bio/appl/hmmer/report.rb - hmmsearch, hmmpfam parserer
Copyright: | Copyright (C) 2002 Hiroshi Suga <suga@biophys.kyoto-u.ac.jp>,
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Copyright: | Copyright (C) 2005 Masashi Fujita <fujita@kuicr.kyoto-u.ac.jp>
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License: | The Ruby License
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$Id:$
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