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#
# = sample/demo_psort.rb - demonstration of Bio::PSORT, client for PSORT WWW server
#
# Copyright:: Copyright (C) 2003-2006
# Mitsuteru C. Nakao <n@bioruby.org>
# License:: The Ruby License
#
#
# == Description
#
# Demonstration of Bio::PSORT, client for PSORT (protein sorting site
# prediction systems) WWW server.
#
# == Requirements
#
# Internet connection is needed.
#
# == Usage
#
# Simply run this script.
#
# $ ruby demo_psort.rb
#
# == Development information
#
# The code was moved from lib/bio/appl/psort.rb.
#
require 'bio'
#if __FILE__ == $0
#begin
# require 'psort/report.rb'
#rescue LoadError
#end
seq = ">hoge mit
MALEPIDYTT RDEDDLDENE LLMKISNAAG SSRVNDNNDD LTFVENDKII
ARYSIQTSSK QQGKASTPPV EEAEEAAPQL PSRSSAAPPP PPRRATPEKK
DVKDLKSKFE GLAASEKEEE EMENKFAPPP KKSEPTIISP KPFSKPQEPV
FKGYHVQVTA HSREIDAEYL KIVRGSDPDT TWLIISPNAK KEYEPESTGS
KKSFTPSKSP APVSKKEPVK TPSPAPAAKI PKENPWATAE YDYDAAEDNE
NIEFVDDDWW LGELEKDGSK GLFPSNYVSL LPSRNVASGA PVQKEEPEQE
SFHDFLQLFD ETKVQYGLAR RKAKQNSGNA ETKAEAPKPE VPEDEPEGEP
DDWNEPELKE RDFDQAPLKP NQSSYKPIGK IDLQKVIAEE KAKEDPRLVQ
DYKKIGNPLP GMHIEADNEE EPEENDDDWD DDEDEAAQPP ANFAAVANNL
KPTAAGSKID DDKVIKGFRN EKSPAQLWAE VSPPGSDVEK IIIIGWCPDS
APLKTRASFA PSSDIANLKN ESKLKRDSEF NSFLGTTKPP SMTESSLKND
KAEEAEQPKT EIAPSLPSRN SIPAPKQEEA PEQAPEEEIE GN
"
Seq1 = ">hgoe
LTFVENDKII NI
"
puts "\n Bio::PSORT::PSORT"
puts "\n ==> p serv = Bio::PSORT::PSORT.imsut"
p serv = Bio::PSORT::PSORT1.imsut
puts "\n ==> p serv.class "
p serv.class
puts "\n ==> p serv.title = 'Query_title_splited_by_white space'"
p serv.title = 'Query_title_splited_by_white space'
puts "\n ==> p serv.exec(seq, false) "
p serv.exec(seq, false)
puts "\n ==> p serv.exec(seq) "
p serv.exec(seq)
puts "\n ==> p report = serv.exec(Bio::FastaFormat.new(seq)) "
p report = serv.exec(Bio::FastaFormat.new(seq))
puts "\n ==> p report.class"
p report.class
puts "\n ==> p report_raw = serv.exec(Bio::FastaFormat.new(seq), false) "
p report_raw = serv.exec(Bio::FastaFormat.new(seq), false)
puts "\n ==> p report_raw.class"
p report_raw.class
puts "\n ==> p report.methods"
p report.methods
methods = ['entry_id', 'origin', 'title', 'sequence','result_info',
'reasoning', 'final_result', 'raw']
methods.each do |method|
puts "\n ==> p report.#{method}"
p eval("report.#{method}")
end
puts "\n Bio::PSORT::PSORT2"
puts "\n ==> p serv = Bio::PSORT::PSORT2.imsut"
p serv = Bio::PSORT::PSORT2.imsut
puts "\n ==> p serv.class "
p serv.class
puts "\n ==> p seq "
p seq
puts "\n ==> p serv.title = 'Query_title_splited_by_white space'"
p serv.title = 'Query_title_splited_by_white space'
puts "\n ==> p serv.exec(seq) # parsed report"
p serv.exec(seq)
puts "\n ==> p report = serv.exec(Bio::FastaFormat.new(seq)) # parsed report"
p report = serv.exec(Bio::FastaFormat.new(seq))
puts "\n ==> p serv.exec(seq, false) # report in plain text"
p serv.exec(seq, false)
puts "\n ==> p report_raw = serv.exec(Bio::FastaFormat.new(seq), false) # report in plain text"
p report_raw = serv.exec(Bio::FastaFormat.new(seq), false)
puts "\n ==> p report.methods"
p report.methods
methods = ['entry_id', 'scl', 'definition', 'seq', 'features', 'prob', 'pred', 'k', 'raw']
methods.each do |method|
puts "\n ==> p report.#{method}"
p eval("report.#{method}")
end
#end
|
