From sgujja at broad.mit.edu Tue Jan 8 14:03:54 2008 From: sgujja at broad.mit.edu (Sharvari Gujja) Date: Tue, 08 Jan 2008 14:03:54 -0500 Subject: [BioRuby] help wtih bioruby wrapper for emboss tools... Message-ID: <4783C91A.2030503@broad.mit.edu> Hi all, I am trying to use emboss tool "water" in bioruby. However when I try to run the following script I get the error as : uninitialized constant Bio::EBI (NameError). Do I need to import any files? #!/usr/bin/env ruby require 'bio' require 'base64' emboss = Bio::EBI::SOAP::Emboss.new emboss.list_methods hash = { "tool" => "water", "asequence" => "uniprot:alk1_human", "bsequence" => "uniprot:alk1_mouse", "email" => "ebisoap at example.org" } poll = emboss.run(hash, []) emboss.checkStatus(poll) base = emboss.poll(poll, "tooloutput") puts Base64.decode64(base) Thanks -S From ktym at hgc.jp Tue Jan 8 20:56:40 2008 From: ktym at hgc.jp (Toshiaki Katayama) Date: Wed, 9 Jan 2008 10:56:40 +0900 Subject: [BioRuby] help wtih bioruby wrapper for emboss tools... In-Reply-To: <4783C91A.2030503@broad.mit.edu> References: <4783C91A.2030503@broad.mit.edu> Message-ID: <4746BAE5-C90E-493C-8FD6-C20CE5D25E4E@hgc.jp> Hi Sharvari, What version of the BioRuby are you using? When I tried interactively, SOAP query to EBI was successfully submitted. ------------------------------------------------------------ ktym at toge9064:~% bioruby Loading config (/Users/ktym/.bioruby/shell/session/config) ... done Loading object (/Users/ktym/.bioruby/shell/session/object) ... done Loading history (/Users/ktym/.bioruby/shell/session/history) ... done . . . B i o R u b y i n t h e s h e l l . . . Version : BioRuby 1.2.1 / Ruby 1.8.6 bioruby> emboss = Bio::EBI::SOAP::Emboss.new ignored attr: {}nillable ==> #>, @log=nil, @wsdl="http://www.ebi.ac.uk/Tools/webservices/wsdl/WSEmboss.wsdl"> bioruby> emboss.list_methods ==> ["run", "checkStatus", "getResults", "getTools", "poll", "getInfo"] bioruby> hash = { bioruby+ "tool" => "water", bioruby+ "asequence" => "uniprot:alk1_human", bioruby+ "bsequence" => "uniprot:alk1_mouse", bioruby+ "email" => "ebisoap at example.org" } ==> {"asequence"=>"uniprot:alk1_human", "tool"=>"water", "bsequence"=>"uniprot:alk1_mouse", "email"=>"ebisoap at example.org"} bioruby> poll = emboss.run(hash, []) ==> "emboss-20080108-19402170" bioruby> emboss.checkStatus(poll) ==> "RUNNING" ------------------------------------------------------------ Real problem here is that the EBI server never finishes this work... 5 hours later, the process is still (reported to be) running thus I can't obtain the result yet. ------------------------------------------------------------ bioruby> emboss.checkStatus(poll) ==> "RUNNING" bioruby> base = emboss.poll(poll, "tooloutput") ==> nil ------------------------------------------------------------ Regards, Toshiaki Katayama On 2008/01/09, at 4:03, Sharvari Gujja wrote: > Hi all, > > I am trying to use emboss tool "water" in bioruby. However when I try to run the following script I get the error as : uninitialized constant Bio::EBI (NameError). > > Do I need to import any files? > > #!/usr/bin/env ruby > require 'bio' > require 'base64' > emboss = Bio::EBI::SOAP::Emboss.new > > emboss.list_methods > > hash = { > "tool" => "water", > "asequence" => "uniprot:alk1_human", > "bsequence" => "uniprot:alk1_mouse", > "email" => "ebisoap at example.org" > } > poll = emboss.run(hash, []) > emboss.checkStatus(poll) > base = emboss.poll(poll, "tooloutput") > puts Base64.decode64(base) > > > Thanks > -S > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From ktym at hgc.jp Tue Jan 8 21:04:23 2008 From: ktym at hgc.jp (Toshiaki Katayama) Date: Wed, 9 Jan 2008 11:04:23 +0900 Subject: [BioRuby] help wtih bioruby wrapper for emboss tools... In-Reply-To: <4746BAE5-C90E-493C-8FD6-C20CE5D25E4E@hgc.jp> References: <4783C91A.2030503@broad.mit.edu> <4746BAE5-C90E-493C-8FD6-C20CE5D25E4E@hgc.jp> Message-ID: Hi, On 2008/01/09, at 10:56, Toshiaki Katayama wrote: > Real problem here is that the EBI server never finishes this work... > 5 hours later, the process is still (reported to be) running > thus I can't obtain the result yet. This was due to the change of the entry name in Swiss-Prot as described at http://www.expasy.org/cgi-bin/idtracker?id=ALK1_HUMAN > The ID: ALK1_HUMAN is no longer valid. > > ALK1_HUMAN (associated with primary accession number: P03973 from release 9.0) was renamed to SLPI_HUMAN in release 52.0. > > ALK1_HUMAN was associated with 1 accession number: P07757 from release 12.0. > > P07757 is now a secondary accession number of SLPI_HUMAN (primary accession number: P03973). So, when I specify the USAs as 'uniprot:slpi_human' and 'uniprot:slpi_mouse' instead of 'uniprot:alk1_human' and 'uniprot:alk1_mouse', I could obtain the proper result. Toshiaki ktym at toge9064:~% bioruby Loading config (/Users/ktym/.bioruby/shell/session/config) ... done Loading object (/Users/ktym/.bioruby/shell/session/object) ... done Loading history (/Users/ktym/.bioruby/shell/session/history) ... done . . . B i o R u b y i n t h e s h e l l . . . Version : BioRuby 1.2.1 / Ruby 1.8.6 bioruby> emboss = Bio::EBI::SOAP::Emboss.new ignored attr: {}nillable ==> #>, @log=nil, @wsdl="http://www.ebi.ac.uk/Tools/webservices/wsdl/WSEmboss.wsdl"> bioruby> hash = { bioruby+ "tool" => "water", bioruby+ "asequence" => "uniprot:slpi_human", bioruby+ "bsequence" => "uniprot:slpi_mouse", bioruby+ "email" => "ebisoap at example.org" } ==> {"asequence"=>"uniprot:slpi_human", "tool"=>"water", "bsequence"=>"uniprot :slpi_mouse", "email"=>"ebisoap at example.org"} bioruby> poll = emboss.run(hash, []) ==> "emboss-20080109-01550394" bioruby> emboss.checkStatus(poll) ==> "DONE" bioruby> base = emboss.poll(poll, "tooloutput") ==> "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" bioruby> require 'base64' ==> true bioruby> puts Base64.decode64(base) ######################################## # Program: water # Rundate: Wed Jan 09 01:55:06 2008 # Align_format: srspair # Report_file: /ebi/extserv/old-work/emboss-20080109-01550394.output ######################################## #======================================= # # Aligned_sequences: 2 # 1: SLPI_HUMAN # 2: SLPI_MOUSE # Matrix: EBLOSUM62 # Gap_penalty: 10.0 # Extend_penalty: 0.5 # # Length: 132 # Identity: 79/132 (59.8%) # Similarity: 96/132 (72.7%) # Gaps: 3/132 ( 2.3%) # Score: 464.5 # # #======================================= SLPI_HUMAN 1 MKSSGLFPFLVLLALGTLAPWAVEGSGK--SFKAGVCPPKKSAQCLRYKK 48 |||.||.||.||||||.||||.||| || :.|.|.||.||.||||:.:| SLPI_MOUSE 1 MKSCGLLPFTVLLALGILAPWTVEG-GKNDAIKIGACPAKKPAQCLKLEK 49 SLPI_HUMAN 49 PECQSDWQCPGKKRCCPDTCGIKCLDPVDTPNPTRRKPGKCPVTYGQCLM 98 |:|::||:||||:|||.|.||.||::||....|..||||:|..|..:|:| SLPI_MOUSE 50 PQCRTDWECPGKQRCCQDACGSKCVNPVPIRKPVWRKPGRCVKTQARCMM 99 SLPI_HUMAN 99 LNPPNFCEMDGQCKRDLKCCMGMCGKSCVSPV 130 |||||.|:.||||....|||.|:|||.|:.|: SLPI_MOUSE 100 LNPPNVCQRDGQCDGKYKCCEGICGKVCLPPM 131 #--------------------------------------- #--------------------------------------- ==> nil From ktym at hgc.jp Tue Jan 8 21:42:12 2008 From: ktym at hgc.jp (Toshiaki Katayama) Date: Wed, 9 Jan 2008 11:42:12 +0900 Subject: [BioRuby] Help using EMBOSS in Bioruby... In-Reply-To: <477BEB9F.5010407@broad.mit.edu> References: <477BEB9F.5010407@broad.mit.edu> Message-ID: Sharvari, Sorry, I missed your previous mails. On 2008/01/03, at 4:53, Sharvari Gujja wrote: > Hi, > > I was wondering how to use water and needle emboss tools in Bioruby. I am aware that the class Bio::EMBOSS exists with methods: > > *entret*(arg) src > *new*(cmd_line) src > > *seqret*(arg) src > > > *exec*() src > > I would like to know how to use water and needle tools.I really appreciate your help. > > Thanks > Sharvari On 2008/01/08, at 5:47, Sharvari Gujja wrote: > Hello Mr.Toshiaki, > > First off, I'd like to thank you for all your help. > > I have just one more question for you. I am trying to see how to use Smith-Waterman / Needleman Wunch alignment in Bioruby. > I really appreciate any input from you. > > Thanks > Sharvari There are several ways to do it. Simplest version would be result = `water -asequence 'swissprot:slpi_human' -bsequence 'swissprot:slpi_mouse' -stdout -auto` and usage of the Bio::EMBOSS class is well documented in the source code. http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/bioruby//lib/bio/appl/emboss.rb?rev=1.8&cvsroot=bioruby bioruby> puts Bio::EMBOSS.new("water -asequence 'swissprot:slpi_human' -bsequence 'swissprot:slpi_mouse'").exec ######################################## # Program: water # Rundate: Wed 9 Jan 2008 11:22:59 # Commandline: water # -asequence swissprot:slpi_human # -bsequence swissprot:slpi_mouse # -stdout # -auto # Align_format: srspair # Report_file: stdout ######################################## #======================================= # # Aligned_sequences: 2 # 1: SLPI_HUMAN # 2: SLPI_MOUSE # Matrix: EBLOSUM62 # Gap_penalty: 10.0 # Extend_penalty: 0.5 # # Length: 132 # Identity: 79/132 (59.8%) # Similarity: 96/132 (72.7%) # Gaps: 3/132 ( 2.3%) # Score: 464.5 # # #======================================= SLPI_HUMAN 1 MKSSGLFPFLVLLALGTLAPWAVEGSGK--SFKAGVCPPKKSAQCLRYKK 48 |||.||.||.||||||.||||.||| || :.|.|.||.||.||||:.:| SLPI_MOUSE 1 MKSCGLLPFTVLLALGILAPWTVEG-GKNDAIKIGACPAKKPAQCLKLEK 49 SLPI_HUMAN 49 PECQSDWQCPGKKRCCPDTCGIKCLDPVDTPNPTRRKPGKCPVTYGQCLM 98 |:|::||:||||:|||.|.||.||::||....|..||||:|..|..:|:| SLPI_MOUSE 50 PQCRTDWECPGKQRCCQDACGSKCVNPVPIRKPVWRKPGRCVKTQARCMM 99 SLPI_HUMAN 99 LNPPNFCEMDGQCKRDLKCCMGMCGKSCVSPV 130 |||||.|:.||||....|||.|:|||.|:.|: SLPI_MOUSE 100 LNPPNVCQRDGQCDGKYKCCEGICGKVCLPPM 131 #--------------------------------------- #--------------------------------------- ==> nil From ktym at hgc.jp Wed Jan 9 12:13:14 2008 From: ktym at hgc.jp (Toshiaki Katayama) Date: Thu, 10 Jan 2008 02:13:14 +0900 Subject: [BioRuby] help wtih bioruby wrapper for emboss tools... In-Reply-To: <4784DC8C.7010506@broad.mit.edu> References: <4783C91A.2030503@broad.mit.edu> <4746BAE5-C90E-493C-8FD6-C20CE5D25E4E@hgc.jp> <4784DC8C.7010506@broad.mit.edu> Message-ID: <285CC958-A7EB-4860-8BE9-7C2AD8AC86E5@hgc.jp> Sharvari, Please write back to the mailing list. > bioruby> puts Bio::EMBOSS.new("water -asequence 'swissprot:slpi_human' -bsequence 'swissprot:slpi_mouse'").exec > sh: water: command not found You need to install EMBOSS suites in your local environment. > bioruby> emboss = Bio::EBI::SOAP::Emboss.new > NameError: uninitialized constant Bio::EBI Use BioRuby 1.2.1 instead of 1.0.0. > Also where can I find documentation to use other tools in Emboss? Consult the EMBOSS manual. Toshiaki On 2008/01/09, at 23:39, Sharvari Gujja wrote: > Toshiaki Katayama wrote: >> Hi Sharvari, >> >> What version of the BioRuby are you using? >> >> When I tried interactively, SOAP query to EBI was successfully submitted. >> >> ------------------------------------------------------------ >> ktym at toge9064:~% bioruby >> Loading config (/Users/ktym/.bioruby/shell/session/config) ... done >> Loading object (/Users/ktym/.bioruby/shell/session/object) ... done >> Loading history (/Users/ktym/.bioruby/shell/session/history) ... done >> >> . . . B i o R u b y i n t h e s h e l l . . . >> >> Version : BioRuby 1.2.1 / Ruby 1.8.6 >> >> bioruby> emboss = Bio::EBI::SOAP::Emboss.new >> ignored attr: {}nillable >> ==> #>, @log=nil, @wsdl="http://www.ebi.ac.uk/Tools/webservices/wsdl/WSEmboss.wsdl"> >> bioruby> emboss.list_methods >> ==> ["run", "checkStatus", "getResults", "getTools", "poll", "getInfo"] >> bioruby> hash = { >> bioruby+ "tool" => "water", >> bioruby+ "asequence" => "uniprot:alk1_human", >> bioruby+ "bsequence" => "uniprot:alk1_mouse", >> bioruby+ "email" => "ebisoap at example.org" >> } >> ==> {"asequence"=>"uniprot:alk1_human", "tool"=>"water", "bsequence"=>"uniprot:alk1_mouse", "email"=>"ebisoap at example.org"} >> bioruby> poll = emboss.run(hash, []) >> ==> "emboss-20080108-19402170" >> bioruby> emboss.checkStatus(poll) >> ==> "RUNNING" >> ------------------------------------------------------------ >> >> Real problem here is that the EBI server never finishes this work... >> 5 hours later, the process is still (reported to be) running >> thus I can't obtain the result yet. >> >> ------------------------------------------------------------ >> bioruby> emboss.checkStatus(poll) >> ==> "RUNNING" >> bioruby> base = emboss.poll(poll, "tooloutput") >> ==> nil >> ------------------------------------------------------------ >> >> Regards, >> Toshiaki Katayama >> >> >> On 2008/01/09, at 4:03, Sharvari Gujja wrote: >> >> >>> Hi all, >>> >>> I am trying to use emboss tool "water" in bioruby. However when I try to run the following script I get the error as : uninitialized constant Bio::EBI (NameError). >>> >>> Do I need to import any files? >>> >>> #!/usr/bin/env ruby >>> require 'bio' >>> require 'base64' >>> emboss = Bio::EBI::SOAP::Emboss.new >>> >>> emboss.list_methods >>> >>> hash = { >>> "tool" => "water", >>> "asequence" => "uniprot:alk1_human", >>> "bsequence" => "uniprot:alk1_mouse", >>> "email" => "ebisoap at example.org" >>> } >>> poll = emboss.run(hash, []) >>> emboss.checkStatus(poll) >>> base = emboss.poll(poll, "tooloutput") >>> puts Base64.decode64(base) >>> >>> >>> Thanks >>> -S >>> >>> _______________________________________________ >>> BioRuby mailing list >>> BioRuby at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioruby >>> >> >> >> _______________________________________________ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> > Hello Mr.Toshiaki, > > Thank you for the reply. This is what I get when I do the same: > > bioruby:14:Warning: require_gem is obsolete. Use gem instead. > Loading config (session/config) ... done > Loading object (session/object) ... done > Loading history (session/history) ... done > > . . . B i o R u b y i n t h e s h e l l . . . > > Version : BioRuby 1.0.0 / Ruby 1.8.6 > > bioruby> puts Bio::EMBOSS.new("water -asequence 'swissprot:slpi_human' -bsequence 'swissprot:slpi_mouse'").exec > sh: water: command not found > > bioruby> emboss = Bio::EBI::SOAP::Emboss.new > NameError: uninitialized constant Bio::EBI > from (irb):2 > > I am trying to download the latest version 1.2.0 and I get the tar file.I was wondering how to proceed from there. > > Also where can I find documentation to use other tools in Emboss? > > I really appreciate your help. > > Thanks > Sharvari From sgujja at broad.mit.edu Wed Jan 9 12:15:58 2008 From: sgujja at broad.mit.edu (Sharvari Gujja) Date: Wed, 09 Jan 2008 12:15:58 -0500 Subject: [BioRuby] How to install EMBOSS suites in my local environment? Message-ID: <4785014E.50208@broad.mit.edu> Hi, I am trying to use Emboss tools in bioruby1.2.1 and would like to know how to install Emboss suite in my local environment Thanks -S From ktym at hgc.jp Wed Jan 9 12:23:39 2008 From: ktym at hgc.jp (Toshiaki Katayama) Date: Thu, 10 Jan 2008 02:23:39 +0900 Subject: [BioRuby] How to install EMBOSS suites in my local environment? In-Reply-To: <4785014E.50208@broad.mit.edu> References: <4785014E.50208@broad.mit.edu> Message-ID: <038F9448-45A1-44DD-9BE7-A967C6E85A79@hgc.jp> http://www.google.com/ http://emboss.sourceforge.net/ On 2008/01/10, at 2:15, Sharvari Gujja wrote: > Hi, > > I am trying to use Emboss tools in bioruby1.2.1 and would like to know how to install Emboss suite in my local environment > > Thanks > -S > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From sgujja at broad.mit.edu Wed Jan 9 16:24:52 2008 From: sgujja at broad.mit.edu (Sharvari Gujja) Date: Wed, 09 Jan 2008 16:24:52 -0500 Subject: [BioRuby] How to install EMBOSS suites in my local environment? In-Reply-To: <038F9448-45A1-44DD-9BE7-A967C6E85A79@hgc.jp> References: <4785014E.50208@broad.mit.edu> <038F9448-45A1-44DD-9BE7-A967C6E85A79@hgc.jp> Message-ID: <47853BA4.5000407@broad.mit.edu> Toshiaki Katayama wrote: > http://www.google.com/ > http://emboss.sourceforge.net/ > > On 2008/01/10, at 2:15, Sharvari Gujja wrote: > > >> Hi, >> >> I am trying to use Emboss tools in bioruby1.2.1 and would like to know how to install Emboss suite in my local environment >> >> Thanks >> -S >> _______________________________________________ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> > > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > Hi, when I use the exec command in bioruby1.2.1 , i get the following error: C:/Program Files/ruby/lib/ruby/site_ruby/1.8/bio/appl/emboss.rb:135:in `exec': undefined method `close' for nil:NilClass (NoMethodError) from Z:/emboss1.rb:11 obj_A = Bio::EMBOSS.new('transeq -sbegin 110 -send 1171 embl:xlrhodop') obj_A.exec puts obj_A.result #=> a FASTA-formatted sequence Really appreciate any input. Thanks Sharvari PS: bioruby version is 1.2.1 ruby version 1.8.6 the script i am running is: From sgujja at broad.mit.edu Wed Jan 9 18:12:05 2008 From: sgujja at broad.mit.edu (Sharvari Gujja) Date: Wed, 09 Jan 2008 18:12:05 -0500 Subject: [BioRuby] help wtih bioruby wrapper for emboss tools... In-Reply-To: References: <4783C91A.2030503@broad.mit.edu> <4746BAE5-C90E-493C-8FD6-C20CE5D25E4E@hgc.jp> Message-ID: <478554C5.2060104@broad.mit.edu> Toshiaki Katayama wrote: > Hi, > > On 2008/01/09, at 10:56, Toshiaki Katayama wrote: > >> Real problem here is that the EBI server never finishes this work... >> 5 hours later, the process is still (reported to be) running >> thus I can't obtain the result yet. >> > > This was due to the change of the entry name in Swiss-Prot as described at > > http://www.expasy.org/cgi-bin/idtracker?id=ALK1_HUMAN > > >> The ID: ALK1_HUMAN is no longer valid. >> >> ALK1_HUMAN (associated with primary accession number: P03973 from release 9.0) was renamed to SLPI_HUMAN in release 52.0. >> >> ALK1_HUMAN was associated with 1 accession number: P07757 from release 12.0. >> >> P07757 is now a secondary accession number of SLPI_HUMAN (primary accession number: P03973). >> > > So, when I specify the USAs as 'uniprot:slpi_human' and 'uniprot:slpi_mouse' > instead of 'uniprot:alk1_human' and 'uniprot:alk1_mouse', > I could obtain the proper result. > > Toshiaki > > > ktym at toge9064:~% bioruby > Loading config (/Users/ktym/.bioruby/shell/session/config) ... done > Loading object (/Users/ktym/.bioruby/shell/session/object) ... done > Loading history (/Users/ktym/.bioruby/shell/session/history) ... done > > . . . B i o R u b y i n t h e s h e l l . . . > > Version : BioRuby 1.2.1 / Ruby 1.8.6 > > bioruby> emboss = Bio::EBI::SOAP::Emboss.new > ignored attr: {}nillable > ==> #>, @log=nil, @wsdl="http://www.ebi.ac.uk/Tools/webservices/wsdl/WSEmboss.wsdl"> > bioruby> hash = { > bioruby+ "tool" => "water", > bioruby+ "asequence" => "uniprot:slpi_human", > bioruby+ "bsequence" => "uniprot:slpi_mouse", > bioruby+ "email" => "ebisoap at example.org" > } > ==> {"asequence"=>"uniprot:slpi_human", "tool"=>"water", "bsequence"=>"uniprot > :slpi_mouse", "email"=>"ebisoap at example.org"} > bioruby> poll = emboss.run(hash, []) > ==> "emboss-20080109-01550394" > bioruby> emboss.checkStatus(poll) > ==> "DONE" > bioruby> base = emboss.poll(poll, "tooloutput") > ==> "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! > 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" > bioruby> require 'base64' > ==> true > bioruby> puts Base64.decode64(base) > ######################################## > # Program: water > # Rundate: Wed Jan 09 01:55:06 2008 > # Align_format: srspair > # Report_file: /ebi/extserv/old-work/emboss-20080109-01550394.output > ######################################## > > #======================================= > # > # Aligned_sequences: 2 > # 1: SLPI_HUMAN > # 2: SLPI_MOUSE > # Matrix: EBLOSUM62 > # Gap_penalty: 10.0 > # Extend_penalty: 0.5 > # > # Length: 132 > # Identity: 79/132 (59.8%) > # Similarity: 96/132 (72.7%) > # Gaps: 3/132 ( 2.3%) > # Score: 464.5 > # > # > #======================================= > > SLPI_HUMAN 1 MKSSGLFPFLVLLALGTLAPWAVEGSGK--SFKAGVCPPKKSAQCLRYKK 48 > |||.||.||.||||||.||||.||| || :.|.|.||.||.||||:.:| > SLPI_MOUSE 1 MKSCGLLPFTVLLALGILAPWTVEG-GKNDAIKIGACPAKKPAQCLKLEK 49 > > SLPI_HUMAN 49 PECQSDWQCPGKKRCCPDTCGIKCLDPVDTPNPTRRKPGKCPVTYGQCLM 98 > |:|::||:||||:|||.|.||.||::||....|..||||:|..|..:|:| > SLPI_MOUSE 50 PQCRTDWECPGKQRCCQDACGSKCVNPVPIRKPVWRKPGRCVKTQARCMM 99 > > SLPI_HUMAN 99 LNPPNFCEMDGQCKRDLKCCMGMCGKSCVSPV 130 > |||||.|:.||||....|||.|:|||.|:.|: > SLPI_MOUSE 100 LNPPNVCQRDGQCDGKYKCCEGICGKVCLPPM 131 > > > #--------------------------------------- > #--------------------------------------- > ==> nil > > > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > Hi, How can I use fasta files from NCBI as input to asequence and bsequence? For examples , I have 2 fasta files BA000002.fasta and CP000030.fasta Thanks -S From ktym at hgc.jp Sat Jan 12 17:44:27 2008 From: ktym at hgc.jp (Toshiaki Katayama) Date: Sun, 13 Jan 2008 07:44:27 +0900 Subject: [BioRuby] How to install EMBOSS suites in my local environment? In-Reply-To: <47853BA4.5000407@broad.mit.edu> References: <4785014E.50208@broad.mit.edu> <038F9448-45A1-44DD-9BE7-A967C6E85A79@hgc.jp> <47853BA4.5000407@broad.mit.edu> Message-ID: <81A85D52-B100-4DA1-A99E-CF7547830D38@hgc.jp> On 2008/01/10, at 6:24, Sharvari Gujja wrote: > when I use the exec command in bioruby1.2.1 , i get the following error: > > C:/Program Files/ruby/lib/ruby/site_ruby/1.8/bio/appl/emboss.rb:135:in `exec': undefined method `close' for nil:NilClass (NoMethodError) > from Z:/emboss1.rb:11 I suspect that the EMBOSS command couldn't be found. Firstly, please confirm you can run the command in the terminal. Secondary, check the command search path. > transeq -sbegin 110 -send 1171 embl:xlrhodop Then, On 2008/01/10, at 8:12, Sharvari Gujja wrote: > How can I use fasta files from NCBI as input to asequence and bsequence? > > For examples , I have 2 fasta files BA000002.fasta and CP000030.fasta learn EMBOSS USA (Uniform Sequence Address) at http://emboss.sourceforge.net/docs/ http://emboss.sourceforge.net/docs/themes/UniformSequenceAddress.html Toshiaki From agrobertson at telus.net Sun Jan 13 23:02:24 2008 From: agrobertson at telus.net (Gordon Robertson) Date: Sun, 13 Jan 2008 20:02:24 -0800 Subject: [BioRuby] Bio::Sequence forces a DNA sequence to lowercase? Message-ID: I'm new to BioRuby, so apologize for asking about something that's very basic, and that likely was discussed and resolved in the distant past. I'm parsing PWM scan 'hits' from a report. The hit sequences have the form "accattAATTAt", where the uppercase letters mark the positions corrsponding to the five most highly conserved bases in the PWM. Given the output format of the PWM scanner, which I don't control, I need to reverse-complement the (-)-strand hits. And I want to preserve the uppercase characters, getting 'aTAATTaatggt' back. I could write something to do this, but thought that this might be a good time to simplify things by using BioRuby. However, when I load BioRuby 1.2.1 into 'irb', and start to look at Bio::Sequence methods, I find that the example code given at http://dev.bioruby.org/wiki/en/? Tutorial.rd immediately forces the input sequence to lowercase - require 'bio' seq = Bio::Sequence::NA.new("atgcATGcaaaa") "atgcatgcaaaa" Inspecting the list of methods available (seq.methods.sort), I see several standard case-control methods, but nothing that appears to permit me to 'lock' or 'freeze' the cases of the input sequence letters, in order that lowercase and uppercase letters are returned appropriately. Is there such a method, or another (simple) way to have upper and lower case characters passed through DNA/RNA methods? G -- Gordon Robertson Canada's Michael Smith Genome Sciences Centre Vancouver BC Canada From raoul.bonnal at itb.cnr.it Tue Jan 15 06:35:10 2008 From: raoul.bonnal at itb.cnr.it (Raoul Jean Pierre Bonnal) Date: Tue, 15 Jan 2008 12:35:10 +0100 Subject: [BioRuby] Count homopolymers Message-ID: <1200396910.10862.24.camel@Graco> This is a raw way for counting homopolymers in a sequence. homopolymersInfo = Hash.new{|hash_bases, key_base| hash_bases[key_base] = Hash.new{|hash_types, key_type| hash_types[key_type] = Array.new;}} "aggagagatgggggataaaaaatttttaaaaagggatagatgggggaattcccccaccccccaaaattttttgggggggggccccccaaaaa".scan(/a{3,}|c{3,}|g{3,}|t{3,}/i){|m| homopolymersInfo[$&.squeeze][$&.length] << [$~.begin(0),$~.end(0)]} homopolymersInfo.each_pair{|base,types| types.each_pair{|type,positions| puts "#{base}, #{type}, #{positions.size}"}} a, 5, 2 a, 6, 1 a, 4, 1 c, 5, 1 c, 6, 2 g, 5, 2 g, 3, 1 g, 9, 1 t, 5, 1 t, 6, 1 ==> {"a"=>{5=>[[27, 32], [87, 92]], 6=>[[16, 22]], 4=>[[62, 66]]}, "c"=>{5=>[[50, 55]], 6=>[[56, 62], [81, 87]]}, "g"=>{5=>[[9, 14], [41, 46]], 3=>[[32, 35]], 9=>[[72, 81]]}, "t"=>{5=>[[22, 27]], 6=>[[66, 72]]}} Positions is an Array of start/end coordinates I could use sym in hash, would be better. -- Ra From jan.aerts at bbsrc.ac.uk Mon Jan 28 09:47:59 2008 From: jan.aerts at bbsrc.ac.uk (Jan Aerts) Date: Mon, 28 Jan 2008 14:47:59 +0000 Subject: [BioRuby] new release Bio::Graphics Message-ID: <1201531679.6583.30.camel@rilxvm05> All, I've uploaded a new version of Bio::Graphics on http://bio-graphics.rubyforge.org. Current version now is 1.4. Most notable new features: * drawing of composite features (such as transcripts) * drawing of vertical pictures * easier assignment of optional arguments: these now use keywords * users can easily create their own glyphs just by creating a file describing them A small example (adapted from the homepage): 1000) # Create the tracks generic_track = my_panel.add_track('generic', :label => false) directed_spliced_track = my_panel.add_track('directed_spliced', :label => false, :glyph => :directed_spliced, :colour => [1,0,1]) # Add features to each track generic_track.add_feature(Bio::Feature.new('clone', '250..375'), :link => 'http://www.newsforge.com') generic_track.add_feature(Bio::Feature.new('clone', '54..124'), :glyph => :line) generic_track.add_feature(Bio::Feature.new('clone', '100..449'), :colour => [1,1,0], :glyph => :box) directed_spliced_track.add_feature(Bio::Feature.new('cds','join(34..52,109..183)'), :link => 'http://www.google.com') directed_spliced_track.add_feature(Bio::Feature.new('cds', 'complement(join(170..231,264..299,350..360,409..445))'), :link => 'http://bioinformatics.roslin.ac.uk') my_panel.draw('glyph_showcase.png') A major effort has been put into this release by Charles Comstock. Thanks Charles. I'll try and find some time to further improve the library. But if anyone is willing to put a bit of effort in it: that'd be great. There are still a few things to be done, including speeding things up and drawing continuous features (e.g. GC content). Any questions/suggestions, please let me know. jan. -- Dr Jan Aerts Bioinformatics Group Roslin Institute Roslin EH25 9PS Scotland, UK tel: +44 131 527 4198 ----...and the obligatory disclaimer---- Roslin Institute is a company limited by guarantee, registered in Scotland (registered number SC157100) and a Scottish Charity (registered number SC023592). Our registered office is at Roslin, Midlothian, EH25 9PS. VAT registration number 847380013. The information contained in this e-mail (including any attachments) is confidential and is intended for the use of the addressee only. The opinions expressed within this e-mail (including any attachments) are the opinions of the sender and do not necessarily constitute those of Roslin Institute (Edinburgh) ("the Institute") unless specifically stated by a sender who is duly authorised to do so on behalf of the Institute. From raoul.bonnal at itb.cnr.it Tue Jan 29 05:40:31 2008 From: raoul.bonnal at itb.cnr.it (Raoul Jean Pierre Bonnal) Date: Tue, 29 Jan 2008 11:40:31 +0100 Subject: [BioRuby] BioRuby Shell Rails Generator Bug ? Message-ID: <1201603231.7826.15.camel@Graco> [root at Graco febo]# gem install bio Updating metadata for 30 gems from http://gems.rubyforge.org .............................. complete Successfully installed bio-1.2.1 1 gem installed ---- [febo at Graco Projects]$ bioruby -r testrb Creating directory (/home/febo/Work/Projects/testrb/shell/session) ... done Creating directory (/home/febo/Work/Projects/testrb/shell/plugin) ... done Creating directory (/home/febo/Work/Projects/testrb/data) ... done Installing Rails application for BioRuby shell ... exists a lot of create .... done Installing Rails plugin for BioRuby shell ... Couldn't find 'bioruby' generator done Then Rails starts. ---------- So digging into the installation tree I found /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/shell/rails/vendor/plugins/generators/bioruby/ and taking as example uniprot plugins [root at Graco febo]# ll /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/shell/rails/vendor/plugins/generators/bioruby/ [root at Graco febo]# mkdir /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/shell/rails/vendor/plugins/bioruby [root at Graco febo]# mv /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/shell/rails/vendor/plugins/generators /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/shell/rails/vendor/plugins/bioruby [root at Graco febo]# ll /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/shell/rails/vendor/plugins/ totale 1 drwxr-xr-x 3 root root 1024 2008-01-29 11:37 bioruby/ [febo at Graco Projects]$ bioruby -r testrb Creating directory (/home/febo/Work/Projects/testrb/shell/session) ... done Creating directory (/home/febo/Work/Projects/testrb/shell/plugin) ... done Creating directory (/home/febo/Work/Projects/testrb/data) ... done Installing Rails application for BioRuby shell ... exists create app/controllers create app/helpers create app/models create app/views/layouts create config/environments create config/initializers create db create doc create lib create lib/tasks create log create public/images create public/javascripts create public/stylesheets create script/performance create script/process create test/fixtures create test/functional create test/integration create test/mocks/development create test/mocks/test create test/unit create vendor create vendor/plugins create tmp/sessions create tmp/sockets create tmp/cache create tmp/pids create Rakefile create README create app/controllers/application.rb create app/helpers/application_helper.rb create test/test_helper.rb create config/database.yml create config/routes.rb create public/.htaccess create config/initializers/inflections.rb create config/initializers/mime_types.rb create config/boot.rb create config/environment.rb create config/environments/production.rb create config/environments/development.rb create config/environments/test.rb create script/about create script/console create script/destroy create script/generate create script/performance/benchmarker create script/performance/profiler create script/performance/request create script/process/reaper create script/process/spawner create script/process/inspector create script/runner create script/server create script/plugin create public/dispatch.rb create public/dispatch.cgi create public/dispatch.fcgi create public/404.html create public/422.html create public/500.html create public/index.html create public/favicon.ico create public/robots.txt create public/images/rails.png create public/javascripts/prototype.js create public/javascripts/effects.js create public/javascripts/dragdrop.js create public/javascripts/controls.js create public/javascripts/application.js create doc/README_FOR_APP create log/server.log create log/production.log create log/development.log create log/test.log done Installing Rails plugin for BioRuby shell ... exists app/controllers exists app/helpers create app/views/bioruby exists app/views/layouts create public/images/bioruby exists public/stylesheets create app/controllers/bioruby_controller.rb create app/helpers/bioruby_helper.rb create app/views/bioruby/_methods.rhtml create app/views/bioruby/_classes.rhtml create app/views/bioruby/_modules.rhtml create app/views/bioruby/_log.rhtml create app/views/bioruby/_variables.rhtml create app/views/bioruby/commands.rhtml create app/views/bioruby/history.rhtml create app/views/bioruby/index.rhtml create app/views/layouts/bioruby.rhtml create public/images/bioruby/spinner.gif create public/images/bioruby/gem.png create public/images/bioruby/link.gif create public/images/bioruby/bg.gif create public/stylesheets/bioruby.css done >>> >>> open http://localhost:3000/bioruby >>> (You can change the port number by adding "-- -p 4000" option) . . . B i o R u b y i n t h e s h e l l . . . Version : BioRuby 1.2.1 / Ruby 1.8.6 => Booting WEBrick... => Rails application started on http://0.0.0.0:3000 => Ctrl-C to shutdown server; call with --help for options [2008-01-29 11:37:51] INFO WEBrick 1.3.1 [2008-01-29 11:37:51] INFO ruby 1.8.6 (2007-03-13) [i586-linux-gnu] [2008-01-29 11:37:51] INFO WEBrick::HTTPServer#start: pid=9210 port=3000 WORKS ! -- Ra From georgkam at gmail.com Wed Jan 30 07:01:46 2008 From: georgkam at gmail.com (George Githinji) Date: Wed, 30 Jan 2008 15:01:46 +0300 Subject: [BioRuby] bio blast Message-ID: <55915f820801300401s79aed759k2921da0fdff5a05a@mail.gmail.com> Hello , Am running this code on ruby 1.8.6, bioruby 1.2.1 on a windows xp platform, require 'bio' #seq_to_blast = "DIADIIRGKDLYLGDQERKQHLEKRLETMFEKIQKNNNNKLSNLSTKEVREYWWALNRDQVWKAITCDAGAADEYFKKSGKLEFEFTGGQCGRDGENVPTYLDYVPQFFR" #program = "blastp" db = "f:/var_blast_datasets/Kenyan_field_var_PR.txt" factory = Bio::Blast.new("blastp","#{db}","-m 0", "local") result = factory.query ('DIADIIRGKDLYLGDQERKQHLEKRLETMFEKIQKNNNNKLSNLSTKEVREYWWALNRDQVWKAITCDAGAADEYFKKSGKLEFEFTGGQCGRDGENVPTYLDYVPQFFR') result.each do |hit| puts hit.bit_score # bit score (*) puts hit.query_seq # query sequence (TRANSLATOR'S NOTE: sequence of homologous region of query sequence) puts hit.midline # middle line string of alignment of homologous region (*) puts hit.target_seq # hit sequence (TRANSLATOR'S NOTE: sequence of homologous region of query sequence) puts hit.evalue # E-value puts hit.identity # % identity puts hit.overlap # length of overlapping region puts hit.query_id # identifier of query sequence puts hit.query_def # definition(comment line) of query sequence puts hit.query_len # length of query sequence puts hit.target_id # identifier of hit sequence puts hit.target_def # definition(comment line) of hit sequence puts hit.target_len # length of hit sequence puts hit.query_start # start position of homologous region in query sequence puts hit.query_end # end position of homologous region in query sequence puts hit.target_start # start position of homologous region in hit(target) sequence puts hit.target_end # end position of homologous region in hit(target) sequence puts hit.lap_at # array of above four numbers end But instead i get this error: C:/ruby-1.8.6/ruby/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/blast/format8.rb:70:in `tab_parse_hsp': undefined method `strip' for nil:NilClass (NoMethodError) from C:/ruby-1.8.6/ruby/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/blast/format8.rb:32:in `tab_parse' from C:/ruby-1.8.6/ruby/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/blast/format8.rb:30:in `each' from C:/ruby-1.8.6/ruby/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/blast/format8.rb:30:in `tab_parse' from C:/ruby-1.8.6/ruby/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/blast/report.rb:71:in `auto_parse' from C:/ruby-1.8.6/ruby/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/blast/report.rb:89:in `initialize' from C:/ruby-1.8.6/ruby/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/blast.rb:232:in `new' from C:/ruby-1.8.6/ruby/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/blast.rb:232:in `parse_result' from C:/ruby-1.8.6/ruby/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/blast.rb:246:in `exec_local' from C:/ruby-1.8.6/ruby/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/blast.rb:212:in `send' from C:/ruby-1.8.6/ruby/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/blast.rb:212:in `query' from F:/Netbeans_folder/vargene/lib/bio_blast.rb:8 Where could i be messing up? Thank you. From robert.citek at gmail.com Wed Jan 30 10:56:45 2008 From: robert.citek at gmail.com (Robert Citek) Date: Wed, 30 Jan 2008 09:56:45 -0600 Subject: [BioRuby] Bio::Sequence forces a DNA sequence to lowercase? In-Reply-To: References: Message-ID: <4145b6790801300756g4acf774fifb50fcba88db84e8@mail.gmail.com> On Jan 13, 2008 10:02 PM, Gordon Robertson wrote: > I'm new to BioRuby, so apologize for asking about something that's > very basic, and that likely was discussed and resolved in the distant > past. This is a perfectly valid question. IMHO, no need to apologize. > ... > I find that the example code given at http://dev.bioruby.org/wiki/en/? > Tutorial.rd immediately forces the input sequence to lowercase - > require 'bio' > seq = Bio::Sequence::NA.new("atgcATGcaaaa") > "atgcatgcaaaa" > ... > Is there such a method, or another (simple) way to have upper and > lower case characters passed through DNA/RNA methods? I can repeat the phenomenon using bioruby on Ubuntu: $ ruby -rbio -e 'puts Bio::Sequence::NA.new("atgcATGcaaaa") ' atgcatgcaaaa How does one preserve the case of the sequence? Regards, - Robert From jan.aerts at bbsrc.ac.uk Wed Jan 30 11:10:58 2008 From: jan.aerts at bbsrc.ac.uk (Jan Aerts) Date: Wed, 30 Jan 2008 16:10:58 +0000 Subject: [BioRuby] Bio::Sequence forces a DNA sequence to lowercase? In-Reply-To: <4145b6790801300756g4acf774fifb50fcba88db84e8@mail.gmail.com> References: <4145b6790801300756g4acf774fifb50fcba88db84e8@mail.gmail.com> Message-ID: <1201709458.7069.22.camel@rilxvm05> > > I find that the example code given at http://dev.bioruby.org/wiki/en/? > > Tutorial.rd immediately forces the input sequence to lowercase - > > require 'bio' > > seq = Bio::Sequence::NA.new("atgcATGcaaaa") > > "atgcatgcaaaa" > > ... > > Is there such a method, or another (simple) way to have upper and > > lower case characters passed through DNA/RNA methods? The very first thing that happens when you create a new sequence is a downcase on it. That actually makes sense in the way that a Bio::Sequence is just that: a sequence. The ATG in your example above should be seen as a "feature" on the "sequence". So the 'right' way to do it is to create a Bio::Sequence object as you did above and then attach a Bio::Feature object to it describing the start codon. However, it's understandable that you'd like to keep the upper/lowercase information after you've made the Bio::Sequence object. The person who'll have to look into that will be Toshiaki. The change might just be a bit more difficult than it looks at first sight. jan. -- Dr Jan Aerts Bioinformatics Group Roslin Institute Roslin EH25 9PS Scotland, UK tel: +44 131 527 4198 ----...and the obligatory disclaimer---- Roslin Institute is a company limited by guarantee, registered in Scotland (registered number SC157100) and a Scottish Charity (registered number SC023592). Our registered office is at Roslin, Midlothian, EH25 9PS. VAT registration number 847380013. The information contained in this e-mail (including any attachments) is confidential and is intended for the use of the addressee only. The opinions expressed within this e-mail (including any attachments) are the opinions of the sender and do not necessarily constitute those of Roslin Institute (Edinburgh) ("the Institute") unless specifically stated by a sender who is duly authorised to do so on behalf of the Institute. From n at bioruby.org Wed Jan 30 11:28:52 2008 From: n at bioruby.org (Mitsuteru Nakao) Date: Thu, 31 Jan 2008 01:28:52 +0900 Subject: [BioRuby] bio blast In-Reply-To: <55915f820801300401s79aed759k2921da0fdff5a05a@mail.gmail.com> References: <55915f820801300401s79aed759k2921da0fdff5a05a@mail.gmail.com> Message-ID: <90ca35f70801300828y520186ci4673fd2d763b825d@mail.gmail.com> Hi If you remove the options "-m 0", you may get the search result without the error. # Because I don't have Windows.:-( > factory = Bio::Blast.new("blastp","#{db}","", "local") And thank you for your bug report. this is a bug in the Bio::Blast::Report class. > factory = Bio::Blast.new("blastp","#{db}","-m 0", "local") hanks. Mitsuteru, - Mitsuteru Nakao, Ph.D. n at bioruby.org / mn at kazusa.or.jp From sgujja at broad.mit.edu Thu Jan 31 17:19:44 2008 From: sgujja at broad.mit.edu (Sharvari Gujja) Date: Thu, 31 Jan 2008 17:19:44 -0500 Subject: [BioRuby] Bioruby and KEGG Message-ID: <47A24980.9090107@broad.mit.edu> Hi, I am trying to do KEGG analysis on protein multi fasta file(input file) in bioruby to get KO description for all the orfs in the fasta file. Appreciate any input on this. Thanks Sharvari PS: Version : BioRuby 1.2.1 / Ruby 1.8.6 From ktym at hgc.jp Thu Jan 31 19:15:03 2008 From: ktym at hgc.jp (Toshiaki Katayama) Date: Fri, 1 Feb 2008 09:15:03 +0900 Subject: [BioRuby] BioRuby Shell Rails Generator Bug ? In-Reply-To: <1201603231.7826.15.camel@Graco> References: <1201603231.7826.15.camel@Graco> Message-ID: <5EA1E3E5-9E75-4EB5-9E5F-524B2A6D425D@hgc.jp> Hmm, it is working in my environment without any changes. What version of rails are you using? By the way, rails mode (bioruby -r) is not yet tested with Rails 2.x and may not work. Regards, Toshiaki Katayama On 2008/01/29, at 19:40, Raoul Jean Pierre Bonnal wrote: > [root at Graco febo]# gem install bio > Updating metadata for 30 gems from http://gems.rubyforge.org > .............................. > complete > Successfully installed bio-1.2.1 > 1 gem installed > ---- > [febo at Graco Projects]$ bioruby -r testrb > Creating directory (/home/febo/Work/Projects/testrb/shell/session) ... > done > Creating directory (/home/febo/Work/Projects/testrb/shell/plugin) ... > done > Creating directory (/home/febo/Work/Projects/testrb/data) ... done > Installing Rails application for BioRuby shell ... > exists > a lot of create .... > > done > Installing Rails plugin for BioRuby shell ... > Couldn't find 'bioruby' generator > done > Then Rails starts. > ---------- > > So digging into the installation tree I > found /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/shell/rails/vendor/plugins/generators/bioruby/ > > and taking as example uniprot plugins > > > [root at Graco febo]# > ll /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/shell/rails/vendor/plugins/generators/bioruby/ > [root at Graco febo]# > mkdir /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/shell/rails/vendor/plugins/bioruby > [root at Graco febo]# > mv /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/shell/rails/vendor/plugins/generators /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/shell/rails/vendor/plugins/bioruby > [root at Graco febo]# > ll /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/shell/rails/vendor/plugins/ > totale 1 > drwxr-xr-x 3 root root 1024 2008-01-29 11:37 bioruby/ > > > [febo at Graco Projects]$ bioruby -r testrb > Creating directory (/home/febo/Work/Projects/testrb/shell/session) ... > done > Creating directory (/home/febo/Work/Projects/testrb/shell/plugin) ... > done > Creating directory (/home/febo/Work/Projects/testrb/data) ... done > Installing Rails application for BioRuby shell ... > exists > create app/controllers > create app/helpers > create app/models > create app/views/layouts > create config/environments > create config/initializers > create db > create doc > create lib > create lib/tasks > create log > create public/images > create public/javascripts > create public/stylesheets > create script/performance > create script/process > create test/fixtures > create test/functional > create test/integration > create test/mocks/development > create test/mocks/test > create test/unit > create vendor > create vendor/plugins > create tmp/sessions > create tmp/sockets > create tmp/cache > create tmp/pids > create Rakefile > create README > create app/controllers/application.rb > create app/helpers/application_helper.rb > create test/test_helper.rb > create config/database.yml > create config/routes.rb > create public/.htaccess > create config/initializers/inflections.rb > create config/initializers/mime_types.rb > create config/boot.rb > create config/environment.rb > create config/environments/production.rb > create config/environments/development.rb > create config/environments/test.rb > create script/about > create script/console > create script/destroy > create script/generate > create script/performance/benchmarker > create script/performance/profiler > create script/performance/request > create script/process/reaper > create script/process/spawner > create script/process/inspector > create script/runner > create script/server > create script/plugin > create public/dispatch.rb > create public/dispatch.cgi > create public/dispatch.fcgi > create public/404.html > create public/422.html > create public/500.html > create public/index.html > create public/favicon.ico > create public/robots.txt > create public/images/rails.png > create public/javascripts/prototype.js > create public/javascripts/effects.js > create public/javascripts/dragdrop.js > create public/javascripts/controls.js > create public/javascripts/application.js > create doc/README_FOR_APP > create log/server.log > create log/production.log > create log/development.log > create log/test.log > done > Installing Rails plugin for BioRuby shell ... > exists app/controllers > exists app/helpers > create app/views/bioruby > exists app/views/layouts > create public/images/bioruby > exists public/stylesheets > create app/controllers/bioruby_controller.rb > create app/helpers/bioruby_helper.rb > create app/views/bioruby/_methods.rhtml > create app/views/bioruby/_classes.rhtml > create app/views/bioruby/_modules.rhtml > create app/views/bioruby/_log.rhtml > create app/views/bioruby/_variables.rhtml > create app/views/bioruby/commands.rhtml > create app/views/bioruby/history.rhtml > create app/views/bioruby/index.rhtml > create app/views/layouts/bioruby.rhtml > create public/images/bioruby/spinner.gif > create public/images/bioruby/gem.png > create public/images/bioruby/link.gif > create public/images/bioruby/bg.gif > create public/stylesheets/bioruby.css > done > >>>> >>>> open http://localhost:3000/bioruby >>>> > > (You can change the port number by adding "-- -p 4000" option) > > > . . . B i o R u b y i n t h e s h e l l . . . > > Version : BioRuby 1.2.1 / Ruby 1.8.6 > > => Booting WEBrick... > => Rails application started on http://0.0.0.0:3000 > => Ctrl-C to shutdown server; call with --help for options > [2008-01-29 11:37:51] INFO WEBrick 1.3.1 > [2008-01-29 11:37:51] INFO ruby 1.8.6 (2007-03-13) [i586-linux-gnu] > [2008-01-29 11:37:51] INFO WEBrick::HTTPServer#start: pid=9210 > port=3000 > > > WORKS ! > > -- > Ra > From ktym at hgc.jp Thu Jan 31 20:10:11 2008 From: ktym at hgc.jp (Toshiaki Katayama) Date: Fri, 1 Feb 2008 10:10:11 +0900 Subject: [BioRuby] Bioruby and KEGG In-Reply-To: <47A24980.9090107@broad.mit.edu> References: <47A24980.9090107@broad.mit.edu> Message-ID: Hi, It depends on what kind of sequences in your multi fasta file, but I can recommend you to try KAAS with SBH (single best hit) method. http://www.genome.jp/kegg/kaas/ Regards, Toshiaki Katayama On 2008/02/01, at 7:19, Sharvari Gujja wrote: > Hi, > > I am trying to do KEGG analysis on protein multi fasta file(input file) > in bioruby to get KO description for all the orfs in the fasta file. > > Appreciate any input on this. > > Thanks > Sharvari > > PS: Version : BioRuby 1.2.1 / Ruby 1.8.6 > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby