From hlapp at drycafe.net Fri Jun 1 10:48:43 2012 From: hlapp at drycafe.net (Hilmar Lapp) Date: Fri, 1 Jun 2012 10:48:43 -0400 Subject: [Bioperl-l] Google groups bioperl-l mirror issue In-Reply-To: References: Message-ID: <6C2BCB18-5691-4DB1-AA1F-CA25D890F854@drycafe.net> Apparently the new Google Groups doesn't support this anymore (or not yet). The admin interface under the respective tab says "This group is configured to archive another mailing () list. This feature is not supported in the new groups UI." It then provides a link to the managing this in the old UI, but there is no such option for setting the remote archive anymore. Bummer. -hilmar On May 31, 2012, at 8:56 AM, Paolo Pavan wrote: > Hello everybody, > This message is just to point out that google groups bioperl-l mirror seems > to not receive threads since about a month. > There is any reason that I have missed for that or is just an issue? > > Regards, > Paolo > > http://groups.google.com/group/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 drycafe dot net : =========================================================== From cjfields at illinois.edu Fri Jun 1 15:22:52 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Fri, 1 Jun 2012 19:22:52 +0000 Subject: [Bioperl-l] Google groups bioperl-l mirror issue In-Reply-To: <6C2BCB18-5691-4DB1-AA1F-CA25D890F854@drycafe.net> References: <6C2BCB18-5691-4DB1-AA1F-CA25D890F854@drycafe.net> Message-ID: <1CB4A8B9-77B3-48C6-92F9-3747537CDFB3@illinois.edu> This also happened with the maker-devel list, but they managed to get things working again. I can look into it. chris On Jun 1, 2012, at 9:48 AM, Hilmar Lapp wrote: > Apparently the new Google Groups doesn't support this anymore (or not yet). The admin interface under the respective tab says "This group is configured to archive another mailing () list. This feature is not supported in the new groups UI." It then provides a link to the managing this in the old UI, but there is no such option for setting the remote archive anymore. > > Bummer. > > -hilmar > > On May 31, 2012, at 8:56 AM, Paolo Pavan wrote: > >> Hello everybody, >> This message is just to point out that google groups bioperl-l mirror seems >> to not receive threads since about a month. >> There is any reason that I have missed for that or is just an issue? >> >> Regards, >> Paolo >> >> http://groups.google.com/group/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 drycafe dot net : > =========================================================== > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From hlapp at drycafe.net Fri Jun 1 15:39:40 2012 From: hlapp at drycafe.net (Hilmar Lapp) Date: Fri, 1 Jun 2012 15:39:40 -0400 Subject: [Bioperl-l] Google groups bioperl-l mirror issue In-Reply-To: <1CB4A8B9-77B3-48C6-92F9-3747537CDFB3@illinois.edu> References: <6C2BCB18-5691-4DB1-AA1F-CA25D890F854@drycafe.net> <1CB4A8B9-77B3-48C6-92F9-3747537CDFB3@illinois.edu> Message-ID: <4CD6BB7B-E4D9-4AE7-A61A-B6D0EEDF0A42@drycafe.net> Maybe they managed to notice and fix it before the option disappeared from the old UI ... On Jun 1, 2012, at 3:22 PM, Fields, Christopher J wrote: > This also happened with the maker-devel list, but they managed to get things working again. I can look into it. > > chris > > On Jun 1, 2012, at 9:48 AM, Hilmar Lapp wrote: > >> Apparently the new Google Groups doesn't support this anymore (or not yet). The admin interface under the respective tab says "This group is configured to archive another mailing () list. This feature is not supported in the new groups UI." It then provides a link to the managing this in the old UI, but there is no such option for setting the remote archive anymore. >> >> Bummer. >> >> -hilmar >> >> On May 31, 2012, at 8:56 AM, Paolo Pavan wrote: >> >>> Hello everybody, >>> This message is just to point out that google groups bioperl-l mirror seems >>> to not receive threads since about a month. >>> There is any reason that I have missed for that or is just an issue? >>> >>> Regards, >>> Paolo >>> >>> http://groups.google.com/group/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 drycafe 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 drycafe dot net : =========================================================== From cjfields at illinois.edu Fri Jun 1 16:00:25 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Fri, 1 Jun 2012 20:00:25 +0000 Subject: [Bioperl-l] Google groups bioperl-l mirror issue In-Reply-To: <4CD6BB7B-E4D9-4AE7-A61A-B6D0EEDF0A42@drycafe.net> References: <6C2BCB18-5691-4DB1-AA1F-CA25D890F854@drycafe.net> <1CB4A8B9-77B3-48C6-92F9-3747537CDFB3@illinois.edu> <4CD6BB7B-E4D9-4AE7-A61A-B6D0EEDF0A42@drycafe.net> Message-ID: Looks as if the email address for the google groups account went inactive. Just re-upped it, let's see if anything shows up? chris On Jun 1, 2012, at 2:39 PM, Hilmar Lapp wrote: > Maybe they managed to notice and fix it before the option disappeared from the old UI ... > > On Jun 1, 2012, at 3:22 PM, Fields, Christopher J wrote: > >> This also happened with the maker-devel list, but they managed to get things working again. I can look into it. >> >> chris >> >> On Jun 1, 2012, at 9:48 AM, Hilmar Lapp wrote: >> >>> Apparently the new Google Groups doesn't support this anymore (or not yet). The admin interface under the respective tab says "This group is configured to archive another mailing () list. This feature is not supported in the new groups UI." It then provides a link to the managing this in the old UI, but there is no such option for setting the remote archive anymore. >>> >>> Bummer. >>> >>> -hilmar >>> >>> On May 31, 2012, at 8:56 AM, Paolo Pavan wrote: >>> >>>> Hello everybody, >>>> This message is just to point out that google groups bioperl-l mirror seems >>>> to not receive threads since about a month. >>>> There is any reason that I have missed for that or is just an issue? >>>> >>>> Regards, >>>> Paolo >>>> >>>> http://groups.google.com/group/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 drycafe 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 drycafe dot net : > =========================================================== > > > > From cjfields at illinois.edu Fri Jun 1 16:03:39 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Fri, 1 Jun 2012 20:03:39 +0000 Subject: [Bioperl-l] Google groups bioperl-l mirror issue In-Reply-To: References: <6C2BCB18-5691-4DB1-AA1F-CA25D890F854@drycafe.net> <1CB4A8B9-77B3-48C6-92F9-3747537CDFB3@illinois.edu> <4CD6BB7B-E4D9-4AE7-A61A-B6D0EEDF0A42@drycafe.net> Message-ID: <62412A5B-A978-45F8-86CD-A4DA6C273F04@illinois.edu> Tada: https://groups.google.com/forum/?hl=en&fromgroups#!topic/bioperl-l/p2gUTNLYA04 chris On Jun 1, 2012, at 3:00 PM, Fields, Christopher J wrote: > Looks as if the email address for the google groups account went inactive. Just re-upped it, let's see if anything shows up? > > chris > > On Jun 1, 2012, at 2:39 PM, Hilmar Lapp wrote: > >> Maybe they managed to notice and fix it before the option disappeared from the old UI ... >> >> On Jun 1, 2012, at 3:22 PM, Fields, Christopher J wrote: >> >>> This also happened with the maker-devel list, but they managed to get things working again. I can look into it. >>> >>> chris >>> >>> On Jun 1, 2012, at 9:48 AM, Hilmar Lapp wrote: >>> >>>> Apparently the new Google Groups doesn't support this anymore (or not yet). The admin interface under the respective tab says "This group is configured to archive another mailing () list. This feature is not supported in the new groups UI." It then provides a link to the managing this in the old UI, but there is no such option for setting the remote archive anymore. >>>> >>>> Bummer. >>>> >>>> -hilmar >>>> >>>> On May 31, 2012, at 8:56 AM, Paolo Pavan wrote: >>>> >>>>> Hello everybody, >>>>> This message is just to point out that google groups bioperl-l mirror seems >>>>> to not receive threads since about a month. >>>>> There is any reason that I have missed for that or is just an issue? >>>>> >>>>> Regards, >>>>> Paolo >>>>> >>>>> http://groups.google.com/group/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 drycafe 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 drycafe dot net : >> =========================================================== >> >> >> >> > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From hlapp at drycafe.net Fri Jun 1 16:19:40 2012 From: hlapp at drycafe.net (Hilmar Lapp) Date: Fri, 1 Jun 2012 16:19:40 -0400 Subject: [Bioperl-l] Google groups bioperl-l mirror issue In-Reply-To: <62412A5B-A978-45F8-86CD-A4DA6C273F04@illinois.edu> References: <6C2BCB18-5691-4DB1-AA1F-CA25D890F854@drycafe.net> <1CB4A8B9-77B3-48C6-92F9-3747537CDFB3@illinois.edu> <4CD6BB7B-E4D9-4AE7-A61A-B6D0EEDF0A42@drycafe.net> <62412A5B-A978-45F8-86CD-A4DA6C273F04@illinois.edu> Message-ID: <9D401A68-91AF-4E07-9B66-8FAA266B130E@drycafe.net> Cool - great detective work, Chris! On Jun 1, 2012, at 4:03 PM, Fields, Christopher J wrote: > Tada: > > https://groups.google.com/forum/?hl=en&fromgroups#!topic/bioperl-l/p2gUTNLYA04 > > chris > > On Jun 1, 2012, at 3:00 PM, Fields, Christopher J wrote: > >> Looks as if the email address for the google groups account went inactive. Just re-upped it, let's see if anything shows up? >> >> chris >> >> On Jun 1, 2012, at 2:39 PM, Hilmar Lapp wrote: >> >>> Maybe they managed to notice and fix it before the option disappeared from the old UI ... >>> >>> On Jun 1, 2012, at 3:22 PM, Fields, Christopher J wrote: >>> >>>> This also happened with the maker-devel list, but they managed to get things working again. I can look into it. >>>> >>>> chris >>>> >>>> On Jun 1, 2012, at 9:48 AM, Hilmar Lapp wrote: >>>> >>>>> Apparently the new Google Groups doesn't support this anymore (or not yet). The admin interface under the respective tab says "This group is configured to archive another mailing () list. This feature is not supported in the new groups UI." It then provides a link to the managing this in the old UI, but there is no such option for setting the remote archive anymore. >>>>> >>>>> Bummer. >>>>> >>>>> -hilmar >>>>> >>>>> On May 31, 2012, at 8:56 AM, Paolo Pavan wrote: >>>>> >>>>>> Hello everybody, >>>>>> This message is just to point out that google groups bioperl-l mirror seems >>>>>> to not receive threads since about a month. >>>>>> There is any reason that I have missed for that or is just an issue? >>>>>> >>>>>> Regards, >>>>>> Paolo >>>>>> >>>>>> http://groups.google.com/group/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 drycafe 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 drycafe 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 drycafe dot net : =========================================================== From cjfields at illinois.edu Fri Jun 1 16:26:06 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Fri, 1 Jun 2012 20:26:06 +0000 Subject: [Bioperl-l] Google groups bioperl-l mirror issue In-Reply-To: <9D401A68-91AF-4E07-9B66-8FAA266B130E@drycafe.net> References: <6C2BCB18-5691-4DB1-AA1F-CA25D890F854@drycafe.net> <1CB4A8B9-77B3-48C6-92F9-3747537CDFB3@illinois.edu> <4CD6BB7B-E4D9-4AE7-A61A-B6D0EEDF0A42@drycafe.net> <62412A5B-A978-45F8-86CD-A4DA6C273F04@illinois.edu> <9D401A68-91AF-4E07-9B66-8FAA266B130E@drycafe.net> Message-ID: We'll lose the intervening month or so of email, unfortunately, don't think Google has a way of pulling those posts in. chris On Jun 1, 2012, at 3:19 PM, Hilmar Lapp wrote: > Cool - great detective work, Chris! > > On Jun 1, 2012, at 4:03 PM, Fields, Christopher J wrote: > >> Tada: >> >> https://groups.google.com/forum/?hl=en&fromgroups#!topic/bioperl-l/p2gUTNLYA04 >> >> chris >> >> On Jun 1, 2012, at 3:00 PM, Fields, Christopher J wrote: >> >>> Looks as if the email address for the google groups account went inactive. Just re-upped it, let's see if anything shows up? >>> >>> chris >>> >>> On Jun 1, 2012, at 2:39 PM, Hilmar Lapp wrote: >>> >>>> Maybe they managed to notice and fix it before the option disappeared from the old UI ... >>>> >>>> On Jun 1, 2012, at 3:22 PM, Fields, Christopher J wrote: >>>> >>>>> This also happened with the maker-devel list, but they managed to get things working again. I can look into it. >>>>> >>>>> chris >>>>> >>>>> On Jun 1, 2012, at 9:48 AM, Hilmar Lapp wrote: >>>>> >>>>>> Apparently the new Google Groups doesn't support this anymore (or not yet). The admin interface under the respective tab says "This group is configured to archive another mailing () list. This feature is not supported in the new groups UI." It then provides a link to the managing this in the old UI, but there is no such option for setting the remote archive anymore. >>>>>> >>>>>> Bummer. >>>>>> >>>>>> -hilmar >>>>>> >>>>>> On May 31, 2012, at 8:56 AM, Paolo Pavan wrote: >>>>>> >>>>>>> Hello everybody, >>>>>>> This message is just to point out that google groups bioperl-l mirror seems >>>>>>> to not receive threads since about a month. >>>>>>> There is any reason that I have missed for that or is just an issue? >>>>>>> >>>>>>> Regards, >>>>>>> Paolo >>>>>>> >>>>>>> http://groups.google.com/group/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 drycafe 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 drycafe 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 drycafe dot net : > =========================================================== > > > > From hnorpois at googlemail.com Tue Jun 5 17:10:13 2012 From: hnorpois at googlemail.com (Hermann Norpois) Date: Tue, 5 Jun 2012 23:10:13 +0200 Subject: [Bioperl-l] (no subject) Message-ID: Hello, actually I wish to get ensembl transcript IDs for some gene names. For addressing this I tried some syntax ( to become more familiar with bioperl and ensembl) but it doesnt work even for easier things, for instance for getting DBEntries. So I guess there is a principal mistake in my script. Can anybody help me? Thanks, Hermann Norpois #!/bin/perl -w use strict; use Bio::EnsEMBL::Registry; my $registry = 'Bio::EnsEMBL::Registry'; $registry->load_registry_from_db( -host => 'ensembldb.ensembl.org', # alternatively ' useastdb.ensembl.org' -user => 'anonymous' ); #my $name = "Bdnf"; my $gene_adaptor = $registry -> get_adaptor( 'Mouse', 'Core', 'Gene'); my $gene = $gene_adaptor->fetch_by_stable_id('ENSG00000184129'); #my $gene = $gene_adaptor -> fetch_all_by_external_name ($name); my @dbentries = @{ $gene->get_all_DBEntries() }; my $info = join (":", @dbentries); print "$info\n"; # print $gene -> seq(), "\n"; From cjfields at illinois.edu Tue Jun 5 17:20:15 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 5 Jun 2012 21:20:15 +0000 Subject: [Bioperl-l] (no subject) In-Reply-To: References: Message-ID: Hermann, You may get an answer here, but for Ensemble-related questions you should post to the Ensembl mail list. Ensembl uses very old (and no longer actively supported) version of BioPerl. chris On Jun 5, 2012, at 4:10 PM, Hermann Norpois wrote: > Hello, > > actually I wish to get ensembl transcript IDs for some gene names. For > addressing this I tried some syntax ( to become more familiar with bioperl > and ensembl) but it doesnt work even for easier things, for instance for > getting DBEntries. So I guess there is a principal mistake in my script. > Can anybody help me? > > Thanks, > Hermann Norpois > > > > #!/bin/perl -w > > use strict; > > > use Bio::EnsEMBL::Registry; > > > my $registry = 'Bio::EnsEMBL::Registry'; > > $registry->load_registry_from_db( > -host => 'ensembldb.ensembl.org', # alternatively ' > useastdb.ensembl.org' > -user => 'anonymous' > ); > > #my $name = "Bdnf"; > my $gene_adaptor = $registry -> get_adaptor( 'Mouse', 'Core', 'Gene'); > my $gene = $gene_adaptor->fetch_by_stable_id('ENSG00000184129'); > #my $gene = $gene_adaptor -> fetch_all_by_external_name ($name); > my @dbentries = @{ $gene->get_all_DBEntries() }; > my $info = join (":", @dbentries); > print "$info\n"; > # print $gene -> seq(), "\n"; > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From miguel.pignatelli at uv.es Wed Jun 6 04:36:55 2012 From: miguel.pignatelli at uv.es (Miguel Pignatelli) Date: Wed, 06 Jun 2012 09:36:55 +0100 Subject: [Bioperl-l] (no subject) In-Reply-To: References: Message-ID: <4FCF16A7.7070600@uv.es> Hi Hermann, Sounds like a problem with the registry. Make sure you have the latest ensembl code and it is accessible via the PERL5LIB. Try to diagnose the problem using the -verbose => 1 flag in load_registry_from_db or by running the script in running ensembl/misc-scripts/ping_ensembl.pl (which tries to diagnose setup problems). You can also try calling a specific version of ensembl and see if there is any difference: $registry->load_registry_from_db( -host => 'ensembldb.ensembl.org', -user => 'anonymous', -verbose => 1, -db_version => 67, ); Hope this helps, M; On 05/06/12 22:10, Hermann Norpois wrote: > use strict; > > > use Bio::EnsEMBL::Registry; > > > my $registry = 'Bio::EnsEMBL::Registry'; > > $registry->load_registry_from_db( > -host => 'ensembldb.ensembl.org', # alternatively' > useastdb.ensembl.org' > -user => 'anonymous' > ); > > #my $name = "Bdnf"; > my $gene_adaptor = $registry -> get_adaptor( 'Mouse', 'Core', 'Gene'); > my $gene = $gene_adaptor->fetch_by_stable_id('ENSG00000184129'); > #my $gene = $gene_adaptor -> fetch_all_by_external_name ($name); > my @dbentries = @{ $gene->get_all_DBEntries() }; > my $info = join (":", @dbentries); > print "$info\n"; > # print $gene -> seq(), "\n"; From jason.stajich at gmail.com Wed Jun 6 18:20:49 2012 From: jason.stajich at gmail.com (Jason Stajich) Date: Wed, 6 Jun 2012 15:20:49 -0700 Subject: [Bioperl-l] Fwd: question References: Message-ID: Please ask your question on the bioperl list too. However, I don't really understand your question. What do you want your output to look like that is difference from this. You should show what code you have been trying so someone can help correct it. Begin forwarded message: > From: Paz Tapia Ram?rez > Subject: Fwd: question > Date: June 6, 2012 3:08:41 PM PDT > To: > > Hello, I've been reading some answers from you in creating of genbank > files with bioperl . I have a question, how it is to set ORGANISM > before FEATURES? > > > SOURCE "My organism" > ORGANISM "My organism" > > FEATURES Location/Qualifiers > source 1..76453 > /organism="Dekkera bruxellensis" > /organelle="mitochondrion" > /mol_type="genomic DNA" > /strain="CBS 2499" > /db_xref="taxon:5007" > gene 1..3643 > /gene="rnl" > > Please help me, > > Best Regards, > > Paz Jason Stajich jason.stajich at gmail.com jason at bioperl.org From Russell.Smithies at agresearch.co.nz Wed Jun 6 21:49:34 2012 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Thu, 7 Jun 2012 13:49:34 +1200 Subject: [Bioperl-l] Fwd: question In-Reply-To: References: Message-ID: <18DF7D20DFEC044098A1062202F5FFF34CCEFC4353@exchsth.agresearch.co.nz> If I read the question right, you want to set the "SOURCE" and "ORGANISM" tags above the "FEATURE" tag. Try here: http://www.bioperl.org/wiki/HOWTO:Feature-Annotation#The_Species_Object Though I note it's deprecated so someone else may be able to offer some assistance. --Russell -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Jason Stajich Sent: Thursday, 7 June 2012 10:21 a.m. To: BioPerl List; Paz Tapia Ram?rez Subject: [Bioperl-l] Fwd: question Please ask your question on the bioperl list too. However, I don't really understand your question. What do you want your output to look like that is difference from this. You should show what code you have been trying so someone can help correct it. Begin forwarded message: > From: Paz Tapia Ram?rez > Subject: Fwd: question > Date: June 6, 2012 3:08:41 PM PDT > To: > > Hello, I've been reading some answers from you in creating of genbank > files with bioperl . I have a question, how it is to set ORGANISM > before FEATURES? > > > SOURCE "My organism" > ORGANISM "My organism" > > FEATURES Location/Qualifiers > source 1..76453 > /organism="Dekkera bruxellensis" > /organelle="mitochondrion" > /mol_type="genomic DNA" > /strain="CBS 2499" > /db_xref="taxon:5007" > gene 1..3643 > /gene="rnl" > > Please help me, > > Best Regards, > > Paz Jason Stajich jason.stajich at gmail.com jason at bioperl.org _______________________________________________ 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 paolo.pavan at gmail.com Thu Jun 7 04:09:42 2012 From: paolo.pavan at gmail.com (Paolo Pavan) Date: Thu, 7 Jun 2012 10:09:42 +0200 Subject: [Bioperl-l] Fwd: Bio::Seq issue In-Reply-To: References: Message-ID: Hello, I have the feeling that the email below was blocked by the mailer daemon because "has a suspicious header", I believe most because has a "patch" file attached so forgive me as I am sending it again. If someone is interested to the file, I can send it not throught the mailing list. Regards, Paolo ---------- Forwarded message ---------- From: Paolo Pavan Date: 2012/5/31 Subject: Bio::Seq issue To: bioperl-l at lists.open-bio.org Hello everyone again, By the way, I think I have encountered a minor issue in the method Bio::Seq->is_circular(), that is defined in the file Bio/Seq.pm as a pure getter as: sub is_circular { shift->primary_seq->is_circular } while it's counterpart in Bio/PrimarySeq.pm is defined as a getter/setter as: sub is_circular{ my $self = shift; return $self->{'is_circular'} = shift if @_; return $self->{'is_circular'}; } the result is that if you have a Bio::Seq object, for instance read by Bio::SeqIO you can't change any more the property (well, unless you do $seq->primary_seq->is_circular($is_circular) ). Do someone agree that they should have the same behaviour? It the case, attached patch file applied to Bio/Seq.pm file should do the job. Best regards, Paolo From l.m.timmermans at students.uu.nl Thu Jun 7 06:04:17 2012 From: l.m.timmermans at students.uu.nl (Leon Timmermans) Date: Thu, 7 Jun 2012 12:04:17 +0200 Subject: [Bioperl-l] Bio::Seq issue In-Reply-To: References: Message-ID: On Thu, May 31, 2012 at 5:34 PM, Paolo Pavan wrote: > Do someone agree that they should have the same behaviour? > It the case, attached patch file applied to Bio/Seq.pm file should do the > job. I agree, but your patch is flawed. Peeking and poking into the internals of another object is a bad idea from a maintenance point of view, it should probably look like sub is_circular { shift->primary_seq->is_circular(@_) } Leon From paolo.pavan at gmail.com Thu Jun 7 06:37:36 2012 From: paolo.pavan at gmail.com (Paolo Pavan) Date: Thu, 7 Jun 2012 12:37:36 +0200 Subject: [Bioperl-l] Bio::Seq issue In-Reply-To: References: Message-ID: No, I didn't already send the patch because the mailer daemon blocked it. It should be like this, also according to the programming style of the PrimarySeq.pm file: 802,803c802,806 < sub is_circular { shift->primary_seq->is_circular } < --- > sub is_circular { > my $self = shift; > return $self->primary_seq->{'is_circular'} = shift if @_; > return $self->primary_seq->{'is_circular'}; > } 2012/6/7 Leon Timmermans > On Thu, May 31, 2012 at 5:34 PM, Paolo Pavan > wrote: > > Do someone agree that they should have the same behaviour? > > It the case, attached patch file applied to Bio/Seq.pm file should do the > > job. > > I agree, but your patch is flawed. Peeking and poking into the > internals of another object is a bad idea from a maintenance point of > view, it should probably look like > > sub is_circular { shift->primary_seq->is_circular(@_) } > > Leon > From p.j.a.cock at googlemail.com Thu Jun 7 06:46:42 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 7 Jun 2012 11:46:42 +0100 Subject: [Bioperl-l] Bio::Seq issue In-Reply-To: References: Message-ID: On Thu, Jun 7, 2012 at 11:37 AM, Paolo Pavan wrote: > No, I didn't already send the patch because the mailer daemon blocked it. > No, it just was just delayed for moderation. It made it to the list: http://lists.open-bio.org/pipermail/bioperl-l/2012-May/036593.html In general any attachment seems to trigger this. Peter From roy.chaudhuri at gmail.com Thu Jun 7 06:42:47 2012 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Thu, 07 Jun 2012 11:42:47 +0100 Subject: [Bioperl-l] Bio::Seq issue In-Reply-To: References: Message-ID: <4FD085A7.6080209@gmail.com> Hi Paolo, I received the first patch from the mailing list, so I think you are mistaken about the mailer daemon. I agree with Leon that it would be better to delegate to Bio::PrimarySeq rather than duplicating the code. Cheers, Roy. On 07/06/2012 11:37, Paolo Pavan wrote: > No, I didn't already send the patch because the mailer daemon blocked it. > > It should be like this, also according to the programming style of the > PrimarySeq.pm file: > > 802,803c802,806 > < sub is_circular { shift->primary_seq->is_circular } > < > --- >> sub is_circular { >> my $self = shift; >> return $self->primary_seq->{'is_circular'} = shift if @_; >> return $self->primary_seq->{'is_circular'}; >> } > > > 2012/6/7 Leon Timmermans > >> On Thu, May 31, 2012 at 5:34 PM, Paolo Pavan >> wrote: >>> Do someone agree that they should have the same behaviour? >>> It the case, attached patch file applied to Bio/Seq.pm file should do the >>> job. >> >> I agree, but your patch is flawed. Peeking and poking into the >> internals of another object is a bad idea from a maintenance point of >> view, it should probably look like >> >> sub is_circular { shift->primary_seq->is_circular(@_) } >> >> Leon >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From paolo.pavan at gmail.com Thu Jun 7 08:20:38 2012 From: paolo.pavan at gmail.com (Paolo Pavan) Date: Thu, 7 Jun 2012 14:20:38 +0200 Subject: [Bioperl-l] Bio::Seq issue In-Reply-To: References: Message-ID: Ah! Ok, I see. You use the primarySeq method instead, I agree, my fault. Actually I meant to write that but I didn't and perl of course does never complain! ;-) And forgive me for the duplicate post, I wasn't sure it was delivered. Bye, Paolo 2012/6/7 Peter Cock > On Thu, Jun 7, 2012 at 11:37 AM, Paolo Pavan > wrote: > > No, I didn't already send the patch because the mailer daemon blocked it. > > > > No, it just was just delayed for moderation. It made it to the list: > http://lists.open-bio.org/pipermail/bioperl-l/2012-May/036593.html > > In general any attachment seems to trigger this. > > Peter > From cjfields at illinois.edu Sat Jun 9 22:45:27 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Sun, 10 Jun 2012 02:45:27 +0000 Subject: [Bioperl-l] EU Codefest Message-ID: <30CAF1E9-8B8F-498C-98BE-32812F18AF97@illinois.edu> Just a reminder that the EU Codefest is coming up! Registration form is here: http://www.open-bio.org/wiki/EU_Codefest_2012 Three main topics will be worked on during the CodeFest: NGS and high performance parsers for OpenBio projects. RDF and semantic web for bioinformatics. Bioinformatics pipelines definition, execution and distribution. but other tracks are more than welcome! chris From hlapp at drycafe.net Sun Jun 10 15:02:51 2012 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sun, 10 Jun 2012 15:02:51 -0400 Subject: [Bioperl-l] Bio::Seq issue In-Reply-To: References: Message-ID: Hi Paolo, Do you have some experience with using git and github? If you fork the repository, make your change, and then send us a pull request, your fix tracks under your username, rather than only a mention in text in a commit message if we applied a patch. See here for documentation: http://www.bioperl.org/wiki/Using_Git#Forking_and_Pull_Requests -hilmar On Jun 7, 2012, at 8:20 AM, Paolo Pavan wrote: > Ah! Ok, I see. You use the primarySeq method instead, I agree, my fault. > Actually I meant to write that but I didn't and perl of course does never > complain! ;-) > And forgive me for the duplicate post, I wasn't sure it was delivered. > > Bye, > Paolo > > 2012/6/7 Peter Cock > >> On Thu, Jun 7, 2012 at 11:37 AM, Paolo Pavan >> wrote: >>> No, I didn't already send the patch because the mailer daemon blocked it. >>> >> >> No, it just was just delayed for moderation. It made it to the list: >> http://lists.open-bio.org/pipermail/bioperl-l/2012-May/036593.html >> >> In general any attachment seems to trigger this. >> >> Peter >> > _______________________________________________ > 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 drycafe dot net : =========================================================== From paolo.pavan at gmail.com Mon Jun 11 09:41:54 2012 From: paolo.pavan at gmail.com (Paolo Pavan) Date: Mon, 11 Jun 2012 15:41:54 +0200 Subject: [Bioperl-l] Bio::Seq issue In-Reply-To: References: Message-ID: Ok, I can do it. Bye bye, Paolo 2012/6/10 Hilmar Lapp > Hi Paolo, > > Do you have some experience with using git and github? If you fork the > repository, make your change, and then send us a pull request, your fix > tracks under your username, rather than only a mention in text in a commit > message if we applied a patch. > > See here for documentation: > http://www.bioperl.org/wiki/Using_Git#Forking_and_Pull_Requests > > -hilmar > > On Jun 7, 2012, at 8:20 AM, Paolo Pavan wrote: > > > Ah! Ok, I see. You use the primarySeq method instead, I agree, my fault. > > Actually I meant to write that but I didn't and perl of course does never > > complain! ;-) > > And forgive me for the duplicate post, I wasn't sure it was delivered. > > > > Bye, > > Paolo > > > > 2012/6/7 Peter Cock > > > >> On Thu, Jun 7, 2012 at 11:37 AM, Paolo Pavan > >> wrote: > >>> No, I didn't already send the patch because the mailer daemon blocked > it. > >>> > >> > >> No, it just was just delayed for moderation. It made it to the list: > >> http://lists.open-bio.org/pipermail/bioperl-l/2012-May/036593.html > >> > >> In general any attachment seems to trigger this. > >> > >> Peter > >> > > _______________________________________________ > > 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 drycafe dot net : > =========================================================== > > > > > From mathematisch at gmail.com Tue Jun 12 06:27:40 2012 From: mathematisch at gmail.com (math math) Date: Tue, 12 Jun 2012 11:27:40 +0100 Subject: [Bioperl-l] seq object usage Message-ID: Hi, consider the following case: A seq object's string field (ie the sequence part) needs to be filled gradually in a PERL loop. The seq object(s) can be hundreds of millions bases long at the end of this loop. The final goal is to write this seq object(s) to an output file (in multi-fasta format). My question is, how can one append progressively more sequence to a seq object (i.e. instead of all at once, to minimize memory), and make sure that these get written to a file. Thanks. From fs5 at sanger.ac.uk Tue Jun 12 09:28:30 2012 From: fs5 at sanger.ac.uk (Frank Schwach) Date: Tue, 12 Jun 2012 14:28:30 +0100 Subject: [Bioperl-l] seq object usage In-Reply-To: References: Message-ID: <4FD743FE.2020504@sanger.ac.uk> the Bio::Seq's "seq" method doesn't take an argument to set a new sequence, so I think you would have to do it like this: $bio_seq_obj->primary_seq( Bio:PrimarySeq->new( -seq => $bio_seq_obj->seq .$some_addition_seq ) ); but it wouldn't save you any memory because you still have the whole sequence in memory. On 12/06/12 11:27, math math wrote: > Hi, > > consider the following case: > > A seq object's string field (ie the sequence part) needs to be filled > gradually in a PERL loop. The seq object(s) can be hundreds of millions > bases long at the end of this loop. The final goal is to write this seq > object(s) to an output file (in multi-fasta format). > > My question is, how can one append progressively more sequence to a seq > object (i.e. instead of all at once, to minimize memory), and make sure > that these get written to a file. > > Thanks. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From challa.ghanashyam at gmail.com Mon Jun 4 23:28:03 2012 From: challa.ghanashyam at gmail.com (Ghana Shyam Challa) Date: Mon, 4 Jun 2012 20:28:03 -0700 (PDT) Subject: [Bioperl-l] Bioper-run installation failed on Mac OS X Lion Message-ID: Hi: I am trying to install bioperl-run on mac os x lion. Bioperl is running on the machine. All the tests failed. Tried installing using CPAN and building it both didn't worked for me. Please help me in this. Challa From kevinfarq at gmail.com Thu Jun 7 15:56:47 2012 From: kevinfarq at gmail.com (Kevin Farquhar) Date: Thu, 7 Jun 2012 14:56:47 -0500 Subject: [Bioperl-l] Issue with HOWTO Beginners Examples from "Retrieving a sequence from a database" and beyond Message-ID: Hi, My Bioperl version is 1.6.1 and it runs on a Windows 7 64 bit Ultimate OS. I'm trying to receive a sequence from the genbank database, but am having no luck. What should I do? Attached to this email is the pl I'm using Here are the errors: C:\Users\Kevin>perl C:\Perl64\lib\Perl\secondbioperl3.pl Name "main::seq_obj" used only once: possible typo at C:\Perl64\lib\Perl\secondb ioperl3.pl line 7. Replacement list is longer than search list at C:/Perl64/site/lib/Bio/Range.pm l ine 251. UNIVERSAL->import is deprecated and will be removed in a future perl at C:/Perl6 4/site/lib/Bio/Tree/TreeFunctionsI.pm line 94 Subroutine new redefined at C:/Perl64/site/lib/Bio\Location\Simple.pm line 93, < GEN1> line 22. Subroutine start redefined at C:/Perl64/site/lib/Bio\Location\Simple.pm line 115 , line 22. Subroutine end redefined at C:/Perl64/site/lib/Bio\Location\Simple.pm line 144, line 22. Subroutine length redefined at C:/Perl64/site/lib/Bio\Location\Simple.pm line 19 0, line 22. Subroutine location_type redefined at C:/Perl64/site/lib/Bio\Location\Simple.pm line 281, line 22. Subroutine to_FTstring redefined at C:/Perl64/site/lib/Bio\Location\Simple.pm li ne 328, line 22. Subroutine trunc redefined at C:/Perl64/site/lib/Bio\Location\Simple.pm line 370 , line 22. C:\Users\Kevin> -------------- next part -------------- A non-text attachment was scrubbed... Name: secondbioperl3.pl Type: application/octet-stream Size: 122 bytes Desc: not available URL: From roy.chaudhuri at gmail.com Tue Jun 12 09:54:55 2012 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Tue, 12 Jun 2012 14:54:55 +0100 Subject: [Bioperl-l] seq object usage In-Reply-To: <4FD743FE.2020504@sanger.ac.uk> References: <4FD743FE.2020504@sanger.ac.uk> Message-ID: <4FD74A2F.5000305@gmail.com> Bio::Seq's seq method just delegates to Bio::PrimarySeq: http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Seq.html#CODE2 So this should work: $bio_seq_obj->seq($bio_seq_obj->seq.$some_addition_seq) You're right about the memory thing though. Math, couldn't you just print out a Fasta file directly rather than using BioPerl? Cheers, Roy. On 12/06/2012 14:28, Frank Schwach wrote: > the Bio::Seq's "seq" method doesn't take an argument to set a new > sequence, so I think you would have to do it like this: > > $bio_seq_obj->primary_seq( > Bio:PrimarySeq->new( > -seq => $bio_seq_obj->seq .$some_addition_seq > ) > ); > > but it wouldn't save you any memory because you still have the whole > sequence in memory. > > > > > On 12/06/12 11:27, math math wrote: >> Hi, >> >> consider the following case: >> >> A seq object's string field (ie the sequence part) needs to be filled >> gradually in a PERL loop. The seq object(s) can be hundreds of millions >> bases long at the end of this loop. The final goal is to write this seq >> object(s) to an output file (in multi-fasta format). >> >> My question is, how can one append progressively more sequence to a seq >> object (i.e. instead of all at once, to minimize memory), and make sure >> that these get written to a file. >> >> Thanks. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Tue Jun 12 11:16:29 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 12 Jun 2012 15:16:29 +0000 Subject: [Bioperl-l] Issue with HOWTO Beginners Examples from "Retrieving a sequence from a database" and beyond In-Reply-To: References: Message-ID: <26249E31-55C1-4C12-9561-FD96E166347E@illinois.edu> Kevin, This is no longer the latest release, but I don't think we have a newer PPM available yet (at least, I don't think we do). The latest on CPAN is v1.6.901. This release updated the code to be compliant with perl 5.12 and up and fixed a few minor bugs, including the 'replacement list' one. IIRC, ActivePerl and Strawberry Perl allow you to install from CPAN. Also, the 'subroutine redefined' errors are generally Windows-specific and are from using the '-w' flag in the script shebang line. Try removing that and see if things quiet down a bit. Regardless, these are simply warnings, not errors. chris On Jun 7, 2012, at 2:56 PM, Kevin Farquhar wrote: > Hi, > > My Bioperl version is 1.6.1 and it runs on a Windows 7 64 bit Ultimate OS. > I'm trying to receive a sequence from the genbank database, but am having > no luck. What should I do? > Attached to this email is the pl I'm using > Here are the errors: > > C:\Users\Kevin>perl C:\Perl64\lib\Perl\secondbioperl3.pl > Name "main::seq_obj" used only once: possible typo at > C:\Perl64\lib\Perl\secondb > ioperl3.pl line 7. > Replacement list is longer than search list at > C:/Perl64/site/lib/Bio/Range.pm l > ine 251. > UNIVERSAL->import is deprecated and will be removed in a future perl at > C:/Perl6 > 4/site/lib/Bio/Tree/TreeFunctionsI.pm line 94 > Subroutine new redefined at C:/Perl64/site/lib/Bio\Location\Simple.pm line > 93, < > GEN1> line 22. > Subroutine start redefined at C:/Perl64/site/lib/Bio\Location\Simple.pm > line 115 > , line 22. > Subroutine end redefined at C:/Perl64/site/lib/Bio\Location\Simple.pm line > 144, > line 22. > Subroutine length redefined at C:/Perl64/site/lib/Bio\Location\Simple.pm > line 19 > 0, line 22. > Subroutine location_type redefined at > C:/Perl64/site/lib/Bio\Location\Simple.pm > line 281, line 22. > Subroutine to_FTstring redefined at > C:/Perl64/site/lib/Bio\Location\Simple.pm li > ne 328, line 22. > Subroutine trunc redefined at C:/Perl64/site/lib/Bio\Location\Simple.pm > line 370 > , line 22. > > C:\Users\Kevin> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From scott at scottcain.net Tue Jun 12 11:24:26 2012 From: scott at scottcain.net (Scott Cain) Date: Tue, 12 Jun 2012 11:24:26 -0400 Subject: [Bioperl-l] Bioper-run installation failed on Mac OS X Lion In-Reply-To: References: Message-ID: HI Chalia, Sorry I missed this in the moderation queue for a week. I don't know much about bioperl-run, but I do have suggestion for your request for help: please provide the complete output from running the tests. It will make it much easier to help you, since you've basically told us nothing about what is going wrong so far. Scott On Mon, Jun 4, 2012 at 11:28 PM, Ghana Shyam Challa wrote: > Hi: > I am trying to install bioperl-run on mac os x lion. Bioperl is > running on the machine. All the tests failed. Tried installing using > CPAN and building it both didn't worked for me. Please help me in > this. > > > Challa > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- ------------------------------------------------------------------------ Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087 Ontario Institute for Cancer Research From cjfields at illinois.edu Tue Jun 12 11:26:49 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 12 Jun 2012 15:26:49 +0000 Subject: [Bioperl-l] seq object usage In-Reply-To: <4FD74A2F.5000305@gmail.com> References: <4FD743FE.2020504@sanger.ac.uk> <4FD74A2F.5000305@gmail.com> Message-ID: <25EBA07A-FF11-4155-AAFB-742F9A94522D@illinois.edu> Bio::LiveSeq is supposed to handle cases like this: http://www.bioperl.org/wiki/HOWTO:Bioperl_Objects#LiveSeq ...but it is severely undocumented. This is one we're planning on pulling out of core and releasing on its own. The code hasn't been updated in quite a while, but it's better than starting from scratch if anyone wants to take it. chris On Jun 12, 2012, at 8:54 AM, Roy Chaudhuri wrote: > Bio::Seq's seq method just delegates to Bio::PrimarySeq: > http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Seq.html#CODE2 > > So this should work: > $bio_seq_obj->seq($bio_seq_obj->seq.$some_addition_seq) > > You're right about the memory thing though. Math, couldn't you just print out a Fasta file directly rather than using BioPerl? > > Cheers, > Roy. > > > On 12/06/2012 14:28, Frank Schwach wrote: >> the Bio::Seq's "seq" method doesn't take an argument to set a new >> sequence, so I think you would have to do it like this: >> >> $bio_seq_obj->primary_seq( >> Bio:PrimarySeq->new( >> -seq => $bio_seq_obj->seq .$some_addition_seq >> ) >> ); >> >> but it wouldn't save you any memory because you still have the whole >> sequence in memory. >> >> >> >> >> On 12/06/12 11:27, math math wrote: >>> Hi, >>> >>> consider the following case: >>> >>> A seq object's string field (ie the sequence part) needs to be filled >>> gradually in a PERL loop. The seq object(s) can be hundreds of millions >>> bases long at the end of this loop. The final goal is to write this seq >>> object(s) to an output file (in multi-fasta format). >>> >>> My question is, how can one append progressively more sequence to a seq >>> object (i.e. instead of all at once, to minimize memory), and make sure >>> that these get written to a file. >>> >>> Thanks. >>> _______________________________________________ >>> 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 illinois.edu Tue Jun 12 11:31:32 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 12 Jun 2012 15:31:32 +0000 Subject: [Bioperl-l] seq object usage In-Reply-To: <25EBA07A-FF11-4155-AAFB-742F9A94522D@illinois.edu> References: <4FD743FE.2020504@sanger.ac.uk> <4FD74A2F.5000305@gmail.com> <25EBA07A-FF11-4155-AAFB-742F9A94522D@illinois.edu> Message-ID: <6F2B1443-268A-45B5-97D5-176C7D832131@illinois.edu> Bio::Seq::LargePrimarySeq/LargeSeq actually is a better fit here than my previous suggestion; note the 'add_sequence_as_string' method: http://search.cpan.org/~cjfields/BioPerl-1.6.901/Bio/Seq/LargeSeq.pm#add_sequence_as_string chris On Jun 12, 2012, at 10:26 AM, Christopher Fields wrote: > Bio::LiveSeq is supposed to handle cases like this: > > http://www.bioperl.org/wiki/HOWTO:Bioperl_Objects#LiveSeq > > ...but it is severely undocumented. This is one we're planning on pulling out of core and releasing on its own. The code hasn't been updated in quite a while, but it's better than starting from scratch if anyone wants to take it. > > chris > > On Jun 12, 2012, at 8:54 AM, Roy Chaudhuri wrote: > >> Bio::Seq's seq method just delegates to Bio::PrimarySeq: >> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Seq.html#CODE2 >> >> So this should work: >> $bio_seq_obj->seq($bio_seq_obj->seq.$some_addition_seq) >> >> You're right about the memory thing though. Math, couldn't you just print out a Fasta file directly rather than using BioPerl? >> >> Cheers, >> Roy. >> >> >> On 12/06/2012 14:28, Frank Schwach wrote: >>> the Bio::Seq's "seq" method doesn't take an argument to set a new >>> sequence, so I think you would have to do it like this: >>> >>> $bio_seq_obj->primary_seq( >>> Bio:PrimarySeq->new( >>> -seq => $bio_seq_obj->seq .$some_addition_seq >>> ) >>> ); >>> >>> but it wouldn't save you any memory because you still have the whole >>> sequence in memory. >>> >>> >>> >>> >>> On 12/06/12 11:27, math math wrote: >>>> Hi, >>>> >>>> consider the following case: >>>> >>>> A seq object's string field (ie the sequence part) needs to be filled >>>> gradually in a PERL loop. The seq object(s) can be hundreds of millions >>>> bases long at the end of this loop. The final goal is to write this seq >>>> object(s) to an output file (in multi-fasta format). >>>> >>>> My question is, how can one append progressively more sequence to a seq >>>> object (i.e. instead of all at once, to minimize memory), and make sure >>>> that these get written to a file. >>>> >>>> Thanks. >>>> _______________________________________________ >>>> 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 alexeymorozov1991 at gmail.com Wed Jun 13 02:27:48 2012 From: alexeymorozov1991 at gmail.com (Alexey Morozov) Date: Wed, 13 Jun 2012 15:27:48 +0900 Subject: [Bioperl-l] Phylogenetic networks. Message-ID: Sup colleagues. I think we could use a couple of things. First, the phylogentic networks. Not the interaction/regulation networks (which is implemented), but generalization of concept of tree (see eg D. Huson et al "Phylogenetic networks: concepts, algorithms and applications"). Seems like network object may inherit from Bio::Tree, though actually it's other way around, and then several objects like splits (aka bifurcations) and maybe some others can be necessary. Second, dealing with genomic rearrangements: at least IO, like writing GRIMM- or MGR-compatible files from genomic RichSeqs, maybe distance metrics and other simple algorithms. I see that both are pretty obscure phylogenetic toys, but they still might get useful. Alexey Morozov LIN SB RAS From l.m.timmermans at students.uu.nl Wed Jun 13 10:19:36 2012 From: l.m.timmermans at students.uu.nl (Leon Timmermans) Date: Wed, 13 Jun 2012 16:19:36 +0200 Subject: [Bioperl-l] Bioper-run installation failed on Mac OS X Lion In-Reply-To: References: Message-ID: On Tue, Jun 5, 2012 at 5:28 AM, Ghana Shyam Challa wrote: > Hi: > I am trying to install bioperl-run on mac os x lion. Bioperl is > running on the machine. All the tests failed. Tried installing using > CPAN and building it both didn't worked for me. Please help me in > this. This is a documented issue. BioPerl-Run depends on external tools, many/most of which are probably not installed on your computer. This is a rather unfortunate situation, and any help changing that by splitting it up into pieces that each only depend on one toolset would probably be most welcome. Leon From cjfields at illinois.edu Wed Jun 13 12:18:29 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Wed, 13 Jun 2012 16:18:29 +0000 Subject: [Bioperl-l] Bioper-run installation failed on Mac OS X Lion In-Reply-To: References: Message-ID: <58169881-0F3D-4A53-966D-93A61EFF028B@illinois.edu> On Jun 13, 2012, at 9:19 AM, Leon Timmermans wrote: > On Tue, Jun 5, 2012 at 5:28 AM, Ghana Shyam Challa > wrote: >> Hi: >> I am trying to install bioperl-run on mac os x lion. Bioperl is >> running on the machine. All the tests failed. Tried installing using >> CPAN and building it both didn't worked for me. Please help me in >> this. > > This is a documented issue. BioPerl-Run depends on external tools, > many/most of which are probably not installed on your computer. This > is a rather unfortunate situation, and any help changing that by > splitting it up into pieces that each only depend on one toolset would > probably be most welcome. > > Leon Agreed, I think we should work on this soon, maybe wrap in relevant parsers and classes if needed (lots of these tie together). It will require a bit of git magic but it is possible. chris From challa.ghanashyam at gmail.com Thu Jun 14 15:19:23 2012 From: challa.ghanashyam at gmail.com (challa.ghanashyam at gmail.com) Date: Thu, 14 Jun 2012 12:19:23 -0700 (PDT) Subject: [Bioperl-l] Bioper-run installation failed on Mac OS X Lion In-Reply-To: References: Message-ID: <48281ec1-0c82-4cd9-95a2-82ef500af444@googlegroups.com> Finally it worked after repeating the force install. I couldn't install XML::Twig on my mac. May be this doesn't allowed the Bioperl run to install smoothly. Thank you all for the help. I appreciate your time. On Monday, June 4, 2012 10:28:03 PM UTC-5, Ghana Shyam Challa wrote: > > Hi: > I am trying to install bioperl-run on mac os x lion. Bioperl is > running on the machine. All the tests failed. Tried installing using > CPAN and building it both didn't worked for me. Please help me in > this. > > > Challa > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From scott at scottcain.net Thu Jun 14 22:17:54 2012 From: scott at scottcain.net (Scott Cain) Date: Thu, 14 Jun 2012 22:17:54 -0400 Subject: [Bioperl-l] GMOD Summer School now accepting applications Message-ID: Applications are now being accepted for the 2012 GMOD Summer School course, a five-day hands-on school aimed at teaching new GMOD administrators how to install, configure and integrate popular GMOD Components. The course will be held August 25-29 at the US National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina. https://docs.google.com/a/scottcain.net/spreadsheet/embeddedform?formkey=dG5hNGFiQ3UwYTV2LUZxZW04Qm1yZXc6MQ These components will be covered at the school: Apollo or WebApollo - genome annotation editor Chado - biological database schema Galaxy - workflow system GBrowse - genome viewer GBrowse_syn - synteny viewer GFF3 - genome annotation file format and tools InterMine - biological data mining system JBrowse - next generation genome browser MAKER - genome annotation pipeline Tripal - web front end to Chado databases The deadline for applying is the end of July 9, 2012. Admission is competitive and is based on the strength of the application, especially the statement of interest. The 2011 school had over 70 applicants for the 25 slots. Any application received after deadline will be automatically placed on the waiting list. The course requires some knowledge of Linux as a prerequisite. The registration fee will be $300 (only $60 per day). There will be a limited number of scholarships available. Thanks, Scott Cain -- ------------------------------------------------------------------------ Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087 Ontario Institute for Cancer Research From du at ibio.jp Fri Jun 15 22:49:23 2012 From: du at ibio.jp (Du, Peng) Date: Sat, 16 Jun 2012 11:49:23 +0900 Subject: [Bioperl-l] Error during installation Message-ID: Hi Bioperl Team, Sorry for sending again. This is a newbie, I encountered a problem while installing bioperl-ext. The error message is : /usr/bin/ld: libs/libsw.a(aln.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC libs/libsw.a: could not read symbols: Bad value collect2: ld returned 1 exit status I googled some solutions, but all of them are confusing, could you tell me where exactly should I add the -fPIC? In the makefile under the bioperl-ext-1.4 directory? I tried to add this to the CCCDLFLAGS, CCDLFLAGS, LDDLFLAGS and LDFLAGS in that file. But it still doesn't work. Could you tell me what to do or where could I find the answer? Thank you very much. Best Regards, Peng -- Peng Du Graduate School of Information Science and Technology, Hokkaido University Kita 14 Nishi 9 Kita-ku, Sapporo, Japan ?060-0814 Email: du at ibio.jp Tel: +81 80 3268 9713 From du at ibio.jp Fri Jun 15 23:28:47 2012 From: du at ibio.jp (Du, Peng) Date: Sat, 16 Jun 2012 12:28:47 +0900 Subject: [Bioperl-l] error during installation Message-ID: Hi everybody, I am a newbie, I encountered a problem while installing bioperl-ext. The error message is : /usr/bin/ld: libs/libsw.a(aln.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC libs/libsw.a: could not read symbols: Bad value collect2: ld returned 1 exit status I googled some solutions, but all of them are confusing, could you tell me where exactly should I add the -fPIC? In the makefile under the bioperl-ext-1.4 directory? I tried to add this to the CCCDLFLAGS, CCDLFLAGS, LDDLFLAGS and LDFLAGS in that file. But it still doesn't work. Could you tell me what to do or where could I find the answer? Thank you very much. Best Regards, Peng -- Peng Du Graduate School of Information Science and Technology, Hokkaido University Kita 14 Nishi 9 Kita-ku, Sapporo, Japan ?060-0814 Email: du at ibio.jp Tel: +81 80 3268 9713 From du at ibio.jp Sat Jun 16 03:57:09 2012 From: du at ibio.jp (Du, Peng) Date: Sat, 16 Jun 2012 16:57:09 +0900 Subject: [Bioperl-l] error during installation In-Reply-To: References: Message-ID: Hi everybody, I fixed this problem by replacing 'libs/libsw$(LIB_EXT)' with '\'-fPIC libs/libsw$(LIB_EXT)\'' in the file bioperl-ext-14.2/Bio/Ext/Align/Makefile.PL according to one post by a kind man ^_^. Many thanks to him. But, when I did make test. Some other errors occurred: chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl 1..2 Can't load '../blib/arch/auto/Bio/Ext/Align/Align.so' for module Bio::Ext::Align: ../blib/arch/auto/Bio/Ext/Align/Align.so: undefined symbol: bp_sw_show_simple_PackAln at /usr/lib/perl/5.14/DynaLoader.pm line 184. at test.pl line 10. Compilation failed in require at test.pl line 10. BEGIN failed--compilation aborted at test.pl line 10. not ok 1 make[1]: *** [test_dynamic] Error 2 Could anybody tell me what I should do next? Thank you, all your replies will be appreciated~~~ On Sat, Jun 16, 2012 at 12:28 PM, Du, Peng wrote: > Hi everybody, > > I am a newbie, I encountered a problem while installing bioperl-ext. > The error message is : > > > /usr/bin/ld: libs/libsw.a(aln.o): relocation R_X86_64_32 against > `.rodata.str1.8' can not be used when making a shared object; > recompile with -fPIC > libs/libsw.a: could not read symbols: Bad value > collect2: ld returned 1 exit status > > I googled some solutions, but all of them are confusing, could you > tell me where exactly should I add the -fPIC? In the makefile under > the bioperl-ext-1.4 directory? ?I tried to add this to the CCCDLFLAGS, > CCDLFLAGS, LDDLFLAGS and LDFLAGS in that file. But it still doesn't > work. > > Could you tell me what to do or where could I find the answer? > > Thank you very much. > > Best Regards, > Peng > > -- > > Peng Du > Graduate School of Information Science and Technology, Hokkaido University > Kita 14 Nishi 9 Kita-ku, Sapporo, Japan ?060-0814 > Email: du at ibio.jp Tel: +81 80 3268 9713 -- Peng Du Graduate School of Information Science and Technology, Hokkaido University Kita 14 Nishi 9 Kita-ku, Sapporo, Japan ?060-0814 Email: du at ibio.jp Tel: +81 80 3268 9713 From l.m.timmermans at students.uu.nl Sat Jun 16 04:50:35 2012 From: l.m.timmermans at students.uu.nl (Leon Timmermans) Date: Sat, 16 Jun 2012 10:50:35 +0200 Subject: [Bioperl-l] error during installation In-Reply-To: References: Message-ID: On Sat, Jun 16, 2012 at 5:28 AM, Du, Peng wrote: > Hi everybody, > > I am a newbie, I encountered a problem while installing bioperl-ext. > The error message is : > > > /usr/bin/ld: libs/libsw.a(aln.o): relocation R_X86_64_32 against > `.rodata.str1.8' can not be used when making a shared object; > recompile with -fPIC > libs/libsw.a: could not read symbols: Bad value > collect2: ld returned 1 exit status > > I googled some solutions, but all of them are confusing, could you > tell me where exactly should I add the -fPIC? In the makefile under > the bioperl-ext-1.4 directory? ?I tried to add this to the CCCDLFLAGS, > CCDLFLAGS, LDDLFLAGS and LDFLAGS in that file. But it still doesn't > work. >f > Could you tell me what to do or where could I find the answer? > > Thank you very much. > > Best Regards, > Peng You should not install it in the first place. BioPerl-ext has been partly merged into the main Bioperl distribution, and partly spun off into its own dists (Bio::Tools::HMM, not released yet AFAIK). You should just install the former, or help release the latter. Leon From cjfields at illinois.edu Sat Jun 16 13:43:26 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Sat, 16 Jun 2012 17:43:26 +0000 Subject: [Bioperl-l] error during installation In-Reply-To: References: Message-ID: <38A300A1-F7E0-40FA-A5A7-8D72CCE65A44@illinois.edu> On Jun 16, 2012, at 3:50 AM, Leon Timmermans wrote: > On Sat, Jun 16, 2012 at 5:28 AM, Du, Peng wrote: >> Hi everybody, >> >> I am a newbie, I encountered a problem while installing bioperl-ext. >> The error message is : >> >> >> /usr/bin/ld: libs/libsw.a(aln.o): relocation R_X86_64_32 against >> `.rodata.str1.8' can not be used when making a shared object; >> recompile with -fPIC >> libs/libsw.a: could not read symbols: Bad value >> collect2: ld returned 1 exit status >> >> I googled some solutions, but all of them are confusing, could you >> tell me where exactly should I add the -fPIC? In the makefile under >> the bioperl-ext-1.4 directory? I tried to add this to the CCCDLFLAGS, >> CCDLFLAGS, LDDLFLAGS and LDFLAGS in that file. But it still doesn't >> work. >> f >> Could you tell me what to do or where could I find the answer? >> >> Thank you very much. >> >> Best Regards, >> Peng > > You should not install it in the first place. BioPerl-ext has been > partly merged into the main Bioperl distribution, and partly spun off > into its own dists (Bio::Tools::HMM, not released yet AFAIK). You > should just install the former, or help release the latter. > > Leon For all intents and purposes I would consider all parts (past and present) of bioperl-ext deprecated, unless we can find someone willing to take them on. And, with that in mind, frankly I would be much more amenable to supporting XS (or similar) interfaces to common bioinformatics libraries (Bio::DB::Sam as an example) than ones specifically designed with bioperl in mind. The latter (bioperl-ext) have significantly bit-rotted to the point I'm not sure whether they would be worth keeping around. chris From du at ibio.jp Sat Jun 16 18:15:49 2012 From: du at ibio.jp (Peng Du) Date: Sun, 17 Jun 2012 07:15:49 +0900 Subject: [Bioperl-l] error during installation In-Reply-To: <38A300A1-F7E0-40FA-A5A7-8D72CCE65A44@illinois.edu> References: <38A300A1-F7E0-40FA-A5A7-8D72CCE65A44@illinois.edu> Message-ID: Thank you for all your replies. So,what do you suggest me do if I want to do alignment with external tools like clustawl or dpalign? In the current distribution of BioPerl, ext package is still required to do this, I am afraid. Thank you. Sent from my iPhone On 2012/06/17, at 2:43, "Fields, Christopher J" wrote: > On Jun 16, 2012, at 3:50 AM, Leon Timmermans wrote: > >> On Sat, Jun 16, 2012 at 5:28 AM, Du, Peng wrote: >>> Hi everybody, >>> >>> I am a newbie, I encountered a problem while installing bioperl-ext. >>> The error message is : >>> >>> >>> /usr/bin/ld: libs/libsw.a(aln.o): relocation R_X86_64_32 against >>> `.rodata.str1.8' can not be used when making a shared object; >>> recompile with -fPIC >>> libs/libsw.a: could not read symbols: Bad value >>> collect2: ld returned 1 exit status >>> >>> I googled some solutions, but all of them are confusing, could you >>> tell me where exactly should I add the -fPIC? In the makefile under >>> the bioperl-ext-1.4 directory? I tried to add this to the CCCDLFLAGS, >>> CCDLFLAGS, LDDLFLAGS and LDFLAGS in that file. But it still doesn't >>> work. >>> f >>> Could you tell me what to do or where could I find the answer? >>> >>> Thank you very much. >>> >>> Best Regards, >>> Peng >> >> You should not install it in the first place. BioPerl-ext has been >> partly merged into the main Bioperl distribution, and partly spun off >> into its own dists (Bio::Tools::HMM, not released yet AFAIK). You >> should just install the former, or help release the latter. >> >> Leon > > > For all intents and purposes I would consider all parts (past and present) of bioperl-ext deprecated, unless we can find someone willing to take them on. And, with that in mind, frankly I would be much more amenable to supporting XS (or similar) interfaces to common bioinformatics libraries (Bio::DB::Sam as an example) than ones specifically designed with bioperl in mind. The latter (bioperl-ext) have significantly bit-rotted to the point I'm not sure whether they would be worth keeping around. > > chris From cjfields at illinois.edu Sun Jun 17 01:21:36 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Sun, 17 Jun 2012 05:21:36 +0000 Subject: [Bioperl-l] error during installation In-Reply-To: References: <38A300A1-F7E0-40FA-A5A7-8D72CCE65A44@illinois.edu> Message-ID: On Jun 16, 2012, at 5:15 PM, Peng Du wrote: > Thank you for all your replies. > > So,what do you suggest me do if I want to do alignment with external tools like clustawl or dpalign? In the current distribution of BioPerl, ext package is still required to do this, I am afraid. No, you should only need bioperl-run to run clustalw, and bioperl core modules to parse it. If you have anything from those packages that is failing from a lack of bioperl-ext we need to know about it (preferably with code examples and errors encountered). chris > Thank you. > > Sent from my iPhone > > On 2012/06/17, at 2:43, "Fields, Christopher J" wrote: > >> On Jun 16, 2012, at 3:50 AM, Leon Timmermans wrote: >> >>> On Sat, Jun 16, 2012 at 5:28 AM, Du, Peng wrote: >>>> Hi everybody, >>>> >>>> I am a newbie, I encountered a problem while installing bioperl-ext. >>>> The error message is : >>>> >>>> >>>> /usr/bin/ld: libs/libsw.a(aln.o): relocation R_X86_64_32 against >>>> `.rodata.str1.8' can not be used when making a shared object; >>>> recompile with -fPIC >>>> libs/libsw.a: could not read symbols: Bad value >>>> collect2: ld returned 1 exit status >>>> >>>> I googled some solutions, but all of them are confusing, could you >>>> tell me where exactly should I add the -fPIC? In the makefile under >>>> the bioperl-ext-1.4 directory? I tried to add this to the CCCDLFLAGS, >>>> CCDLFLAGS, LDDLFLAGS and LDFLAGS in that file. But it still doesn't >>>> work. >>>> f >>>> Could you tell me what to do or where could I find the answer? >>>> >>>> Thank you very much. >>>> >>>> Best Regards, >>>> Peng >>> >>> You should not install it in the first place. BioPerl-ext has been >>> partly merged into the main Bioperl distribution, and partly spun off >>> into its own dists (Bio::Tools::HMM, not released yet AFAIK). You >>> should just install the former, or help release the latter. >>> >>> Leon >> >> >> For all intents and purposes I would consider all parts (past and present) of bioperl-ext deprecated, unless we can find someone willing to take them on. And, with that in mind, frankly I would be much more amenable to supporting XS (or similar) interfaces to common bioinformatics libraries (Bio::DB::Sam as an example) than ones specifically designed with bioperl in mind. The latter (bioperl-ext) have significantly bit-rotted to the point I'm not sure whether they would be worth keeping around. >> >> chris From du at ibio.jp Sun Jun 17 01:37:03 2012 From: du at ibio.jp (Du, Peng) Date: Sun, 17 Jun 2012 14:37:03 +0900 Subject: [Bioperl-l] Fwd: error during installation In-Reply-To: References: <38A300A1-F7E0-40FA-A5A7-8D72CCE65A44@illinois.edu> Message-ID: ---------- Forwarded message ---------- From: Du, Peng Date: Sun, Jun 17, 2012 at 2:33 PM Subject: Re: [Bioperl-l] error during installation To: "Fields, Christopher J" Thank you, the current code is use Bio::Root::IO; use Bio::SearchIO; use Bio::Seq; use Bio::SeqIO; use File::Spec; use Params::Check; use Bio::Factory::ApplicationFactoryI; use Bio::SeqFeature::Gene::Transcript; use Bio::EnsEMBL::Registry; use Getopt::Long; use Bio::SimpleAlign; use Bio::Tools::dpAlign; use Bio::Tools::AlignFactory; use Bio::Ext::Align; use Bio::Tools::RepeatMasker; use Bio::LocatableSeq ; use Bio::Tools::Run::Alignment::Clustalw; # some other codes if($align_method eq "dpAlign"){ ? ? ? ? ? ? ? ?$factory= new Bio::Tools::dpAlign(-match => 3, ? ? ? ? ? ? ? ? ? ? -mismatch => -1,# change this to avoid the mismatch to see what is going to happen ? ? ? ? ? ? ? ? ? ? -gap => 3, ? ? ? ? ? ? ? ? ? ? -ext => 1, ? ? ? ? ? ? ? ? ? ? -alg => Bio::Tools::dpAlign::DPALIGN_GLOBAL_MILLER_MYERS);#Or, we should use global ? ? ? ?} ? ? ? ?else { ? ? ? ? ? ? ? ?$factory = Bio::Tools::Run::Alignment::Clustalw->new(); ? ? ? ?} if($align_method eq "dpAlign"){ $alignment=$factory->pairwise_alignment($seq_one, $seq_two); ? ? ? ? ? ? ? ? ? ? ? ?} ? ? ? ? ? ? ? ? ? ? ? ?else{ ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?@two_seqs_array=(); ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?@two_seqs_array=($seq_one, $seq_two); ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?$seq_array_ref = \@two_seqs_array; ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?$alignment=$factory->align($seq_array_ref); ? ? ? ? ? ? ? ? ? ? ? ?} At present, I want to use dpAlign, I don't know I still need bio-ext to perform dpAlign or I could modify my code to achieve this without bio-ext package. Thank you. On Sun, Jun 17, 2012 at 2:21 PM, Fields, Christopher J wrote: > On Jun 16, 2012, at 5:15 PM, Peng Du wrote: > >> Thank you for all your replies. >> >> So,what do you suggest me do if I want to do alignment with external tools like clustawl or dpalign? In the current distribution of BioPerl, ext package is still required to do this, I am afraid. > > No, you should only need bioperl-run to run clustalw, and bioperl core modules to parse it. ?If you have anything from those packages that is failing from a lack of bioperl-ext we need to know about it (preferably with code examples and errors encountered). > > chris > >> Thank you. >> >> Sent from my iPhone >> >> On 2012/06/17, at 2:43, "Fields, Christopher J" wrote: >> >>> On Jun 16, 2012, at 3:50 AM, Leon Timmermans wrote: >>> >>>> On Sat, Jun 16, 2012 at 5:28 AM, Du, Peng wrote: >>>>> Hi everybody, >>>>> >>>>> I am a newbie, I encountered a problem while installing bioperl-ext. >>>>> The error message is : >>>>> >>>>> >>>>> /usr/bin/ld: libs/libsw.a(aln.o): relocation R_X86_64_32 against >>>>> `.rodata.str1.8' can not be used when making a shared object; >>>>> recompile with -fPIC >>>>> libs/libsw.a: could not read symbols: Bad value >>>>> collect2: ld returned 1 exit status >>>>> >>>>> I googled some solutions, but all of them are confusing, could you >>>>> tell me where exactly should I add the -fPIC? In the makefile under >>>>> the bioperl-ext-1.4 directory? ?I tried to add this to the CCCDLFLAGS, >>>>> CCDLFLAGS, LDDLFLAGS and LDFLAGS in that file. But it still doesn't >>>>> work. >>>>> f >>>>> Could you tell me what to do or where could I find the answer? >>>>> >>>>> Thank you very much. >>>>> >>>>> Best Regards, >>>>> Peng >>>> >>>> You should not install it in the first place. BioPerl-ext has been >>>> partly merged into the main Bioperl distribution, and partly spun off >>>> into its own dists (Bio::Tools::HMM, not released yet AFAIK). You >>>> should just install the former, or help release the latter. >>>> >>>> Leon >>> >>> >>> For all intents and purposes I would consider all parts (past and present) of bioperl-ext deprecated, unless we can find someone willing to take them on. ?And, with that in mind, frankly I would be much more amenable to supporting XS (or similar) interfaces to common bioinformatics libraries (Bio::DB::Sam as an example) than ones specifically designed with bioperl in mind. ?The latter (bioperl-ext) have significantly bit-rotted to the point I'm not sure whether they would be worth keeping around. >>> >>> chris > -- Peng Du Graduate School of Information Science and Technology, Hokkaido University Kita 14 Nishi 9 Kita-ku, Sapporo, Japan ?060-0814 Email: du at ibio.jp Tel: +81 80 3268 9713 -- Peng Du Graduate School of Information Science and Technology, Hokkaido University Kita 14 Nishi 9 Kita-ku, Sapporo, Japan ?060-0814 Email: du at ibio.jp Tel: +81 80 3268 9713 From l.m.timmermans at students.uu.nl Sun Jun 17 07:01:02 2012 From: l.m.timmermans at students.uu.nl (Leon Timmermans) Date: Sun, 17 Jun 2012 13:01:02 +0200 Subject: [Bioperl-l] error during installation In-Reply-To: References: <38A300A1-F7E0-40FA-A5A7-8D72CCE65A44@illinois.edu> Message-ID: On Sun, Jun 17, 2012 at 7:37 AM, Du, Peng wrote: > At present, I want to use dpAlign, I don't know I still need bio-ext > to perform dpAlign or I could modify my code to achieve this without > bio-ext package. > Thank you. Bio::Tools::dpAlign is in the main BioPerl distribution, as can be seen here: https://metacpan.org/module/Bio::Tools::dpAlign. You will need to take out that ?use Bio::Ext::Align;?, but you don't seem to be using it anyway. Leon From du at ibio.jp Sun Jun 17 07:16:17 2012 From: du at ibio.jp (Du, Peng) Date: Sun, 17 Jun 2012 20:16:17 +0900 Subject: [Bioperl-l] error during installation In-Reply-To: References: <38A300A1-F7E0-40FA-A5A7-8D72CCE65A44@illinois.edu> Message-ID: Sorry for that, actually I am using it, but I forgot to paste the code in which I invoked "pairwise_alignment" with dpAlign. At the same time, I met another problem regarding "ClustalW". The error message was"MSG ClustalW call align crashed -1". It might be because of incorrect installation of BioPerl-run. But, I didn't encounter any error message while installing it. Thank all of you. Peng On Sun, Jun 17, 2012 at 8:01 PM, Leon Timmermans wrote: > On Sun, Jun 17, 2012 at 7:37 AM, Du, Peng wrote: >> At present, I want to use dpAlign, I don't know I still need bio-ext >> to perform dpAlign or I could modify my code to achieve this without >> bio-ext package. >> Thank you. > > Bio::Tools::dpAlign is in the main BioPerl distribution, as can be > seen here: https://metacpan.org/module/Bio::Tools::dpAlign. You will > need to take out that ?use Bio::Ext::Align;?, but you don't seem to be > using it anyway. > > Leon -- Peng Du Graduate School of Information Science and Technology, Hokkaido University Kita 14 Nishi 9 Kita-ku, Sapporo, Japan ?060-0814 Email: du at ibio.jp Tel: +81 80 3268 9713 From bubli_thakur at rediffmail.com Sat Jun 16 23:18:56 2012 From: bubli_thakur at rediffmail.com (subarna thakur) Date: 17 Jun 2012 03:18:56 -0000 Subject: [Bioperl-l] =?utf-8?q?Ks_saturation?= Message-ID: <20120617031856.16345.qmail@f4mail-235-140.rediffmail.com> Dear all,I am trying to calculate dn/ds values of  all orthologous gene pair between a pair of genome using pairwsie_kaks.pl script within bioperl which evokes the codeml program in runmode -2. When I am analyzing the results, some of the genes have anomalously high dS or Ks values and some of them even reaching more than 100 as a result of which the average value of Ks for the whole genome  shots up. These genes are orthologous genes and even share more than 50% sequence identity. Should I consider these genes for the anlysis or left them out. If I left them out, then upto what cutoff value of Ks should I consider for analysis. In some papers, I have found that they have considered Ks values as high as 5.6. Is there a way for determining the cutoff value for Ks? Subarna   From du at ibio.jp Fri Jun 15 22:47:19 2012 From: du at ibio.jp (Du, Peng) Date: Sat, 16 Jun 2012 11:47:19 +0900 Subject: [Bioperl-l] Error occurred during installation Message-ID: Hi Bioperl Team, This is a newbie, I encountered a problem while installing bioperl-ext. The error message is : /usr/bin/ld: libs/libsw.a(aln.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC libs/libsw.a: could not read symbols: Bad value collect2: ld returned 1 exit status I googled some solutions, but all of them are confusing, could you tell me where exactly should I add the -fPIC? In the makefile under the bioperl-ext-1.4 directory? I tried to add this to the CCCDLFLAGS, CCDLFLAGS, LDDLFLAGS and LDFLAGS in that file. But it still doesn't work. Could you tell me what to do or where could I find the answer? Thank you very much. Best Regards, Peng -- Peng Du Graduate School of Information Science and Technology, Hokkaido University Kita 14 Nishi 9 Kita-ku, Sapporo, Japan ?060-0814 Email: du at ibio.jp Tel: +81 80 3268 9713 From roy.chaudhuri at gmail.com Tue Jun 19 09:48:10 2012 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Tue, 19 Jun 2012 14:48:10 +0100 Subject: [Bioperl-l] Ks saturation In-Reply-To: <20120617031856.16345.qmail@f4mail-235-140.rediffmail.com> References: <20120617031856.16345.qmail@f4mail-235-140.rediffmail.com> Message-ID: <4FE0831A.4010403@gmail.com> Hi Subarna, These are PAML specific questions rather than anything directly related to BioPerl (since BioPerl is just acting as a wrapper around codeml), so it would be better to ask your question here: https://www.ucl.ac.uk/discussions/viewforum.php?f=54 Cheers, Roy. On 17/06/2012 04:18, subarna thakur wrote: > > Dear all,I am trying to calculate dn/ds values of  all > orthologous gene pair between a pair of genome using pairwsie_kaks.pl > script within bioperl which evokes the codeml program in runmode -2. > When I am analyzing the results, some of the genes > have anomalously high dS or Ks values and some of them even > reaching more than 100 as a result of which the average value of Ks > for the whole genome  shots up. These genes are orthologous > genes and even share more than 50% sequence identity. Should I > consider these genes for the anlysis or left them out. If I left them > out, then upto what cutoff value of Ks should I consider for > analysis. In some papers, I have found that they have considered Ks > values as high as 5.6. Is there a way for determining the cutoff > value for Ks? Subarna   > _______________________________________________ Bioperl-l mailing > list Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Tue Jun 19 10:14:09 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 19 Jun 2012 14:14:09 +0000 Subject: [Bioperl-l] error during installation In-Reply-To: References: <38A300A1-F7E0-40FA-A5A7-8D72CCE65A44@illinois.edu> Message-ID: <97904033-3500-46D6-872C-C9693DB7E64A@illinois.edu> This seems specifically like a clustalw problem (the error code is a giveaway). What version of clustalw is this? It should run with more recent versions. Re: dpalign, is there something that module specifically does that other tools can't provide? If it proves useful I would rather move it and all related tools into it's own distribution for separate release (so any bugs can be fixed more readily w/o relying on core changes). chris On Jun 17, 2012, at 6:16 AM, Du, Peng wrote: > Sorry for that, actually I am using it, but I forgot to paste the code > in which I invoked "pairwise_alignment" with dpAlign. > At the same time, I met another problem regarding "ClustalW". The > error message was"MSG ClustalW call align crashed -1". It might be > because of incorrect installation of BioPerl-run. But, I didn't > encounter any error message while installing it. > > Thank all of you. > > Peng > > On Sun, Jun 17, 2012 at 8:01 PM, Leon Timmermans > wrote: >> On Sun, Jun 17, 2012 at 7:37 AM, Du, Peng wrote: >>> At present, I want to use dpAlign, I don't know I still need bio-ext >>> to perform dpAlign or I could modify my code to achieve this without >>> bio-ext package. >>> Thank you. >> >> Bio::Tools::dpAlign is in the main BioPerl distribution, as can be >> seen here: https://metacpan.org/module/Bio::Tools::dpAlign. You will >> need to take out that ?use Bio::Ext::Align;?, but you don't seem to be >> using it anyway. >> >> Leon > > > > -- > > Peng Du > Graduate School of Information Science and Technology, Hokkaido University > Kita 14 Nishi 9 Kita-ku, Sapporo, Japan 060-0814 > Email: du at ibio.jp Tel: +81 80 3268 9713 From du at ibio.jp Tue Jun 19 11:25:42 2012 From: du at ibio.jp (Du, Peng) Date: Wed, 20 Jun 2012 00:25:42 +0900 Subject: [Bioperl-l] error during installation In-Reply-To: <97904033-3500-46D6-872C-C9693DB7E64A@illinois.edu> References: <38A300A1-F7E0-40FA-A5A7-8D72CCE65A44@illinois.edu> <97904033-3500-46D6-872C-C9693DB7E64A@illinois.edu> Message-ID: As to the Clustalw problem, it turned out that, I didn't install it in the first place, I am very sorry for the stupid mistake. It is alright now. But, as to dpAlign, I compared the alignment of non coding regions of two species with dpAlign (in an Intel x86 but much slower machine where dpAlign is good) and Clustalw respectively and checked the output, I found that, each with default parameters, the alignments by dpAlign were better than that by Clustalw, and there was a tremendous difference in the outputs in terms of A<=>G, C<=>T, AG<=>CT substitutional rate and divergence by Tamura-Nei Model between the two alignments. The values are much smaller with dpAlign. Since I am a newbie, I don't quite understand why there was such a difference. Is it might because of the Clustalw is designed for multiple alignment or the default parameters are not appropriate? I am now investigating other tools available in the main distribution of BioPerl, but I have no idea whether there is a good substitution of dpAlign in context of non coding region alignment. Thank you very much. On Tue, Jun 19, 2012 at 11:14 PM, Fields, Christopher J wrote: > This seems specifically like a clustalw problem (the error code is a giveaway). ?What version of clustalw is this? ?It should run with more recent versions. > > Re: dpalign, is there something that module specifically does that other tools can't provide? ? If it proves useful I would rather move it and all related tools into it's own distribution for separate release (so any bugs can be fixed more readily w/o relying on core changes). > > chris > > On Jun 17, 2012, at 6:16 AM, Du, Peng wrote: > >> Sorry for that, actually I am using it, but I forgot to paste the code >> in which I invoked "pairwise_alignment" with dpAlign. >> At the same time, I met another problem regarding "ClustalW". The >> error message was"MSG ClustalW call align crashed -1". It might be >> because of incorrect installation of BioPerl-run. But, I didn't >> encounter any error message while installing it. >> >> Thank all of you. >> >> Peng >> >> On Sun, Jun 17, 2012 at 8:01 PM, Leon Timmermans >> wrote: >>> On Sun, Jun 17, 2012 at 7:37 AM, Du, Peng wrote: >>>> At present, I want to use dpAlign, I don't know I still need bio-ext >>>> to perform dpAlign or I could modify my code to achieve this without >>>> bio-ext package. >>>> Thank you. >>> >>> Bio::Tools::dpAlign is in the main BioPerl distribution, as can be >>> seen here: https://metacpan.org/module/Bio::Tools::dpAlign. You will >>> need to take out that ?use Bio::Ext::Align;?, but you don't seem to be >>> using it anyway. >>> >>> Leon >> >> >> >> -- >> >> Peng Du >> Graduate School of Information Science and Technology, Hokkaido University >> Kita 14 Nishi 9 Kita-ku, Sapporo, Japan ?060-0814 >> Email: du at ibio.jp Tel: +81 80 3268 9713 > -- Peng Du Graduate School of Information Science and Technology, Hokkaido University Kita 14 Nishi 9 Kita-ku, Sapporo, Japan ?060-0814 Email: du at ibio.jp Tel: +81 80 3268 9713 From l.m.timmermans at students.uu.nl Tue Jun 19 13:21:47 2012 From: l.m.timmermans at students.uu.nl (Leon Timmermans) Date: Tue, 19 Jun 2012 19:21:47 +0200 Subject: [Bioperl-l] error during installation In-Reply-To: References: <38A300A1-F7E0-40FA-A5A7-8D72CCE65A44@illinois.edu> <97904033-3500-46D6-872C-C9693DB7E64A@illinois.edu> Message-ID: On Tue, Jun 19, 2012 at 5:25 PM, Du, Peng wrote: > As to the Clustalw problem, it turned out that, I didn't install it in > the first place, I am very sorry for the stupid mistake. It is alright > now. But, as to dpAlign, I compared the alignment of non coding > regions of two species with dpAlign (in an Intel x86 but much slower > machine where dpAlign is good) and Clustalw respectively and checked > the output, I found that, each with default parameters, the alignments > by dpAlign were better than that by Clustalw, and there was a > tremendous difference in the outputs in terms of A<=>G, C<=>T, AG<=>CT > substitutional rate and divergence by Tamura-Nei Model between the two > alignments. The values are much smaller with dpAlign. ?Since I am a > newbie, I don't quite understand why there was such a difference. Is > it might because of the Clustalw is designed for multiple alignment or > the default parameters are not appropriate? > > I am now investigating other tools available in the main distribution > of ?BioPerl, but I have no idea whether there is a good substitution > of dpAlign in context of non coding region alignment. ClustalW uses a heuristic algorithm, it cannot produce a solution that is guaranteed to be optimal. dpAlign uses the Miller-Myers algorithm (a variant on Needleman-Wunch), that does make such guarantees. It should be slower but may produce a better alignment. Leon From cjfields at illinois.edu Tue Jun 19 13:38:04 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 19 Jun 2012 17:38:04 +0000 Subject: [Bioperl-l] error during installation In-Reply-To: References: <38A300A1-F7E0-40FA-A5A7-8D72CCE65A44@illinois.edu> <97904033-3500-46D6-872C-C9693DB7E64A@illinois.edu> Message-ID: <0280F56F-B9C2-45FC-8B57-28BAE1DB0A7C@illinois.edu> On Jun 19, 2012, at 12:21 PM, Leon Timmermans wrote: > On Tue, Jun 19, 2012 at 5:25 PM, Du, Peng wrote: >> As to the Clustalw problem, it turned out that, I didn't install it in >> the first place, I am very sorry for the stupid mistake. It is alright >> now. But, as to dpAlign, I compared the alignment of non coding >> regions of two species with dpAlign (in an Intel x86 but much slower >> machine where dpAlign is good) and Clustalw respectively and checked >> the output, I found that, each with default parameters, the alignments >> by dpAlign were better than that by Clustalw, and there was a >> tremendous difference in the outputs in terms of A<=>G, C<=>T, AG<=>CT >> substitutional rate and divergence by Tamura-Nei Model between the two >> alignments. The values are much smaller with dpAlign. Since I am a >> newbie, I don't quite understand why there was such a difference. Is >> it might because of the Clustalw is designed for multiple alignment or >> the default parameters are not appropriate? >> >> I am now investigating other tools available in the main distribution >> of BioPerl, but I have no idea whether there is a good substitution >> of dpAlign in context of non coding region alignment. > > ClustalW uses a heuristic algorithm, it cannot produce a solution that > is guaranteed to be optimal. dpAlign uses the Miller-Myers algorithm > (a variant on Needleman-Wunch), that does make such guarantees. It > should be slower but may produce a better alignment. > > Leon Agreed. I think it would be worth pulling this out and releasing it on it's own, maybe including Bio::Tools::dpAlign with it as well. The key problem is one of maintenance; this code was pretty much written by one developer. I'll see if I can track Yee Man (the developer) down. chris From du at ibio.jp Tue Jun 19 22:20:00 2012 From: du at ibio.jp (Peng Du) Date: Wed, 20 Jun 2012 11:20:00 +0900 Subject: [Bioperl-l] error during installation In-Reply-To: <0280F56F-B9C2-45FC-8B57-28BAE1DB0A7C@illinois.edu> References: <38A300A1-F7E0-40FA-A5A7-8D72CCE65A44@illinois.edu> <97904033-3500-46D6-872C-C9693DB7E64A@illinois.edu> <0280F56F-B9C2-45FC-8B57-28BAE1DB0A7C@illinois.edu> Message-ID: <68F9A8E5-7A51-4BBD-9015-B7C007DCC505@ibio.jp> Thanks for all your kind replies, based on my current knowledge, it might be worth making dpAlign at work even in the absence of BioPerl-ext package. Thank you. Peng On 2012/06/20, at 2:38, "Fields, Christopher J" wrote: > On Jun 19, 2012, at 12:21 PM, Leon Timmermans wrote: > >> On Tue, Jun 19, 2012 at 5:25 PM, Du, Peng wrote: >>> As to the Clustalw problem, it turned out that, I didn't install it in >>> the first place, I am very sorry for the stupid mistake. It is alright >>> now. But, as to dpAlign, I compared the alignment of non coding >>> regions of two species with dpAlign (in an Intel x86 but much slower >>> machine where dpAlign is good) and Clustalw respectively and checked >>> the output, I found that, each with default parameters, the alignments >>> by dpAlign were better than that by Clustalw, and there was a >>> tremendous difference in the outputs in terms of A<=>G, C<=>T, AG<=>CT >>> substitutional rate and divergence by Tamura-Nei Model between the two >>> alignments. The values are much smaller with dpAlign. Since I am a >>> newbie, I don't quite understand why there was such a difference. Is >>> it might because of the Clustalw is designed for multiple alignment or >>> the default parameters are not appropriate? >>> >>> I am now investigating other tools available in the main distribution >>> of BioPerl, but I have no idea whether there is a good substitution >>> of dpAlign in context of non coding region alignment. >> >> ClustalW uses a heuristic algorithm, it cannot produce a solution that >> is guaranteed to be optimal. dpAlign uses the Miller-Myers algorithm >> (a variant on Needleman-Wunch), that does make such guarantees. It >> should be slower but may produce a better alignment. >> >> Leon > > Agreed. I think it would be worth pulling this out and releasing it on it's own, maybe including Bio::Tools::dpAlign with it as well. The key problem is one of maintenance; this code was pretty much written by one developer. I'll see if I can track Yee Man (the developer) down. > > chris From du at ibio.jp Fri Jun 22 00:25:46 2012 From: du at ibio.jp (Du, Peng) Date: Fri, 22 Jun 2012 13:25:46 +0900 Subject: [Bioperl-l] error during installation In-Reply-To: <68F9A8E5-7A51-4BBD-9015-B7C007DCC505@ibio.jp> References: <38A300A1-F7E0-40FA-A5A7-8D72CCE65A44@illinois.edu> <97904033-3500-46D6-872C-C9693DB7E64A@illinois.edu> <0280F56F-B9C2-45FC-8B57-28BAE1DB0A7C@illinois.edu> <68F9A8E5-7A51-4BBD-9015-B7C007DCC505@ibio.jp> Message-ID: Hi everybody, I tried to install this on another machine and also failed. The error message which are the same for the two machines and the cpu information for them are attached below. So, could anybody help me figure out where this is wrong or, if there is any chance that the developers can do something with it? Thank you very much. Machine 0: CPU info. processor : 0 vendor_id : AuthenticAMD cpu family : 15 model : 33 model name : Dual Core AMD Opteron(tm) Processor 280 stepping : 2 microcode : 0x4d cpu MHz : 2405.233 cache size : 1024 KB physical id : 0 siblings : 2 core id : 0 cpu cores : 2 apicid : 0 initial apicid : 0 fpu : yes fpu_exception : yes cpuid level : 1 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt lm 3dnowext 3dnow rep_good nopl pni lahf_lm cmp_legacy bogomips : 4810.46 TLB size : 1024 4K pages clflush size : 64 cache_alignment : 64 address sizes : 40 bits physical, 48 bits virtual power management: ts fid vid ttp Machine 1 CPU info. processor : 0 vendor_id : GenuineIntel cpu family : 6 model : 26 model name : Intel(R) Core(TM) i7 CPU 920 @ 2.67GHz stepping : 5 cpu MHz : 1600.000 cache size : 8192 KB physical id : 0 siblings : 8 core id : 0 cpu cores : 4 apicid : 0 initial apicid : 0 fpu : yes fpu_exception : yes cpuid level : 11 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm sse4_1 sse4_2 popcnt lahf_lm ida tpr_shadow vnmi flexpriority ept vpid bogomips : 5345.11 clflush size : 64 cache_alignment : 64 address sizes : 36 bits physical, 48 bits virtual power management: Error message for both sudo make test make[1]: Entering directory `/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align' DEFINE='-DPOSIX -DNOERROR'; CC='cc'; export DEFINE INC CC; \ cd libs && make CC=cc libsw.a -e make[2]: Entering directory `/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align/libs' make[2]: `libsw.a' is up to date. make[2]: Leaving directory `/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align/libs' DEFINE='-DPOSIX -DNOERROR'; CC='cc'; export DEFINE INC CC; \ cd libs && make CC=cc libsw.a -e make[2]: Entering directory `/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align/libs' make[2]: `libsw.a' is up to date. make[2]: Leaving directory `/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align/libs' rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so rm: cannot remove `../blib/arch/auto/Bio/Ext/Align/Align.so': Permission denied make[1]: *** [../blib/arch/auto/Bio/Ext/Align/Align.so] Error 1 make[1]: Leaving directory `/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align' make: *** [subdirs] Error 2 ibio at ibio-H8DAR-T:~/Downloads/bioperl-ext-1.4/Bio/Ext$ sudo make test make[1]: Entering directory `/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align' DEFINE='-DPOSIX -DNOERROR'; CC='cc'; export DEFINE INC CC; \ cd libs && make CC=cc libsw.a -e make[2]: Entering directory `/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align/libs' make[2]: `libsw.a' is up to date. make[2]: Leaving directory `/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align/libs' DEFINE='-DPOSIX -DNOERROR'; CC='cc'; export DEFINE INC CC; \ cd libs && make CC=cc libsw.a -e make[2]: Entering directory `/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align/libs' make[2]: `libsw.a' is up to date. make[2]: Leaving directory `/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align/libs' rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so cc -shared -O2 -g -L/usr/local/lib -fstack-protector Align.o -o ../blib/arch/auto/Bio/Ext/Align/Align.so '-fPIC libs/libsw.a' \ -lm \ chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so make[1]: Leaving directory `/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align' make[1]: Entering directory `/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align' DEFINE='-DPOSIX -DNOERROR'; CC='cc'; export DEFINE INC CC; \ cd libs && make CC=cc libsw.a -e make[2]: Entering directory `/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align/libs' make[2]: `libsw.a' is up to date. make[2]: Leaving directory `/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align/libs' DEFINE='-DPOSIX -DNOERROR'; CC='cc'; export DEFINE INC CC; \ cd libs && make CC=cc libsw.a -e make[2]: Entering directory `/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align/libs' make[2]: `libsw.a' is up to date. make[2]: Leaving directory `/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align/libs' rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so cc -shared -O2 -g -L/usr/local/lib -fstack-protector Align.o -o ../blib/arch/auto/Bio/Ext/Align/Align.so '-fPIC libs/libsw.a' \ -lm \ chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl 1..2 Can't load '../blib/arch/auto/Bio/Ext/Align/Align.so' for module Bio::Ext::Align: ../blib/arch/auto/Bio/Ext/Align/Align.so: undefined symbol: bp_sw_show_simple_PackAln at /usr/lib/perl/5.14/DynaLoader.pm line 184. at test.pl line 10. Compilation failed in require at test.pl line 10. BEGIN failed--compilation aborted at test.pl line 10. not ok 1 make[1]: *** [test_dynamic] Error 2 make[1]: Leaving directory `/home/ibio/Downloads/bioperl-ext-1.4/Bio/Ext/Align' make: *** [subdirs-test] Error 2 Thanks again. Peng On Wed, Jun 20, 2012 at 11:20 AM, Peng Du wrote: > > Thanks for all your kind replies, based on my current knowledge, it might be worth making dpAlign at work even in the absence of BioPerl-ext package. > Thank you. > > Peng > > On 2012/06/20, at 2:38, "Fields, Christopher J" wrote: > >> On Jun 19, 2012, at 12:21 PM, Leon Timmermans wrote: >> >>> On Tue, Jun 19, 2012 at 5:25 PM, Du, Peng wrote: >>>> As to the Clustalw problem, it turned out that, I didn't install it in >>>> the first place, I am very sorry for the stupid mistake. It is alright >>>> now. But, as to dpAlign, I compared the alignment of non coding >>>> regions of two species with dpAlign (in an Intel x86 but much slower >>>> machine where dpAlign is good) and Clustalw respectively and checked >>>> the output, I found that, each with default parameters, the alignments >>>> by dpAlign were better than that by Clustalw, and there was a >>>> tremendous difference in the outputs in terms of A<=>G, C<=>T, AG<=>CT >>>> substitutional rate and divergence by Tamura-Nei Model between the two >>>> alignments. The values are much smaller with dpAlign. ?Since I am a >>>> newbie, I don't quite understand why there was such a difference. Is >>>> it might because of the Clustalw is designed for multiple alignment or >>>> the default parameters are not appropriate? >>>> >>>> I am now investigating other tools available in the main distribution >>>> of ?BioPerl, but I have no idea whether there is a good substitution >>>> of dpAlign in context of non coding region alignment. >>> >>> ClustalW uses a heuristic algorithm, it cannot produce a solution that >>> is guaranteed to be optimal. dpAlign uses the Miller-Myers algorithm >>> (a variant on Needleman-Wunch), that does make such guarantees. It >>> should be slower but may produce a better alignment. >>> >>> Leon >> >> Agreed. ?I think it would be worth pulling this out and releasing it on it's own, maybe including Bio::Tools::dpAlign with it as well. ?The key problem is one of maintenance; this code was pretty much written by one developer. ?I'll see if I can track Yee Man (the developer) down. >> >> chris -- Peng Du Graduate School of Information Science and Technology, Hokkaido University Kita 14 Nishi 9 Kita-ku, Sapporo, Japan ?060-0814 Email: du at ibio.jp Tel: +81 80 3268 9713 From ankh.egypt.public at googlemail.com Sun Jun 24 09:44:49 2012 From: ankh.egypt.public at googlemail.com (ak2083) Date: Sun, 24 Jun 2012 06:44:49 -0700 (PDT) Subject: [Bioperl-l] get html-output on my prompt Message-ID: <34061631.post@talk.nabble.com> Hello, i try to blast a protein sequence (in sequence.fasta) against the blast-db. If i parse this with the command 'perl file.pl', then the programm displayed html-code on my prompt and the out-file was not created. What could i do so that the results write into the out-file? my $report = $blast_obj->submit_blast('sequence.fasta'); my $x = 0; print STDERR "waiting..." if ($x > 0); while (my @rids = $blast_obj->each_rid() && $x == 5) { foreach my $rid (@rids) { my $rc = $blast_obj->retrieve_blast($rid); if (!ref($rc)) { if ($rc < 0) { $blast_obj->remove_rid($rid); } print STDERR "." if ($x > 0); sleep 5; } else { my $result = $rc->next_result(); my $filename = $result->query_name(), '\.out'; $blast_obj->save_output($filename); $blast_obj->remove_rid($rid); print "\nQuery Name: ", $result->query_name(); while (my $hit = $result->next_hit()) { next unless ($x > 0); print "\thit name is ", $hit->name, "\n"; while (my $hsp = $hit->next_hsp()) { print "\t\tscore is ", $hsp->score(), "\n"; } } } } } -- View this message in context: http://old.nabble.com/get-html-output-on-my-prompt-tp34061631p34061631.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From maquino at knome.com Sun Jun 24 09:51:46 2012 From: maquino at knome.com (Mark Aquino) Date: Sun, 24 Jun 2012 13:51:46 +0000 Subject: [Bioperl-l] get html-output on my prompt In-Reply-To: <34061631.post@talk.nabble.com> References: <34061631.post@talk.nabble.com> Message-ID: <92909D83-ECF8-4D0C-85E8-BA4EB7C0441A@knome.com> Your use of the $x variable prevents you from ever entering the while loop at the beginning of the program. You also use it in loops elsewhere, but nowhere in the code do you have an incrementer. Sent from my iPhone On Jun 24, 2012, at 9:46 AM, "ak2083" wrote: > > Hello, > > i try to blast a protein sequence (in sequence.fasta) against the blast-db. > If i parse this > with the command 'perl file.pl', then the programm displayed html-code on my > prompt and the out-file > was not created. What could i do so that the results write into the > out-file? > > my $report = $blast_obj->submit_blast('sequence.fasta'); > my $x = 0; > print STDERR "waiting..." if ($x > 0); > > while (my @rids = $blast_obj->each_rid() && $x == 5) > { > foreach my $rid (@rids) > { > my $rc = $blast_obj->retrieve_blast($rid); > if (!ref($rc)) > { > if ($rc < 0) > { $blast_obj->remove_rid($rid); } > print STDERR "." if ($x > 0); > sleep 5; > } > else > { > my $result = $rc->next_result(); > my $filename = $result->query_name(), '\.out'; > $blast_obj->save_output($filename); > $blast_obj->remove_rid($rid); > print "\nQuery Name: ", $result->query_name(); > > while (my $hit = $result->next_hit()) > { > next unless ($x > 0); > print "\thit name is ", $hit->name, "\n"; > > while (my $hsp = $hit->next_hsp()) > { > print "\t\tscore is ", $hsp->score(), "\n"; > } > } > } > } > } > -- > View this message in context: http://old.nabble.com/get-html-output-on-my-prompt-tp34061631p34061631.html > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From ankh.egypt.public at googlemail.com Tue Jun 26 13:00:41 2012 From: ankh.egypt.public at googlemail.com (ak2083) Date: Tue, 26 Jun 2012 10:00:41 -0700 (PDT) Subject: [Bioperl-l] blastp results and the scientific name Message-ID: <34073767.post@talk.nabble.com> I've blast a protein sequence with blastp. How could i get the scientific name from these hits? I tried with the accession number but this is unsuccessful. Could someone help me? -- View this message in context: http://old.nabble.com/blastp-results-and-the-scientific-name-tp34073767p34073767.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From jonathanmflowers at gmail.com Tue Jun 26 13:35:49 2012 From: jonathanmflowers at gmail.com (Jonathan Flowers) Date: Tue, 26 Jun 2012 13:35:49 -0400 Subject: [Bioperl-l] blastp results and the scientific name In-Reply-To: <34073767.post@talk.nabble.com> References: <34073767.post@talk.nabble.com> Message-ID: You should first parse the blast report using Bio::SearchIO. Then you can extract a "description" which usually contains the species binomial (genus, species) plus additional information using $hit->description. The first two words of the about string are usually the genus and species but this isn't always the case. As you mentioned, the other approach is to extract the accession using $hit->accession and then query a database with the accession number. On Tue, Jun 26, 2012 at 1:00 PM, ak2083 wrote: > > I've blast a protein sequence with blastp. How could i get the > scientific name from these hits? I tried with the accession number > but this is unsuccessful. Could someone help me? > -- > View this message in context: > http://old.nabble.com/blastp-results-and-the-scientific-name-tp34073767p34073767.html > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From du at ibio.jp Tue Jun 26 21:28:00 2012 From: du at ibio.jp (Du, Peng) Date: Wed, 27 Jun 2012 10:28:00 +0900 Subject: [Bioperl-l] PAML problem Message-ID: Hi everyone, I am using bioperl to parse paml output, and I saw this ------------- EXCEPTION: Bio::Root::NotImplemented ------------- MSG: Unknown format of PAML output did not see seqtype STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368 STACK: Bio::Tools::Phylo::PAML::_parse_summary /usr/local/share/perl/5.10.1/Bio/Tools/Phylo/PAML.pm:461 STACK: Bio::Tools::Phylo::PAML::next_result /usr/local/share/perl/5.10.1/Bio/Tools/Phylo/PAML.pm:270 STACK: main::cal_dn_ds dn_ds.pl:131 STACK: dn_ds.pl:44 ---------------------------------------------------------------- I googled and found that, it was caused by PAML version incompatibility. I tried 3.13, 3.14, 4.1, 4.2, 4.5 and none of them worked. Could someone tell me which version is fine? My bioperl version is 1.006001. Thank you very much. -- Peng Du Graduate School of Information Science and Technology, Hokkaido University Kita 14 Nishi 9 Kita-ku, Sapporo, Japan ?060-0814 Email: du at ibio.jp Tel: +81 80 3268 9713 From jason.stajich at gmail.com Tue Jun 26 21:37:55 2012 From: jason.stajich at gmail.com (Jason Stajich) Date: Tue, 26 Jun 2012 18:37:55 -0700 Subject: [Bioperl-l] PAML problem In-Reply-To: References: Message-ID: <75365EA6-399D-4E89-A8BA-C0E1ED8871E8@gmail.com> Peng - This module needs a person who's sole job is to keep tracking bugs and updating it with new versions of the program. so far it has burned out several developers on working on it since it not stable. I am not sure what the answer is to the problem, but often it depends on the extra parameters used as this changes the order of the output making it hard to parse. So I don't have a solution for you except that you'll have to post the bug and the problem output mlc file to redmine and hope that we can entice some developers to bang their head against this some more. Jason On Jun 26, 2012, at 6:28 PM, Du, Peng wrote: > Hi everyone, > > I am using bioperl to parse paml output, and I saw this > > ------------- EXCEPTION: Bio::Root::NotImplemented ------------- > MSG: Unknown format of PAML output did not see seqtype > STACK: Error::throw > STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368 > STACK: Bio::Tools::Phylo::PAML::_parse_summary > /usr/local/share/perl/5.10.1/Bio/Tools/Phylo/PAML.pm:461 > STACK: Bio::Tools::Phylo::PAML::next_result > /usr/local/share/perl/5.10.1/Bio/Tools/Phylo/PAML.pm:270 > STACK: main::cal_dn_ds dn_ds.pl:131 > STACK: dn_ds.pl:44 > ---------------------------------------------------------------- > > I googled and found that, it was caused by PAML version > incompatibility. I tried 3.13, 3.14, 4.1, 4.2, 4.5 and none of them > worked. Could someone tell me which version is fine? > > My bioperl version is 1.006001. Thank you very much. > > -- > > Peng Du > Graduate School of Information Science and Technology, Hokkaido University > Kita 14 Nishi 9 Kita-ku, Sapporo, Japan 060-0814 > Email: du at ibio.jp Tel: +81 80 3268 9713 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Jason Stajich jason.stajich at gmail.com jason at bioperl.org From ankh.egypt.public at googlemail.com Sun Jun 24 06:29:00 2012 From: ankh.egypt.public at googlemail.com (ak2083) Date: Sun, 24 Jun 2012 03:29:00 -0700 (PDT) Subject: [Bioperl-l] get html-output on my prompt Message-ID: <34061631.post@talk.nabble.com> Hello, i try to blast a protein sequence (in sequence.fasta) against the blast-db. If i parse this with the command 'perl file.pl', then the programm displayed html-code on my prompt and the out-file was not created. What could i do so that the results write into the out-file? my $report = $blast_obj->submit_blast('sequence.fasta'); my $x = 0; print STDERR "waiting..." if ($x > 0); while (my @rids = $blast_obj->each_rid() && $x == 5) { foreach my $rid (@rids) { my $rc = $blast_obj->retrieve_blast($rid); if (!ref($rc)) { if ($rc < 0) { $blast_obj->remove_rid($rid); } print STDERR "." if ($x > 0); sleep 5; } else { my $result = $rc->next_result(); my $filename = $result->query_name(), '\.out'; $blast_obj->save_output($filename); $blast_obj->remove_rid($rid); print "\nQuery Name: ", $result->query_name(); while (my $hit = $result->next_hit()) { next unless ($x > 0); print "\thit name is ", $hit->name, "\n"; while (my $hsp = $hit->next_hsp()) { print "\t\tscore is ", $hsp->score(), "\n"; } } } } } -- View this message in context: http://old.nabble.com/get-html-output-on-my-prompt-tp34061631p34061631.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From kjetil at kjernsmo.net Tue Jun 26 10:06:59 2012 From: kjetil at kjernsmo.net (Kjetil Kjernsmo) Date: Tue, 26 Jun 2012 16:06:59 +0200 Subject: [Bioperl-l] Moving to Moose hackathon Message-ID: <201206261607.01102.kjetil@kjernsmo.net> All, Oslo.pm is organizing a hackathon from August 25th to 30th at Preikestolen Mountain Lodge: http://act.yapc.eu/mtmh2012/ I'm sorry that I didn't think about the Bioperl community earlier, as we officially closed registration yesterday, but we are unofficially able to accept registrations another two days. :-) The main reason why I think it might interest the Bioperl community is that we will do a major reengineering of the RDF code to bring it on the top of the Moose object system. In particular, we will try to create a much more flexible system to better exploit high-performance triple stores. For those who have corporate sponsorships, there are professional tickets, we hope that those who can afford one buys one to support the rest of the efforts. For members of the community, there are these discount codes: Community653cabin3 (Share a 3-bed room, cabin, 653 EUR) Community782cabin2 (Share a 2-bed room, cabin, 782 EUR) Community938cabin1 (Your own room, cabin, 938 EUR) Community955hotel3 (Share a 3-bed room, hotel, 955 EUR) Community1040hotel2 (Share a 2-bed room, hotel, 1040 EUR) Community1300hotel1 (Your own room, hotel, 1300 EUR) Please let me know if there are any questions. Best, Kjetil -- Kjetil Kjernsmo PhD Research Fellow, University of Oslo, Norway Semantic Web / SPARQL Query Federation kjetil at kjernsmo.net http://www.kjetil.kjernsmo.net/ From frech.christian at gmail.com Wed Jun 27 01:58:36 2012 From: frech.christian at gmail.com (Christian Frech) Date: Tue, 26 Jun 2012 22:58:36 -0700 (PDT) Subject: [Bioperl-l] Rendering multi-exon gene models from genbank input file Message-ID: <764d79a5-24a8-4eab-a365-05a388c8e96e@googlegroups.com> Hi all, can someone please lay out the proper BioPerl procedure that renders Bio::Graphics gene models (displaying UTRs, CDS, and introns) given a genbank entry as input? In particular, CDS and mRNA split locations specified as joins() in the genbank entry should be resolved correctly as exons and introns. I am aware of embl2picture.pl and Bio::SeqFeature::Tools::Unflattener, but so far both did not give me a completely satisfactory solution to this problem. Thanks a lot, Christian