bio 1.3.1 → 1.4.0

data/sample/demo_ddbjxml.rb

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+#
+# = sample/demo_ddbjxml.rb - demonstration of Bio::DDBJ::XML, DDBJ SOAP access
+#
+# Copyright::	Copyright (C) 2003, 2004
+#		Toshiaki Katayama <k@bioruby.org>
+# License::	The Ruby License
+#
+#
+#
+# == Description
+#
+# Demonstration of Bio::DDBJ::XML, DDBJ SOAP server access class.
+#
+# == Requirements
+#
+# Internet connection is needed.
+#
+# == Usage
+#
+# Simply run this script.
+#
+#  $ ruby demo_ddbjxml.rb
+#
+# == Notes
+#
+# It can not be run with Ruby 1.9 because SOAP4R (SOAP support for Ruby)
+# currently does not support Ruby 1.9.
+#
+# == Development information
+#
+# The code was moved from lib/bio/io/ddbjxml.rb.
+#
+
+require 'bio'
+
+#if __FILE__ == $0
+
+  begin
+    require 'pp'
+    alias p pp
+  rescue LoadError
+  end
+
+  puts ">>> Bio::DDBJ::XML::Blast"
+  serv = Bio::DDBJ::XML::Blast.new
+# serv.log = STDERR
+
+  query = "MSSRIARALALVVTLLHLTRLALSTCPAACHCPLEAPKCAPGVGLVRDGCGCCKVCAKQL"
+
+  puts "### searchSimple('blastp', 'SWISS', query)"
+  puts serv.searchSimple('blastp', 'SWISS', query)
+
+  puts "### searchParam('tblastn', 'ddbjvrl', query, '-m 8')"
+  puts serv.searchParam('tblastn', 'ddbjvrl', query, '-m 8')
+
+
+  puts ">>> Bio::DDBJ::XML::ClustalW"
+  serv = Bio::DDBJ::XML::ClustalW.new
+
+  query = <<END
+> RABSTOUT   rabbit Guinness receptor
+   LKMHLMGHLKMGLKMGLKGMHLMHLKHMHLMTYTYTTYRRWPLWMWLPDFGHAS
+   ADSCVCAHGFAVCACFAHFDVCFGAVCFHAVCFAHVCFAAAVCFAVCAC
+> MUSNOSE   mouse nose drying factor
+    mhkmmhkgmkhmhgmhmhglhmkmhlkmgkhmgkmkytytytryrwtqtqwtwyt
+    fdgfdsgafdagfdgfsagdfavdfdvgavfsvfgvdfsvdgvagvfdv
+> HSHEAVEN    human Guinness receptor repeat
+ mhkmmhkgmkhmhgmhmhg   lhmkmhlkmgkhmgkmk  ytytytryrwtqtqwtwyt
+ fdgfdsgafdagfdgfsag   dfavdfdvgavfsvfgv  dfsvdgvagvfdv
+ mhkmmhkgmkhmhgmhmhg   lhmkmhlkmgkhmgkmk  ytytytryrwtqtqwtwyt
+ fdgfdsgafdagfdgfsag   dfavdfdvgavfsvfgv  dfsvdgvagvfdv
+END
+
+  puts "### analyzeSimple(query)"
+  puts serv.analyzeSimple(query)
+
+  puts "### analyzeParam(query, '-align -matrix=blosum')"
+  puts serv.analyzeParam(query, '-align -matrix=blosum')
+
+
+  puts ">>> Bio::DDBJ::XML::DDBJ"
+  serv = Bio::DDBJ::XML::DDBJ.new
+
+  puts "### getFFEntry('AB000050')"
+  puts serv.getFFEntry('AB000050')
+
+  puts "### getXMLEntry('AB000050')"
+  puts serv.getXMLEntry('AB000050')
+
+  puts "### getFeatureInfo('AB000050', 'cds')"
+  puts serv.getFeatureInfo('AB000050', 'cds')
+
+  puts "### getAllFeatures('AB000050')"
+  puts serv.getAllFeatures('AB000050')
+
+  puts "### getRelatedFeatures('AL121903', '59000', '64000')"
+  puts serv.getRelatedFeatures('AL121903', '59000', '64000')
+
+  puts "### getRelatedFeaturesSeq('AL121903', '59000', '64000')"
+  puts serv.getRelatedFeaturesSeq('AL121903', '59000', '64000')
+
+
+  puts ">>> Bio::DDBJ::XML::Fasta"
+  serv = Bio::DDBJ::XML::Fasta.new
+
+  query = ">Test\nMSDGAVQPDG GQPAVRNERA TGSGNGSGGG GGGGSGGVGI"
+
+  puts "### searchSimple('fasta34', 'PDB', query)"
+  puts serv.searchSimple('fasta34', 'PDB', query)
+
+  query = ">Test\nAGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC"
+
+  puts "### searchParam('fastx34_t', 'PDB', query, '-n')"
+  puts serv.searchParam('fastx34_t', 'PDB', query, '-n')
+
+
+  puts ">>> Bio::DDBJ::XML::GetEntry"
+  serv = Bio::DDBJ::XML::GetEntry.new
+
+  puts "### getDDBJEntry('AB000050')"
+  puts serv.getDDBJEntry('AB000050')
+
+  puts "### getPDBEntry('1AAR')"
+  puts serv. getPDBEntry('1AAR')
+
+
+  puts ">>> Bio::DDBJ::XML::Gib"
+  serv = Bio::DDBJ::XML::Gib.new
+
+  puts "### getOrganismList"
+  puts serv.getOrganismList
+
+  puts "### getChIDList"
+  puts serv.getChIDList
+
+  puts "### getOrganismNameFromChid('Sent_CT18:')"
+  puts serv.getOrganismNameFromChid('Sent_CT18:')
+
+  puts "### getChIDFromOrganismName('Aquifex aeolicus VF5')"
+  puts serv.getChIDFromOrganismName('Aquifex aeolicus VF5')
+
+  puts "### getAccession('Ecol_K12_MG1655:')"
+  puts serv.getAccession('Ecol_K12_MG1655:')
+
+  puts "### getPieceNumber('Mgen_G37:')"
+  puts serv.getPieceNumber('Mgen_G37:')
+
+  puts "### getDivision('Mgen_G37:')"
+  puts serv.getDivision('Mgen_G37:')
+
+  puts "### getType('Mgen_G37:')"
+  puts serv.getType('Mgen_G37:')
+
+  puts "### getCDS('Aaeo_VF5:ece1')"
+  puts serv.getCDS('Aaeo_VF5:ece1')
+
+  puts "### getFlatFile('Nost_PCC7120:pCC7120zeta')"
+  puts serv.getFlatFile('Nost_PCC7120:pCC7120zeta')
+
+  puts "### getFastaFile('Nost_PCC7120:pCC7120zeta')"
+  puts serv.getFastaFile('Nost_PCC7120:pCC7120zeta', 'cdsaa')
+
+
+  puts ">>> Bio::DDBJ::XML::Gtop"
+  serv = Bio::DDBJ::XML::Gtop.new
+
+  puts "### getOrganismList"
+  puts serv.getOrganismList
+
+  puts "### getMasterInfo"
+  puts serv.getMasterInfo('thrA', 'ecol0')
+
+
+#  puts ">>> Bio::DDBJ::XML::PML"
+#  serv = Bio::DDBJ::XML::PML.new
+#
+#  puts "### getVariation('1')"
+#  puts serv.getVariation('1')
+
+
+  puts ">>> Bio::DDBJ::XML::SRS"
+  serv = Bio::DDBJ::XML::SRS.new
+
+  puts "### searchSimple('[pathway-des:sugar]')"
+  puts serv.searchSimple('[pathway-des:sugar]')
+
+  puts "### searchParam('[swissprot-des:cohesin]', '-f seq -sf fasta')"
+  puts serv.searchParam('[swissprot-des:cohesin]', '-f seq -sf fasta')
+
+
+  puts ">>> Bio::DDBJ::XML::TxSearch"
+  serv = Bio::DDBJ::XML::TxSearch.new
+
+  puts "### searchSimple('*coli')"
+  puts serv.searchSimple('*coli')
+
+  puts "### searchSimple('*tardigrada*')"
+  puts serv.searchSimple('*tardigrada*')
+
+  puts "### getTxId('Escherichia coli')"
+  puts serv.getTxId('Escherichia coli')
+
+  puts "### getTxName('562')"
+  puts serv.getTxName('562')
+
+  query = "Campylobacter coli\nEscherichia coli"
+  rank = "family\ngenus"
+
+  puts "### searchLineage(query, rank, 'Bacteria')"
+  puts serv.searchLineage(query, rank, 'Bacteria')
+
+#end

data/sample/demo_fasta_remote.rb

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+#
+# = sample/demo_fasta_remote.rb - demonstration of FASTA execution using GenomeNet web service
+#
+# Copyright::  Copyright (C) 2001, 2002 Toshiaki Katayama <k@bioruby.org>
+# License::    The Ruby License
+#
+# == Description
+#
+# Demonstration of Bio::Fasta.remote, wrapper class for FASTA execution using
+# GenomeNet fasta.genome.jp web service.
+#
+# == Requirements
+#
+# * Internet connection
+#
+# == Usage
+#
+# Specify a files containing a nucleic acid sequence.
+# The file format should be the fasta format.
+#
+#  $ ruby demo_fasta_remote.rb file.fst
+#
+# Example usage using test data:
+#
+#  $ ruby -Ilib sample/demo_fasta_remote.rb test/data/blast/b0002.faa
+#
+# Note that it may take very long time. Please wait for 3 to 5 minutes.
+#
+# == Development information
+#
+# The code was moved from lib/bio/appl/fasta.rb.
+#
+
+require 'bio'
+
+#if __FILE__ == $0
+  begin
+    require 'pp'
+    alias p pp
+  rescue
+  end
+
+# serv = Bio::Fasta.local('fasta34', 'hoge.nuc')
+# serv = Bio::Fasta.local('fasta34', 'hoge.pep')
+# serv = Bio::Fasta.local('ssearch34', 'hoge.pep')
+
+  # This may take 3 minutes or so.
+  serv = Bio::Fasta.remote('fasta', 'genes')
+  p serv.query(ARGF.read)
+#end
+

data/sample/demo_fastaformat.rb

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+#
+# = sample/demo_fastaformat.rb - demonstration of the FASTA format parser
+#
+# Copyright::  Copyright (C) 2001, 2002
+#              Naohisa Goto <ng@bioruby.org>,
+#              Toshiaki Katayama <k@bioruby.org>
+# License::    The Ruby License
+#
+# $Id:$
+#
+# == Description
+#
+# Demonstration of FASTA format parser.
+#
+# == Usage
+#
+# Simply run the script.
+#
+#  $ ruby demo_fastaformat.rb
+#
+# == Development information
+#
+# The code was moved from lib/bio/db/fasta.rb.
+#
+
+require 'bio'
+
+  f_str = <<END
+>sce:YBR160W  CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]
+MSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEG
+VPSTAIREISLLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYME
+GIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQNLLINKDGNL
+KLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGC
+IFAEMCNRKPIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFP
+QWRRKDLSQVVPSLDPRGIDLLDKLLAYDPINRISARRAAIHPYFQES
+>sce:YBR274W  CHK1; probable serine/threonine-protein kinase [EC:2.7.1.-] [SP:KB9S_YEAST]
+MSLSQVSPLPHIKDVVLGDTVGQGAFACVKNAHLQMDPSIILAVKFIHVP
+TCKKMGLSDKDITKEVVLQSKCSKHPNVLRLIDCNVSKEYMWIILEMADG
+GDLFDKIEPDVGVDSDVAQFYFQQLVSAINYLHVECGVAHRDIKPENILL
+DKNGNLKLADFGLASQFRRKDGTLRVSMDQRGSPPYMAPEVLYSEEGYYA
+DRTDIWSIGILLFVLLTGQTPWELPSLENEDFVFFIENDGNLNWGPWSKI
+EFTHLNLLRKILQPDPNKRVTLKALKLHPWVLRRASFSGDDGLCNDPELL
+AKKLFSHLKVSLSNENYLKFTQDTNSNNRYISTQPIGNELAELEHDSMHF
+QTVSNTQRAFTSYDSNTNYNSGTGMTQEAKWTQFISYDIAALQFHSDEND
+CNELVKRHLQFNPNKLTKFYTLQPMDVLLPILEKALNLSQIRVKPDLFAN
+FERLCELLGYDNVFPLIINIKTKSNGGYQLCGSISIIKIEEELKSVGFER
+KTGDPLEWRRLFKKISTICRDIILIPN
+END
+
+  f = Bio::FastaFormat.new(f_str)
+  puts "### FastaFormat"
+  puts "# entry"
+  puts f.entry
+  puts "# entry_id"
+  p f.entry_id
+  puts "# definition"
+  p f.definition
+  puts "# data"
+  p f.data
+  puts "# seq"
+  p f.seq
+  puts "# seq.type"
+  p f.seq.type
+  puts "# length"
+  p f.length
+  puts "# aaseq"
+  p f.aaseq
+  puts "# aaseq.type"
+  p f.aaseq.type
+  puts "# aaseq.composition"
+  p f.aaseq.composition
+  puts "# aalen"
+  p f.aalen
+
+  puts
+
+  n_str = <<END
+>CRA3575282.F 
+24 15 23 29 20 13 20 21 21 23 22 25 13 22 17 15 25 27 32 26  
+32 29 29 25
+END
+
+  n = Bio::FastaNumericFormat.new(n_str)
+  puts "### FastaNumericFormat"
+  puts "# entry"
+  puts n.entry
+  puts "# entry_id"
+  p n.entry_id
+  puts "# definition"
+  p n.definition
+  puts "# data"
+  p n.data
+  puts "# length"
+  p n.length
+  #puts "# percent to ratio by yield"
+  #n.each do |x|
+  #  p x/100.0
+  #end
+  puts "# first three"
+  p n[0]
+  p n[1]
+  p n[2]
+  puts "# last one"
+  p n[-1]
+

data/sample/demo_genbank.rb

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+#
+# = sample/demo_genbank.rb - demonstration of Bio::GenBank
+#
+# Copyright::  Copyright (C) 2000-2005 Toshiaki Katayama <k@bioruby.org>
+# License::    The Ruby License
+#
+#
+# == Description
+#
+# Demonstration of Bio::GenBank, the parser class for the GenBank entry.
+#
+# == Usage
+#
+# Usage 1: Without arguments, showing demo with a GenBank entry.
+# Internet connection is needed.
+#
+#  $ ruby demo_genbank.rb
+#
+# Usage 2: IDs or accession numbers are given as the arguments.
+# Internet connection is needed.
+#
+#  $ ruby demo_genbank.rb X94434 NM_000669
+#
+# Usage 3: When the first argument is "--files", "-files", "--file", or
+# "-file", filenames are given as the arguments.
+#
+#  $ ruby demo_genbank.rb --files file1.gbk file2.gbk ...
+#
+# == Development information
+#
+# The code was moved from lib/bio/db/genbank/genbank.rb, and modified
+# as below:
+# * To get sequences from the NCBI web service.
+# * By default, arguments are sequence IDs (accession numbers).
+# * New option "--files" (or "-files", "--file", or "-file") to
+#   read sequences from file(s).
+# 
+
+require 'bio'
+
+begin
+  require 'pp'
+  alias p pp
+rescue LoadError
+end
+
+def demo_genbank(gb)
+
+  puts "### GenBank"
+  puts "## LOCUS"
+  puts "# GenBank.locus"
+  p gb.locus
+  puts "# GenBank.entry_id"
+  p gb.entry_id
+  puts "# GenBank.nalen"
+  p gb.nalen
+  puts "# GenBank.strand"
+  p gb.strand
+  puts "# GenBank.natype"
+  p gb.natype
+  puts "# GenBank.circular"
+  p gb.circular
+  puts "# GenBank.division"
+  p gb.division
+  puts "# GenBank.date"
+  p gb.date
+
+  puts "## DEFINITION"
+  p gb.definition
+
+  puts "## ACCESSION"
+  p gb.accession
+
+  puts "## VERSION"
+  p gb.versions
+  p gb.version
+  p gb.gi
+
+  puts "## NID"
+  p gb.nid
+
+  puts "## KEYWORDS"
+  p gb.keywords
+
+  puts "## SEGMENT"
+  p gb.segment
+
+  puts "## SOURCE"
+  p gb.source
+  p gb.common_name
+  p gb.vernacular_name
+  p gb.organism
+  p gb.taxonomy
+
+  puts "## REFERENCE"
+  p gb.references
+
+  puts "## COMMENT"
+  p gb.comment
+
+  puts "## FEATURES"
+  p gb.features
+
+  puts "## BASE COUNT"
+  p gb.basecount
+  p gb.basecount('a')
+  p gb.basecount('A')
+
+  puts "## ORIGIN"
+  p gb.origin
+  p gb.naseq
+
+  puts "=" * 78
+end
+
+case ARGV[0]
+when '-file', '--file', '-files', '--files'
+  ARGV.shift
+  ARGV.each do |filename|
+    Bio::FlatFile.foreach(filename) do |gb|
+      demo_genbank(gb)
+    end
+  end
+else
+  efetch = Bio::NCBI::REST::EFetch.new
+  argv = ARGV.empty? ? [ 'X94434' ] : ARGV
+  argv.each do |id_or_accession|
+    raw = efetch.sequence(id_or_accession)
+    gb = Bio::GenBank.new(raw)
+    demo_genbank(gb)
+  end
+end