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#!/usr/bin/env ruby
#
# enzymes.rb - cut input file using enzyme on command line
#
# Copyright (C) 2006 Pjotr Prins <p@bioruby.org> and Trevor Wennblom <trevor@corevx.com>
#
# 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.
#
# $Id: enzymes.rb,v 1.1 2006/03/03 15:31:06 pjotr Exp $
#
require 'bio/io/flatfile'
require 'bio/util/restriction_enzyme'
include Bio
usage = <<USAGE
Usage: enzymes.rb enzyme1 [enzyme2] infiles
Examples:
Output the primary sequences cut using both BstYI and MseI:
./enzymes.rb BstYI MseI *.seq
or using the actual formats
./enzymes.rb "r^gatcy" "t^taa" *.seq
USAGE
if ARGV.size < 2
print usage
exit 1
end
enzyme1 = ARGV.shift
# ---- Fetch enzyme2 if it is not a file
arg2 = ARGV[0]
if arg2 and !File.exist?(arg2)
enzyme2 = ARGV.shift
end
re1 = Bio::RestrictionEnzyme::DoubleStranded.new(enzyme1)
puts "Enzyme #{enzyme1}: " + re1.primary.with_cut_symbols # e.g. r^gatcy
if (enzyme2)
re2 = Bio::RestrictionEnzyme::DoubleStranded.new(enzyme2)
puts "Enzyme #{enzyme2}: " + re2.primary.with_cut_symbols # e.g. t^taa
end
ARGV.each do | fn |
ff = Bio::FlatFile.auto(fn)
ff.each_entry do |entry|
seq = Bio::Sequence::NA.new(entry.seq)
# puts seq.inspect
seq.cut_with_enzyme(enzyme1).each do | frag1 |
frag = frag1
if enzyme2
seq = Bio::Sequence::NA.new(frag1.primary)
frags2 = seq.cut_with_enzyme(enzyme2)
next if frags2.size == 0
frag = frags2.shift # pick up first fragment
end
print '> '+entry.definition+"\n"
print frag.primary,"\n"
end
end
end
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