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#!/usr/bin/env ruby
#
# pmsearch.rb - generate BibTeX format reference list by PubMed keyword search
#
# Copyright (C) 2002 KATAYAMA Toshiaki <k@bioruby.org>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# $Id:$
#
require 'bio'
Bio::NCBI.default_email = 'staff@bioruby.org'
if ARGV[0] =~ /\A\-f/
ARGV.shift
form = ARGV.shift
else
form = 'bibtex'
end
keywords = ARGV.join(' ')
uids = Bio::PubMed.esearch(keywords)
if uids and !uids.empty? then
entries = Bio::PubMed.efetch(uids)
else
entries = []
end
entries.each do |entry|
case form
when 'medline'
puts entry
else
puts Bio::MEDLINE.new(entry).reference.__send__(form.intern)
end
print "\n"
end
|
