[BioRuby-cvs] bioruby/lib/bio/shell/plugin blast.rb,NONE,1.1

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/shell/plugin
In directory dev.open-bio.org:/tmp/cvs-serv27565/lib/bio/shell/plugin

Added Files:
	blast.rb 
Log Message:
* newly added shell plugin for blast (currently only supports blast
  against KEGG GENES peptides)


--- NEW FILE: blast.rb ---
#
# = bio/shell/plugin/blast.rb - plugin for BLAST services
#
# Copyright::   Copyright (C) 2006
#               Toshiaki Katayama <k at bioruby.org>
# License::     Ruby's
#
# $Id: blast.rb,v 1.1 2006/07/25 18:43:17 k 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 = seq(data.seq)
    else
      desc = "query"
      tmp = seq(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