Sha256: ab085742b7659066c313a6fcfc4c1b063233c173a18f97167add22669cfc0cfe
Contents?: true
Size: 1.17 KB
Versions: 29
Compression:
Stored size: 1.17 KB
Contents
#
# = bio/shell/plugin/psort.rb - plugin for PSORT
#
# Copyright:: Copyright (C) 2006
# Toshiaki Katayama <k@bioruby.org>
# License:: The Ruby License
#
# $Id: psort.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
#
module Bio::Shell
private
def psort1(str)
seq = getseq(str)
if seq.is_a?(Bio::Sequence::NA)
seq = seq.translate
end
psort = Bio::PSORT::PSORT1.imsut
fasta = seq.to_fasta
results = psort.exec(fasta).final_result
results.each do |result|
puts "#{result["certainty"].to_f*100.0}\t#{result["prediction"]}"
end
return results.first["prediction"]
end
def psort2(str)
seq = getseq(str)
if seq.is_a?(Bio::Sequence::NA)
seq = seq.translate
end
psort = Bio::PSORT::PSORT2.imsut
fasta = seq.to_fasta
results = psort.exec(fasta).prob.sort_by{|x, y| y}.reverse
results.each do |loc, prob|
next if prob <= 0.0
puts "#{prob}\t#{Bio::PSORT::PSORT2::SclNames[loc]}"
end
return results.first.first
end
def psort2locations
names = Bio::PSORT::PSORT2::SclNames
names.sort.each do |loc, desc|
puts "#{loc}\t#{desc}"
end
return names
end
end
Version data entries
29 entries across 29 versions & 6 rubygems