/usr/bin/br_biogetseq is in ruby-bio 1.5.0-2.
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 | #!/usr/bin/ruby
#
# = biogetseq - OBDA sequence data retrieval (executable)
#
# Copyright:: Copyright (C) 2003
# Toshiaki Katayama <k@bioruby.org>
# License:: The Ruby License
#
# $Id: br_biogetseq.rb,v 1.4 2007/04/05 23:35:39 trevor Exp $
#
require 'bio'
def usage
print <<END
#{$0} --dbname <dbname> [--namespace <namespace>] entry_id [entry_id]
END
exit 1
end
if ARGV.size < 3
usage
end
while ARGV.first =~ /^-/
case ARGV.shift
when /^\-\-format/
ARGV.shift
raise NotImplementedError
when /^\-\-dbname/
dbname = ARGV.shift
when /^\-\-namespace/
namespace = ARGV.shift
end
end
reg = Bio::Registry.new
db = reg.get_database(dbname)
if namespace
db['namespace'] = namespace
end
ARGV.each do |entry|
puts db.get_by_id(entry)
end
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