Sha256: 363a9cd26d862b6fc7d7dd6cba92eb1e5f8a1e85252768e14f22ba6691b141d8
Contents?: true
Size: 789 Bytes
Versions: 29
Compression:
Stored size: 789 Bytes
Contents
#
# = bio/shell/plugin/blast.rb - plugin for BLAST services
#
# Copyright:: Copyright (C) 2006
# Toshiaki Katayama <k@bioruby.org>
# License:: The Ruby License
#
# $Id: blast.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
#
module Bio::Shell
private
# GenomeNet
def keggblast(query)
server = Bio::Blast.remote("blastp", "genes", "", "genomenet_tab")
if query[/^>/]
data = Bio::FastaFormat.new(query)
desc = data.definition
tmp = getseq(data.seq)
else
desc = "query"
tmp = getseq(query)
end
if tmp.respond_to?(:translate)
aaseq = tmp.translate
else
aaseq = tmp
end
fasta = aaseq.to_fasta(desc, 60)
result = server.query(fasta)
puts server.output
return result
end
end
Version data entries
29 entries across 29 versions & 6 rubygems