report.rb

Path: lib/bio/appl/hmmer/report.rb
Last Update: Sun Mar 06 17:42:30 +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   pp   bio/shell/setup   bio/shell/irb   bio/shell/web   bio/shell/script   bio/shell/core   bio/shell/interface   bio/shell/object   bio/shell/demo   bio/shell/plugin/entry   bio/shell/plugin/seq   bio/shell/plugin/midi   bio/shell/plugin/codon   bio/shell/plugin/flatfile   bio/shell/plugin/obda   bio/shell/plugin/das   bio/shell/plugin/keggapi   bio/shell/plugin/soap   bio/shell/plugin/emboss   bio/shell/plugin/blast   bio/shell/plugin/psort   bio/shell/plugin/ncbirest   bio/shell/plugin/togows   irb   irb/completion   ./config/boot   ./config/environment   ./config/boot   commands/server   net/ftp  

External Aliases

pp -> p

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