[BioRuby] efetch/esearch broken
craigknox
craigknox at gmail.com
Thu Mar 5 19:16:23 UTC 2009
Hi Everyone,
I am using the latest bioruby gem (1.3.0) and I am having trouble
running efetch. The following is copied directly from the tutorial on
"http://bioruby.open-bio.org/wiki/BiorubyTutorial". When I run it,
"Bio::PubMed.efetch(entries)" returns a string instead of an array of
strings. Additionally, the "retmax" parameter for esearch is not
working - it is only returning the default of 100 entries.
Is the tutorial just out of date or is this a bug?
Thanks,
Craig Knox
#!/usr/bin/env ruby
require 'bio'
keywords = ARGV.join(' ') # I am using "histamine" here
options = {
'maxdate' => '2003/05/31',
'retmax' => 1000,
}
entries = Bio::PubMed.esearch(keywords, options)
Bio::PubMed.efetch(entries).each do |entry|
medline = Bio::MEDLINE.new(entry)
reference = medline.reference
puts reference.bibtex
end
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