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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
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