[BioRuby] reading multiple hmmpfam reports
George Githinji
georgkam at gmail.com
Thu Jan 15 15:43:05 UTC 2015
With bioruby version 1.4.3.0001, I am not sure what is causing the no
method error with this code taken from the example code.
Running the code below gives a NoMethodError.
undefined method `reports' for Bio::HMMER::Report:Class (NoMethodError)
file = ARGV[0] # a hmmpfam text file with multiple results
Bio::HMMER.reports(File.read(file)) 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
end
--
---------------
Sincerely
George
Skype: george_g2
Blog: http://www.biorelated.com/
Twitter: http://twitter.com/#!/george_l
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