinary Medicine >> University of Cambridge, U.K. >> From cjfields1 at gmail.com Wed Jul 30 15:03:05 2008 From: cjfields1 at gmail.com (Chris Fields) Date: Wed, 30 Jul 2008 14:03:05 -0500 Subject: [Bioperl-l] Issues on Bio::Tools::Primer3->next_primer In-Reply-To: <4D57BD4C-3F0D-4D4D-9F5C-FC85C49F1E75@bioperl.org> References: <5486b2980807281345p3fd2c511u16ba6f4392a882c5@mail.gmail.com> <488EF05A.6030601@gmail.com> <5486b2980807290842i41e85149g13ca374c7eb7713@mail.gmail.com> <488F58A9.9030306@gmail.com> <4890A1DF.9060800@gmail.com> <5486b2980807301133t387c9d53t3ea4c365bc95edef@mail.gmail.com> <4D57BD4C-3F0D-4D4D-9F5C-FC85C49F1E75@bioperl.org> Message-ID: <9CF5B1EC-E871-442D-A7FA-96C06C35C249@gmail.com> My bad; I should have run tests (though the patch seemed to work). I have reverted it and will wait for Roy. chris On Jul 30, 2008, at 1:40 PM, Jason Stajich wrote: > yeah I don't know that the patch went in correctly, not sure if it > was applied against the same version? > Roy can you double check how this should look. > > -jason > On Jul 30, 2008, at 11:33 AM, John M.C. Ma wrote: > >> Hi Roy, >> >> I have checked out this from svn. However, there was a compile-time >> error >> for primer3.pm: >> >> syntax error at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line >> 380, >> near "elsif" >> Global symbol "%args" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 382. >> Global symbol "$key" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 382. >> Global symbol "$self" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 382. >> Can't use global $1 in "my" at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 389, near "=$1" >> Global symbol "$maxlocation" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 390. >> Global symbol "$maxlocation" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 390. >> Global symbol "$location" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 393. >> Global symbol "$location" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394. >> Global symbol "$maxlocation" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394. >> Global symbol "$maxlocation" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394. >> Global symbol "$location" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394. >> Global symbol "$location" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 396. >> Global symbol "%results" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 399. >> Global symbol "$location" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 399. >> Global symbol "$self" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 399. >> syntax error at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line >> 400, >> near "}" >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm has too many errors. >> Compilation failed in require at >> /usr/lib/perl5/site_perl/5.10.0/Bio/Tools/Run/Primer3.pm line 145. >> BEGIN failed--compilation aborted at >> /usr/lib/perl5/site_perl/5.10.0/Bio/Tools/Run/Primer3.pm line 145. >> Compilation failed in require at >> /home/johnma/workspace/NCBI-test/NCBI-test.pl line 9. >> BEGIN failed--compilation aborted at >> /home/johnma/workspace/NCBI-test/NCBI-test.pl line 9. >> >> Best regards, >> >> John >> >> On Wed, Jul 30, 2008 at 12:16 PM, Roy Chaudhuri > >wrote: >> >>> This is now fixed in bioperl-live thanks to Roy's patch (which >>> seemed to >>>> post to bugzilla just fine). >>>> >>> >>> Thanks for adding in the patch. The bugzilla problems were an >>> issue with >>> cookies using Firefox, it worked when I resorted to Internet >>> Explorer. >>> >>> John- I should have mentioned in my previous post, if you have any >>> problems >>> installing the patch (or upgrading from bioperl-live) then >>> creating a >>> Bio::Seq object from your raw sequence and supplying that to the - >>> seq >>> argument of new() is a suitable workaround. >>> >>> >>> Roy. >>> -- >>> Dr. Roy Chaudhuri >>> Department of Veterinary Medicine >>> University of Cambridge, U.K. >>> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > From roy.chaudhuri at gmail.com Wed Jul 30 15:28:53 2008 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Wed, 30 Jul 2008 20:28:53 +0100 Subject: [Bioperl-l] Issues on Bio::Tools::Primer3->next_primer In-Reply-To: <9CF5B1EC-E871-442D-A7FA-96C06C35C249@gmail.com> References: <5486b2980807281345p3fd2c511u16ba6f4392a882c5@mail.gmail.com> <488EF05A.6030601@gmail.com> <5486b2980807290842i41e85149g13ca374c7eb7713@mail.gmail.com> <488F58A9.9030306@gmail.com> <4890A1DF.9060800@gmail.com> <5486b2980807301133t387c9d53t3ea4c365bc95edef@mail.gmail.com> <4D57BD4C-3F0D-4D4D-9F5C-FC85C49F1E75@bioperl.org> <9CF5B1EC-E871-442D-A7FA-96C06C35C249@gmail.com> Message-ID: <4890C0F5.5000706@gmail.com> > My bad; I should have run tests (though the patch seemed to work). I > have reverted it and will wait for Roy. Sorry, the patch is for Bio::Tools::Run::Primer3 (in bioperl-run), it looks like it has been applied to Bio::Tools::Primer3 (in bioperl-live). Roy. -- Dr. Roy Chaudhuri Department of Veterinary Medicine University of Cambridge, U.K. From cjfields at uiuc.edu Wed Jul 30 15:28:31 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 30 Jul 2008 14:28:31 -0500 Subject: [Bioperl-l] Issues on Bio::Tools::Primer3->next_primer In-Reply-To: <4D57BD4C-3F0D-4D4D-9F5C-FC85C49F1E75@bioperl.org> References: <5486b2980807281345p3fd2c511u16ba6f4392a882c5@mail.gmail.com> <488EF05A.6030601@gmail.com> <5486b2980807290842i41e85149g13ca374c7eb7713@mail.gmail.com> <488F58A9.9030306@gmail.com> <4890A1DF.9060800@gmail.com> <5486b2980807301133t387c9d53t3ea4c365bc95edef@mail.gmail.com> <4D57BD4C-3F0D-4D4D-9F5C-FC85C49F1E75@bioperl.org> Message-ID: Okay, patched the correct one (Bio::Tools::Run::Primer3); I previously patched Bio::Tools::Primer3 (and the patch succeeded!). Ran tests and everything passes. John can you try this one out to see if that fixes everything? chris On Jul 30, 2008, at 1:40 PM, Jason Stajich wrote: > yeah I don't know that the patch went in correctly, not sure if it > was applied against the same version? > Roy can you double check how this should look. > > -jason > On Jul 30, 2008, at 11:33 AM, John M.C. Ma wrote: > >> Hi Roy, >> >> I have checked out this from svn. However, there was a compile-time >> error >> for primer3.pm: >> >> syntax error at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line >> 380, >> near "elsif" >> Global symbol "%args" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 382. >> Global symbol "$key" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 382. >> Global symbol "$self" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 382. >> Can't use global $1 in "my" at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 389, near "=$1" >> Global symbol "$maxlocation" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 390. >> Global symbol "$maxlocation" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 390. >> Global symbol "$location" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 393. >> Global symbol "$location" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394. >> Global symbol "$maxlocation" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394. >> Global symbol "$maxlocation" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394. >> Global symbol "$location" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394. >> Global symbol "$location" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 396. >> Global symbol "%results" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 399. >> Global symbol "$location" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 399. >> Global symbol "$self" requires explicit package name at >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 399. >> syntax error at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line >> 400, >> near "}" >> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm has too many errors. >> Compilation failed in require at >> /usr/lib/perl5/site_perl/5.10.0/Bio/Tools/Run/Primer3.pm line 145. >> BEGIN failed--compilation aborted at >> /usr/lib/perl5/site_perl/5.10.0/Bio/Tools/Run/Primer3.pm line 145. >> Compilation failed in require at >> /home/johnma/workspace/NCBI-test/NCBI-test.pl line 9. >> BEGIN failed--compilation aborted at >> /home/johnma/workspace/NCBI-test/NCBI-test.pl line 9. >> >> Best regards, >> >> John >> >> On Wed, Jul 30, 2008 at 12:16 PM, Roy Chaudhuri > >wrote: >> >>> This is now fixed in bioperl-live thanks to Roy's patch (which >>> seemed to >>>> post to bugzilla just fine). >>>> >>> >>> Thanks for adding in the patch. The bugzilla problems were an >>> issue with >>> cookies using Firefox, it worked when I resorted to Internet >>> Explorer. >>> >>> John- I should have mentioned in my previous post, if you have any >>> problems >>> installing the patch (or upgrading from bioperl-live) then >>> creating a >>> Bio::Seq object from your raw sequence and supplying that to the - >>> seq >>> argument of new() is a suitable workaround. >>> >>> >>> Roy. >>> -- >>> Dr. Roy Chaudhuri >>> Department of Veterinary Medicine >>> University of Cambridge, U.K. >>> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Marie-Claude Hofmann College of Veterinary Medicine University of Illinois Urbana-Champaign From manchunjohn-ma at uiowa.edu Wed Jul 30 16:52:01 2008 From: manchunjohn-ma at uiowa.edu (John M.C. Ma) Date: Wed, 30 Jul 2008 15:52:01 -0500 Subject: [Bioperl-l] Issues on Bio::Tools::Primer3->next_primer In-Reply-To: References: <5486b2980807281345p3fd2c511u16ba6f4392a882c5@mail.gmail.com> <488EF05A.6030601@gmail.com> <5486b2980807290842i41e85149g13ca374c7eb7713@mail.gmail.com> <488F58A9.9030306@gmail.com> <4890A1DF.9060800@gmail.com> <5486b2980807301133t387c9d53t3ea4c365bc95edef@mail.gmail.com> <4D57BD4C-3F0D-4D4D-9F5C-FC85C49F1E75@bioperl.org> Message-ID: <5486b2980807301352hb671b9ap31439e8ca4f0b55f@mail.gmail.com> Hi Chris and everyone, it goes on fine. Thanks for all the help! John On Wed, Jul 30, 2008 at 2:28 PM, Chris Fields wrote: > Okay, patched the correct one (Bio::Tools::Run::Primer3); I previously > patched Bio::Tools::Primer3 (and the patch succeeded!). Ran tests and > everything passes. John can you try this one out to see if that fixes > everything? > > chris > > On Jul 30, 2008, at 1:40 PM, Jason Stajich wrote: > > yeah I don't know that the patch went in correctly, not sure if it was >> applied against the same version? >> Roy can you double check how this should look. >> >> -jason >> On Jul 30, 2008, at 11:33 AM, John M.C. Ma wrote: >> >> Hi Roy, >>> >>> I have checked out this from svn. However, there was a compile-time error >>> for primer3.pm: >>> >>> syntax error at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 380, >>> near "elsif" >>> Global symbol "%args" requires explicit package name at >>> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 382. >>> Global symbol "$key" requires explicit package name at >>> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 382. >>> Global symbol "$self" requires explicit package name at >>> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 382. >>> Can't use global $1 in "my" at >>> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 389, near "=$1" >>> Global symbol "$maxlocation" requires explicit package name at >>> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 390. >>> Global symbol "$maxlocation" requires explicit package name at >>> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 390. >>> Global symbol "$location" requires explicit package name at >>> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 393. >>> Global symbol "$location" requires explicit package name at >>> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394. >>> Global symbol "$maxlocation" requires explicit package name at >>> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394. >>> Global symbol "$maxlocation" requires explicit package name at >>> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394. >>> Global symbol "$location" requires explicit package name at >>> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 394. >>> Global symbol "$location" requires explicit package name at >>> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 396. >>> Global symbol "%results" requires explicit package name at >>> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 399. >>> Global symbol "$location" requires explicit package name at >>> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 399. >>> Global symbol "$self" requires explicit package name at >>> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 399. >>> syntax error at /home/johnma/bioperl-live/Bio/Tools/Primer3.pm line 400, >>> near "}" >>> /home/johnma/bioperl-live/Bio/Tools/Primer3.pm has too many errors. >>> Compilation failed in require at >>> /usr/lib/perl5/site_perl/5.10.0/Bio/Tools/Run/Primer3.pm line 145. >>> BEGIN failed--compilation aborted at >>> /usr/lib/perl5/site_perl/5.10.0/Bio/Tools/Run/Primer3.pm line 145. >>> Compilation failed in require at >>> /home/johnma/workspace/NCBI-test/NCBI-test.pl line 9. >>> BEGIN failed--compilation aborted at >>> /home/johnma/workspace/NCBI-test/NCBI-test.pl line 9. >>> >>> Best regards, >>> >>> John >>> >>> On Wed, Jul 30, 2008 at 12:16 PM, Roy Chaudhuri >> >wrote: >>> >>> This is now fixed in bioperl-live thanks to Roy's patch (which seemed to >>>> >>>>> post to bugzilla just fine). >>>>> >>>>> >>>> Thanks for adding in the patch. The bugzilla problems were an issue with >>>> cookies using Firefox, it worked when I resorted to Internet Explorer. >>>> >>>> John- I should have mentioned in my previous post, if you have any >>>> problems >>>> installing the patch (or upgrading from bioperl-live) then creating a >>>> Bio::Seq object from your raw sequence and supplying that to the -seq >>>> argument of new() is a suitable workaround. >>>> >>>> >>>> Roy. >>>> -- >>>> Dr. Roy Chaudhuri >>>> Department of Veterinary Medicine >>>> University of Cambridge, U.K. >>>> >>>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Marie-Claude Hofmann > College of Veterinary Medicine > University of Illinois Urbana-Champaign > > > > > From mauricio at open-bio.org Thu Jul 31 00:32:05 2008 From: mauricio at open-bio.org (Mauricio Herrera Cuadra) Date: Wed, 30 Jul 2008 23:32:05 -0500 Subject: [Bioperl-l] bioperl 1.6 In-Reply-To: References: Message-ID: <48914045.9040505@open-bio.org> Chris Fields wrote: > Speaking of, I would like to get test coverage running; should this be > set up on portal? I may have my hands full with the bug fixes, so if > anyone would like to step up and take care of that it would be a > tremendous help. There is a ticket in the OBF Helpdesk queue waiting for me to setup this. I'll dedicate some time in the weekend to set it up once for all. Regards, Mauricio. From cjfields at uiuc.edu Thu Jul 31 10:04:35 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 31 Jul 2008 09:04:35 -0500 Subject: [Bioperl-l] bioperl 1.6 In-Reply-To: <48914045.9040505@open-bio.org> References: <48914045.9040505@open-bio.org> Message-ID: On Jul 30, 2008, at 11:32 PM, Mauricio Herrera Cuadra wrote: > Chris Fields wrote: >> Speaking of, I would like to get test coverage running; should this >> be set up on portal? I may have my hands full with the bug fixes, >> so if anyone would like to step up and take care of that it would >> be a tremendous help. > > There is a ticket in the OBF Helpdesk queue waiting for me to setup > this. I'll dedicate some time in the weekend to set it up once for > all. > > Regards, > Mauricio. That would be great! If we get this running could we place relevant code in bioperl-live/maintenance (in case we want to add more functionality in the future)? I plan on adding my nightly build script there once I have it cleaned up, prior to the release. chris From cjfields at uiuc.edu Thu Jul 31 10:26:11 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 31 Jul 2008 09:26:11 -0500 Subject: [Bioperl-l] bioperl 1.6 In-Reply-To: <2bb9b24a0807302318w15d1f764tcb32a6066e330191@mail.gmail.com> References: <48914045.9040505@open-bio.org> <2bb9b24a0807302318w15d1f764tcb32a6066e330191@mail.gmail.com> Message-ID: On Jul 31, 2008, at 1:18 AM, Rutger Vos wrote: > I would be interested to hear what sort of timeline you have in mind > for 1.6. For a while now, Bio::Phylo has been informally compatible > with bioperl, but I'd like to target 1.6 for formal, advertised > interoperability. ... This may depend on Arlin's suggestion of having another phylohackathon, which (if it happens) represents a great opportunity to get together and work out Bio::Phylo and 1.6-related issues. We should probably keep track of Bio::Phylo compatibility somehow, maybe by submitting a ticket to bugzilla or by other means if you want (wiki, your blog, etc). As for 1.6, personally I would like to get it out ASAP (early fall 2008), with a new 1.7 dev series very soon soon after (fall-winter 2008). However, a new release is blocking on some significant issues that need to be resolved. The two foremost in my mind are (1) OBDA compatibility issues between various Bio* (BioRuby, for instance) and (2) bioperl-db problems with recent Bio::Species changes. Both issues have tickets in bugzilla for tracking. chris From rutgeraldo at gmail.com Thu Jul 31 02:18:52 2008 From: rutgeraldo at gmail.com (Rutger Vos) Date: Thu, 31 Jul 2008 02:18:52 -0400 Subject: [Bioperl-l] bioperl 1.6 In-Reply-To: <48914045.9040505@open-bio.org> References: <48914045.9040505@open-bio.org> Message-ID: <2bb9b24a0807302318w15d1f764tcb32a6066e330191@mail.gmail.com> I would be interested to hear what sort of timeline you have in mind for 1.6. For a while now, Bio::Phylo has been informally compatible with bioperl, but I'd like to target 1.6 for formal, advertised interoperability. On Thu, Jul 31, 2008 at 12:32 AM, Mauricio Herrera Cuadra wrote: > Chris Fields wrote: >> >> Speaking of, I would like to get test coverage running; should this be set >> up on portal? I may have my hands full with the bug fixes, so if anyone >> would like to step up and take care of that it would be a tremendous help. > > There is a ticket in the OBF Helpdesk queue waiting for me to setup this. > I'll dedicate some time in the weekend to set it up once for all. > > Regards, > Mauricio. > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Dr. Rutger A. Vos Department of zoology University of British Columbia http://www.nexml.org http://rutgervos.blogspot.com From rutgeraldo at gmail.com Thu Jul 31 10:27:15 2008 From: rutgeraldo at gmail.com (Rutger Vos) Date: Thu, 31 Jul 2008 10:27:15 -0400 Subject: [Bioperl-l] Phyloxml In-Reply-To: <0F8894E4-06DD-4688-B5CE-1A06BF111889@uiuc.edu> References: <672E04DC-9AE9-4DC0-B106-BC4C1510D0D8@nist.gov> <0F8894E4-06DD-4688-B5CE-1A06BF111889@uiuc.edu> Message-ID: <2bb9b24a0807310727r77ef53b3me0aeacdaf0615923@mail.gmail.com> The Bio::Phylo approach is as follows: - Bio::Phylo objects masquerade as BioPerl objects by implementing (and inheriting from) their respective interfaces (e.g. Bio::Phylo::Forest::Tree <-> Bio::Tree::TreeI) - BioPerl objects can be unpacked in a new_from_bioperl constructor which returns a Bio::Phylo object On Wed, Jul 30, 2008 at 11:44 AM, Chris Fields wrote: > > On Jul 30, 2008, at 8:58 AM, Arlin Stoltzfus wrote: > >> Jason, et al-- >> >> In regard to the Bio::NEXUS objects, we (Bio::NEXUS team) have the >> aspiration to integrate with BioPerl objects via some coordinated CDAT >> (character-data-and-trees object) super-object that would allow coordinated >> operations like slicing OTUs X, Y and Z out of both the tree and the >> alignment. >> >> But it hasn't really happened. Aaron suggests that there might be a >> lesson here, and maybe its about the folly of designing one great object >> ("One Thing to rule them all; One Thing to find them; One Thing to gather >> all, and in the darkness, bind them"). Anyway, Aaron suggests we should opt >> for a "dumber" (his words) approach such as treating an alignment as an >> "annotation" of a tree. He and Weigang have done some of that. >> >> Yet, I think Rutger might have worked out a smarter approach in >> Bio::Phylo, which (as I understand it) *does* have bindings to BioPerl >> objects. >> >> It might be worth having a summit meeting to work out some strategy to >> solve this problem. We might be able to get support for a meeting or >> hackathon via NESCent if we write a White Paper that lays out a plan aimed >> at 1) object bindings between Bio::Phylo, BioPerl and Bio::NEXUS and 2) some >> coordinated operations, with or without a super-object. The purpose would >> be to expand the power of these Perl libraries to facilitate evolutionary >> analyses. >> >> Any takers? >> >> Arlin > > A hackathon sounds like a good idea. Would NESCent be up for hosting this? > > chris > -- Dr. Rutger A. Vos Department of zoology University of British Columbia http://www.nexml.org http://rutgervos.blogspot.com From bosborne11 at verizon.net Thu Jul 31 10:37:49 2008 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 31 Jul 2008 10:37:49 -0400 Subject: [Bioperl-l] bioperl 1.6 In-Reply-To: References: <48914045.9040505@open-bio.org> <2bb9b24a0807302318w15d1f764tcb32a6066e330191@mail.gmail.com> Message-ID: <6EA5DAA4-F517-452D-BBD1-E3908D77DFB6@verizon.net> Chris, Yes, I volunteered to look at these, and I did take a look. What's not clear to me though is if BioRuby is saying these issues are "nice to fix" but insubstantial or if they are truly important. I'd hesitate to call these a block to releasing 1.6 if they don't block the use of OBDA, and I have no idea if these "block" anyone over at BioRuby or not. To my knowledge these bugs don't appear when one uses OBDA with Bioperl. Specifically, it would be nice to see the code where these bugs show themselves. Brian O. On Jul 31, 2008, at 10:26 AM, Chris Fields wrote: > The two foremost in my mind are (1) OBDA compatibility issues > between various Bio* (BioRuby, for instance) From manchunjohn-ma at uiowa.edu Thu Jul 31 12:46:41 2008 From: manchunjohn-ma at uiowa.edu (John M.C. Ma) Date: Thu, 31 Jul 2008 11:46:41 -0500 Subject: [Bioperl-l] $query in Bio::Tools::Run::Alignment Message-ID: <5486b2980807310946m547f794bkf2d17c209d0f619c@mail.gmail.com> Hi again, Sorry to come again and ask: is the $DB in Bio::Tools::Run::Alignment->run() accept the same things as the database argument in command line Blat? I tried to run this: use Bio::Seq; use Bio::Tools::Run::Primer3; use Bio::Tools::Primer3; use Bio::Seq::PrimedSeq; use Bio::SeqFeature::Primer; use Bio::Tools::Run::Alignment::Blat; my %gene_info; $gene_info{seq}=Bio::Seq->new(-seq=>'[snip sequence]', -id=>'Akr1c6',); my $primer3_handle=Bio::Tools::Run::Primer3->new(-seq=>$gene_info{seq}, -path=>'/home/johnma/primer3-1.1.4/src/primer3_core'); my $primer3_results=$primer3_handle->run(); for my $primer($primer=$primer3_results->next_primer) { my $left_primer=$primer->get_primer('l')->seq; $left_primer->display_id($gene_info{seq}->primary_id()."_F"); my $blat_handle=Bio::Tools::Run::Alignment::Blat->new; my @blat_result_f=$blat_handle->run($left_primer, '~/Genomes/Rat/Genomic/All_chrs'); } Whereas All_chrs is a text file containing paths for all chromosome 2bit files for each line, per Blat requirment. But the output just gave me the Blat help screen plus: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Blat call (/home/johnma/blatSuite.34/blat -out=psl /tmp/G7dJhcOGZ4 /tmp/lDn680q46z) crashed: 65280 STACK: Error::throw STACK: Bio::Root::Root::throw /home/johnma/bioperl-live/Bio/Root/Root.pm:357 STACK: Bio::Tools::Run::Alignment::Blat::_run /home/johnma/bioperl-run/Bio/Tools/Run/Alignment/Blat.pm:250 STACK: Bio::Tools::Run::Alignment::Blat::run /home/johnma/bioperl-run/Bio/Tools/Run/Alignment/Blat.pm:167 STACK: /home/johnma/workspace/NCBI-test/Blat-test.pl:20 ----------------------------------------------------------- I don't know what should I deal with this... Cheers, John From cjfields at uiuc.edu Thu Jul 31 16:01:02 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 31 Jul 2008 15:01:02 -0500 Subject: [Bioperl-l] bioperl 1.6 In-Reply-To: <6EA5DAA4-F517-452D-BBD1-E3908D77DFB6@verizon.net> References: <48914045.9040505@open-bio.org> <2bb9b24a0807302318w15d1f764tcb32a6066e330191@mail.gmail.com> <6EA5DAA4-F517-452D-BBD1-E3908D77DFB6@verizon.net> Message-ID: <522963EF-F7E1-442E-A60C-A71E15BE3C6C@uiuc.edu> On Jul 31, 2008, at 9:37 AM, Brian Osborne wrote: > Chris, > > Yes, I volunteered to look at these, and I did take a look. What's > not clear to me though is if BioRuby is saying these issues are > "nice to fix" but insubstantial or if they are truly important. > > I'd hesitate to call these a block to releasing 1.6 if they don't > block the use of OBDA, and I have no idea if these "block" anyone > over at BioRuby or not. To my knowledge these bugs don't appear when > one uses OBDA with Bioperl. > > Specifically, it would be nice to see the code where these bugs show > themselves. > > > Brian O. Brian, I agree that these don't block the use of OBDA within BioPerl. However I'm worried they possibly block cross-language OBDA use, for instance if one built the flatfile database in BioPerl and used OBDA- specific flatfile adaptors for BioRuby (and possibly vice versa). I think the bug submitter indicated conflicts with OBDA specifications, though you commented about these issues already in the bug reports. I suspect you (and others involved with OBDA)` can more readily identify whether the bug is ours or in BioRuby code, so this is something we should bring up with the BioRuby folks. Regardless, any bioperl-specific fixes related to this can be included in a later point release on the 1.6 branch. chris PS: for those following, the specific bugs are 2336-2339 in bugzilla, and specifically flatfiles via Bio::DB::Flat. From brunovecchi at yahoo.com.ar Thu Jul 31 23:15:19 2008 From: brunovecchi at yahoo.com.ar (Bruno Vecchi) Date: Fri, 01 Aug 2008 00:15:19 -0300 Subject: [Bioperl-l] Bio::Biblio doesn't find articles Message-ID: <48927FC7.5060103@yahoo.com.ar> Hi everyone, I am trying to retrieve bibliographic data using Bio::Biblio, but so far I haven't got any luck. The following code prints zero results whatever the keyword ("atom" in this example) you choose. Could anyone please point me to my mistake? There are no errors in the output, just no articles found. # Beginning of script #/usr/bin/perl -w use strict; use Bio::Biblio; my $bib_obj = Bio::Biblio->new(); my $biblio_results = $bib_obj->find("atom"); print $biblio_results->get_count; # End of script Calling the Bio::Biblio constructor method without parameters sets them to default values, which are: access: soap location: 'http://www.ebi.ac.uk/openbqs/services/MedlineSRS' I also tried using the example script at http://code.open-bio.org/svnweb/index.cgi/bioperl/view/bioperl-live/trunk/scripts/biblio/biblio.PLS with the same result. For instance, trying: biblio.PLS -find Java -find perl Gave the following output: Looking for 'Java'... Found 0 Looking for 'perl'... Found 0 Maybe the URL of the service is out of date? Thanks a lot in advance! Bruno.