report.rb

Path: lib/bio/appl/hmmer/report.rb
Last Update: Sun Dec 04 02:16:41 +0000 2011

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

Required files

bio/appl/hmmer  

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