From mh6 at sanger.ac.uk Thu Dec 1 11:30:22 2011 From: mh6 at sanger.ac.uk (Michael Paulini) Date: Thu, 01 Dec 2011 16:30:22 +0000 Subject: [BioRuby] EMBL / ENA parser error Message-ID: <4ED7AB9E.7050709@sanger.ac.uk> Hi fellow biorubysts, I tried to parse EMBL/ENA entry DQ471885 with the bioruby EMBL parser, and it dies when it tries to parse: OS uncultured nematode due to the regexp in embl/common.rb being: ================================== if tmp =~ /([A-Z][a-z]* *[\w\d \:\'\+\-]+[\w\d])/ org = $1 tmp =~ /(\(.+\))/ os.push({'name' => $1, 'os' => org}) else raise "Error: OS Line. #{$!}\n#{fetch('OS')}\n" end ================================ as it doesn't start with an uppercase letter. Shouud we change the regexp, or file a bug with ENA? thanks, Michael -- 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 pjotr.public14 at thebird.nl Mon Dec 5 06:51:05 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 5 Dec 2011 12:51:05 +0100 Subject: [BioRuby] Announcing Bio-Affy Message-ID: <20111205115105.GA29115@thebird.nl> Rubyistas, I just released bio-affy, which is a Affymetrix microarray file format parser (CEL/CDF) for Ruby. The plugin uses both Ruby and C. This Biogem is an FFI binding to R/Bioconductor's Affyio package: http://www.bioconductor.org/packages/2.2/bioc/html/affyio.html What is interesting about this Biogem/BioRuby plugin is not only that it uses FFI to map C code to Ruby, but also fires up the R interpreter to support the Affyio internal function calls into Rlib. The FFI binding also accesses internal C structs of my Affyio adapter. See the examples in https://github.com/pjotrp/bioruby-affy/blob/master/spec/bio-affy_spec.rb Pj. PS. We will create Biogem scaffolding for FFI support in the near future, as well as for SWIG and native Ruby extensions. FFI is interesting as it has good support across all Ruby versions (including JRuby). From bonnal at ingm.org Mon Dec 5 10:47:40 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 05 Dec 2011 16:47:40 +0100 Subject: [BioRuby] Announcing Bio-Affy In-Reply-To: <20111205115105.GA29115@thebird.nl> Message-ID: Amazing! Yep, FFI is something we'll support :-) On 05/12/11 12.51, "Pjotr Prins" wrote: > Rubyistas, > > I just released bio-affy, which is a Affymetrix microarray file format > parser (CEL/CDF) for Ruby. The plugin uses both Ruby and C. > > This Biogem is an FFI binding to R/Bioconductor's Affyio package: > > http://www.bioconductor.org/packages/2.2/bioc/html/affyio.html > > What is interesting about this Biogem/BioRuby plugin is not only that > it uses FFI to map C code to Ruby, but also fires up the R interpreter > to support the Affyio internal function calls into Rlib. > > The FFI binding also accesses internal C structs of my Affyio adapter. > See the examples in > > https://github.com/pjotrp/bioruby-affy/blob/master/spec/bio-affy_spec.rb > > Pj. > > PS. We will create Biogem scaffolding for FFI support in the near > future, as well as for SWIG and native Ruby extensions. FFI is > interesting as it has good support across all Ruby versions > (including JRuby). > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From ngoto at gen-info.osaka-u.ac.jp Wed Dec 7 11:32:49 2011 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Thu, 8 Dec 2011 01:32:49 +0900 Subject: [BioRuby] EMBL / ENA parser error In-Reply-To: <4ED7AB9E.7050709@sanger.ac.uk> References: <4ED7AB9E.7050709@sanger.ac.uk> Message-ID: <20111207163250.C42C91CBC3C4@idnmail.gen-info.osaka-u.ac.jp> Hi Michael, We must first read official documents provided by EMBL-EBI. EMBL User Manual: http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html In "3.4.7 The OS Line", two examples that don't start with an uppercase letter are shown. > OS unidentified bacterium B8 > OS uncultured proteobacterium Therefore, the issue should be treated as a bug of BioRuby. The regexp and/or the logic for OS lines will be changed. Thank you for reporting the issue, Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org On Thu, 01 Dec 2011 16:30:22 +0000 Michael Paulini wrote: > Hi fellow biorubysts, > > I tried to parse EMBL/ENA entry DQ471885 with the bioruby EMBL parser, > and it dies when it tries to parse: > OS uncultured nematode > > due to the regexp in embl/common.rb being: > ================================== > if tmp =~ /([A-Z][a-z]* *[\w\d \:\'\+\-]+[\w\d])/ > org = $1 > tmp =~ /(\(.+\))/ > os.push({'name' => $1, 'os' => org}) > else > raise "Error: OS Line. #{$!}\n#{fetch('OS')}\n" > end > ================================ > as it doesn't start with an uppercase letter. > > Shouud we change the regexp, or file a bug with ENA? > > thanks, > > Michael > > > -- > 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. > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From p.j.a.cock at googlemail.com Thu Dec 8 16:34:50 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 8 Dec 2011 21:34:50 +0000 Subject: [BioRuby] BioRuby BuildBot failure report emails? Message-ID: Dear all, Who should we send the BuildBot failure emails to, if anyone? This will be one email per failure - so if there is a problem that affects all N build targets, you'd get N emails. Typically the builds will be run once a day, but can be manually triggered via the web interface, which means extra emails if things fail. For Biopython we're currently sending them just to a couple of key developers and/or buildbot administrators. We felt there would be too many to send to the whole development mailing list. Note that anyone can follow the news feed from http://testing.open-bio.org/bioruby/ by using feed://testing.open-bio.org/bioruby/rss or feed://testing.open-bio.org/bioruby/atom (and similar for Biopython's buildbot too). Regards, Peter From mh6 at sanger.ac.uk Thu Dec 1 16:30:22 2011 From: mh6 at sanger.ac.uk (Michael Paulini) Date: Thu, 01 Dec 2011 16:30:22 +0000 Subject: [BioRuby] EMBL / ENA parser error Message-ID: <4ED7AB9E.7050709@sanger.ac.uk> Hi fellow biorubysts, I tried to parse EMBL/ENA entry DQ471885 with the bioruby EMBL parser, and it dies when it tries to parse: OS uncultured nematode due to the regexp in embl/common.rb being: ================================== if tmp =~ /([A-Z][a-z]* *[\w\d \:\'\+\-]+[\w\d])/ org = $1 tmp =~ /(\(.+\))/ os.push({'name' => $1, 'os' => org}) else raise "Error: OS Line. #{$!}\n#{fetch('OS')}\n" end ================================ as it doesn't start with an uppercase letter. Shouud we change the regexp, or file a bug with ENA? thanks, Michael -- 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 pjotr.public14 at thebird.nl Mon Dec 5 11:51:05 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 5 Dec 2011 12:51:05 +0100 Subject: [BioRuby] Announcing Bio-Affy Message-ID: <20111205115105.GA29115@thebird.nl> Rubyistas, I just released bio-affy, which is a Affymetrix microarray file format parser (CEL/CDF) for Ruby. The plugin uses both Ruby and C. This Biogem is an FFI binding to R/Bioconductor's Affyio package: http://www.bioconductor.org/packages/2.2/bioc/html/affyio.html What is interesting about this Biogem/BioRuby plugin is not only that it uses FFI to map C code to Ruby, but also fires up the R interpreter to support the Affyio internal function calls into Rlib. The FFI binding also accesses internal C structs of my Affyio adapter. See the examples in https://github.com/pjotrp/bioruby-affy/blob/master/spec/bio-affy_spec.rb Pj. PS. We will create Biogem scaffolding for FFI support in the near future, as well as for SWIG and native Ruby extensions. FFI is interesting as it has good support across all Ruby versions (including JRuby). From bonnal at ingm.org Mon Dec 5 15:47:40 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 05 Dec 2011 16:47:40 +0100 Subject: [BioRuby] Announcing Bio-Affy In-Reply-To: <20111205115105.GA29115@thebird.nl> Message-ID: Amazing! Yep, FFI is something we'll support :-) On 05/12/11 12.51, "Pjotr Prins" wrote: > Rubyistas, > > I just released bio-affy, which is a Affymetrix microarray file format > parser (CEL/CDF) for Ruby. The plugin uses both Ruby and C. > > This Biogem is an FFI binding to R/Bioconductor's Affyio package: > > http://www.bioconductor.org/packages/2.2/bioc/html/affyio.html > > What is interesting about this Biogem/BioRuby plugin is not only that > it uses FFI to map C code to Ruby, but also fires up the R interpreter > to support the Affyio internal function calls into Rlib. > > The FFI binding also accesses internal C structs of my Affyio adapter. > See the examples in > > https://github.com/pjotrp/bioruby-affy/blob/master/spec/bio-affy_spec.rb > > Pj. > > PS. We will create Biogem scaffolding for FFI support in the near > future, as well as for SWIG and native Ruby extensions. FFI is > interesting as it has good support across all Ruby versions > (including JRuby). > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From ngoto at gen-info.osaka-u.ac.jp Wed Dec 7 16:32:49 2011 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Thu, 8 Dec 2011 01:32:49 +0900 Subject: [BioRuby] EMBL / ENA parser error In-Reply-To: <4ED7AB9E.7050709@sanger.ac.uk> References: <4ED7AB9E.7050709@sanger.ac.uk> Message-ID: <20111207163250.C42C91CBC3C4@idnmail.gen-info.osaka-u.ac.jp> Hi Michael, We must first read official documents provided by EMBL-EBI. EMBL User Manual: http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html In "3.4.7 The OS Line", two examples that don't start with an uppercase letter are shown. > OS unidentified bacterium B8 > OS uncultured proteobacterium Therefore, the issue should be treated as a bug of BioRuby. The regexp and/or the logic for OS lines will be changed. Thank you for reporting the issue, Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org On Thu, 01 Dec 2011 16:30:22 +0000 Michael Paulini wrote: > Hi fellow biorubysts, > > I tried to parse EMBL/ENA entry DQ471885 with the bioruby EMBL parser, > and it dies when it tries to parse: > OS uncultured nematode > > due to the regexp in embl/common.rb being: > ================================== > if tmp =~ /([A-Z][a-z]* *[\w\d \:\'\+\-]+[\w\d])/ > org = $1 > tmp =~ /(\(.+\))/ > os.push({'name' => $1, 'os' => org}) > else > raise "Error: OS Line. #{$!}\n#{fetch('OS')}\n" > end > ================================ > as it doesn't start with an uppercase letter. > > Shouud we change the regexp, or file a bug with ENA? > > thanks, > > Michael > > > -- > 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. > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From p.j.a.cock at googlemail.com Thu Dec 8 21:34:50 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 8 Dec 2011 21:34:50 +0000 Subject: [BioRuby] BioRuby BuildBot failure report emails? Message-ID: Dear all, Who should we send the BuildBot failure emails to, if anyone? This will be one email per failure - so if there is a problem that affects all N build targets, you'd get N emails. Typically the builds will be run once a day, but can be manually triggered via the web interface, which means extra emails if things fail. For Biopython we're currently sending them just to a couple of key developers and/or buildbot administrators. We felt there would be too many to send to the whole development mailing list. Note that anyone can follow the news feed from http://testing.open-bio.org/bioruby/ by using feed://testing.open-bio.org/bioruby/rss or feed://testing.open-bio.org/bioruby/atom (and similar for Biopython's buildbot too). Regards, Peter