Last Modified
2013-07-22 16:54:01 +0000
Requires
  • bio/appl/hmmer

Description

bio/appl/hmmer/report.rb - hmmsearch, hmmpfam parserer

Copyright

Copyright (C) 2002 Hiroshi Suga <suga@biophys.kyoto-u.ac.jp>,

Copyright

Copyright (C) 2005 Masashi Fujita <fujita@kuicr.kyoto-u.ac.jp>

License

The Ruby License

$Id:$

Description

Parser class for hmmsearch and hmmpfam in the HMMER package.

Examples

#for multiple reports in a single output file (example.hmmpfam)
Bio::HMMER.reports(File.read("example.hmmpfam")) do |report|
  report.program['name']
  report.parameter['HMM file']
  report.query_info['Query sequence']
  report.hits.each do |hit|
    hit.accession
    hit.description
    hit.score
    hit.evalue
    hit.hsps.each do |hsp|
      hsp.accession
      hsp.domain
      hsp.evalue
      hsp.midline
  end
end

References