/usr/bin/br_biofetch is in ruby-bio 1.4.2-2.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 | #!/usr/bin/env ruby
#
# = biofetch - BioFetch client
#
# Copyright:: Copyright (C) 2002
# Toshiaki Katayama <k@bioruby.org>
# License:: The Ruby License
#
# $Id: br_biofetch.rb,v 1.4 2007/04/05 23:35:39 trevor Exp $
#
require 'bio/io/fetch'
def usage
default_url = 'http://bioruby.org/cgi-bin/biofetch.rb'
another_url = 'http://www.ebi.ac.uk/cgi-bin/dbfetch'
puts "#{$0} [-s[erver] #{another_url}] db id [style] [format]"
puts " server : URL of the BioFetch CGI (default is #{default_url})"
puts " db : database name (embl, genbank, etc.)"
puts " id : entry id"
puts " style : 'raw' or 'html' (default is 'raw')"
puts " format : change the output format ('default', 'fasta', etc.)"
end
if ARGV.empty? or ARGV[0] =~ /^--?h/
usage
exit 1
end
case ARGV[0]
when /^--?s/ # User specified server
ARGV.shift
serv = Bio::Fetch.new(ARGV.shift)
puts serv.fetch(*ARGV)
when /^--?e/ # EBI server
ARGV.shift
serv = Bio::Fetch.new('http://www.ebi.ac.uk/cgi-bin/dbfetch')
puts serv.fetch(*ARGV)
when /^--?r/ # BioRuby server
ARGV.shift
serv = Bio::Fetch.new('http://bioruby.org/cgi-bin/biofetch.rb')
puts serv.fetch(*ARGV)
else # Default server
puts Bio::Fetch.query(*ARGV)
end
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