--- /dev/null
+#!/usr/bin/env ruby
+
+# Copyright (C) 2007-2011 Martin A. Hansen.
+
+# 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., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This program is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Determine the frequencies for k-mers in sequences in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+require 'biopieces'
+require 'seq'
+require 'pp'
+
+casts = []
+casts << {:long=>'size', :short=>'s', :type=>'uint', :mandatory=>false, :default=>4, :allowed=>nil, :disallowed=>'0'}
+casts << {:long=>'type', :short=>'t', :type=>'string', :mandatory=>false, :default=>"dna", :allowed=>"dna,rna,protein", :disallowed=>nil}
+
+bp = Biopieces.new
+
+options = bp.parse(ARGV, casts)
+
+oligos = Seq.generate_oligos(options[:size], options[:type])
+
+bp.each_record do |record|
+ if record.has_key? :SEQ
+ kmers = {}
+ oligos.each { |oligo| kmers[oligo.upcase] = 0 }
+
+ (0 ... record[:SEQ].length - options[:size]).each do |i|
+ kmer = record[:SEQ][i .. i + options[:size] - 1].upcase
+ kmers[kmer] += 1 if kmers[kmer]
+ end
+
+ record.merge! kmers
+ end
+
+ bp.puts record
+end
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
--- /dev/null
+#!/bin/bash
+
+source "$BP_DIR/bp_test/lib/test.sh"
+
+run "$bp -I $in -O $tmp"
+assert_no_diff $tmp $out.1
+clean
+
+run "$bp -I $in -s 2 -O $tmp"
+assert_no_diff $tmp $out.2
+clean
+
+run "$bp -I $in -s 2 -t rna -O $tmp"
+assert_no_diff $tmp $out.3
+clean
+
+run "$bp -I $in -s 2 -t protein -O $tmp"
+assert_no_diff $tmp $out.4
+clean
projects / biopieces.git / commitdiff