-#!/usr/bin/env perl
+#!/usr/bin/env ruby
-# Copyright (C) 2007-2009 Martin A. Hansen.
+# Copyright (C) 2007-2012 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
# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# Use BWA to map sequences in the stream against a specified genome or index.
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-use warnings;
-use strict;
-use Data::Dumper;
-use Maasha::Biopieces;
-use Maasha::Common;
-use Maasha::Fastq;
-use Maasha::SAM;
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-my ( $options, $in, $out, $index, $tmp_dir, $tmp_fq, $tmp_sai, $tmp_sam, $fh_in, $fh_out, $record, $entry, $line, @fields, $type, @args, $arg );
-
-$options = Maasha::Biopieces::parse_options(
- [
- { long => 'genome', short => 'g', type => 'genome', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- { long => 'index_name', short => 'i', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- { long => 'mismatches', short => 'm', type => 'uint', mandatory => 'no', default => 0, allowed => "0,1,2,3", disallowed => undef },
- { long => 'max_hits', short => 'h', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 },
- { long => 'cpus', short => 'c', type => 'uint', mandatory => 'no', default => 1, allowed => undef, disallowed => 0 },
- ]
-);
-
-Maasha::Common::error( qq(both --index_name and --genome specified) ) if $options->{ "genome" } and $options->{ "index_name" };
-Maasha::Common::error( qq(no --index_name or --genome specified) ) if not $options->{ "genome" } and not $options->{ "index_name" };
-
-$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
-$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
-
-if ( defined $options->{ 'genome' } ) {
- $index = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/bowtie/$options->{ 'genome' }";
-} elsif (defined $options->{ 'index_name' } ) {
- $index = $options->{ 'index_name' };
-}
-
-$tmp_dir = Maasha::Biopieces::get_tmpdir();
-$tmp_fq = "$tmp_dir/bwa.fq";
-$tmp_sai = "$tmp_dir/bwa.fq.sai";
-$tmp_sam = "$tmp_dir/bwa.fq.sam";
-
-$fh_out = Maasha::Filesys::file_write_open( $tmp_fq );
-
-while ( $record = Maasha::Biopieces::get_record( $in ) )
-{
- if ( $entry = Maasha::Fastq::biopiece2fastq( $record ) ) {
- Maasha::Fastq::put_entry( $entry, $fh_out );
- }
-
- Maasha::Biopieces::put_record( $record, $out );
-}
-
-close $fh_out;
-
-push @args, "-t $options->{ 'cpus' }";
-push @args, "-R $options->{ 'max_hits' }" if $options->{ 'max_hits' };
-
-$arg = join " ", @args;
-
-if ( $options->{ 'verbose' } )
-{
- print STDERR qq(Running: bwa aln $arg $index $tmp_fq > $tmp_sai\n);
- Maasha::Common::run( "bwa", "aln $arg $index $tmp_fq > $tmp_sai" );
- print STDERR qq(Running: bwa samse $index $tmp_sai $tmp_fq > $tmp_sam\n);
- Maasha::Common::run( "bwa", "samse $index $tmp_sai $tmp_fq > $tmp_sam" )
-}
-else
-{
- Maasha::Common::run( "bwa", "aln $arg $index $tmp_fq > $tmp_sai 2> /dev/null" );
- Maasha::Common::run( "bwa", "samse $index $tmp_sai $tmp_fq > $tmp_sam 2> /dev/null" );
-}
-
-$fh_in = Maasha::Filesys::file_read_open( $tmp_sam );
-
-while ( $entry = Maasha::SAM::get_entry( $fh_in ) )
-{
- if ( $record = Maasha::SAM::sam2biopiece( $entry ) ) {
- Maasha::Biopieces::put_record( $record, $out );
- }
-}
-
-close $fh_in;
-
-unlink $tmp_fq;
-unlink $tmp_sai;
-unlink $tmp_sam;
-
-Maasha::Biopieces::close_stream( $in );
-Maasha::Biopieces::close_stream( $out );
-
-
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+# This program is part of the Biopieces framework (www.biopieces.org).
-BEGIN
-{
- Maasha::Biopieces::status_set();
-}
-
-
-END
-{
- Maasha::Biopieces::status_log();
-}
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+# Use BWA to map sequences in the stream against a specified index.
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+require 'maasha/biopieces'
+require 'maasha/seq'
+require 'maasha/fasta'
+require 'maasha/fastq'
+require 'maasha/sam'
+
+casts = []
+casts << {:long=>'index_name', :short=>'i', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'mismatches', :short=>'m', :type=>'uint', :mandatory=>false, :default=>0, :allowed=>"0,1,2,3", :disallowed=>nil}
+casts << {:long=>'max_hits', :short=>'h', :type=>'uint', :mandatory=>false, :default=>30, :allowed=>nil, :disallowed=>'0'}
+casts << {:long=>'cpus', :short=>'c', :type=>'uint', :mandatory=>false, :default=>1, :allowed=>nil, :disallowed=>'0'}
+
+options = Biopieces.options_parse(ARGV, casts)
+
+tmp_dir = Biopieces.mktmpdir
+tmp_fq = File.join(tmp_dir, "bwa.fq")
+tmp_sai = File.join(tmp_dir, "bwa.sai")
+tmp_sam = File.join(tmp_dir, "bwa.sam")
+
+# Class containing methods for executing BWA.
+class BWA
+ def initialize(fq_file, sai_file, sam_file, options)
+ @fq_file = fq_file
+ @sai_file = sai_file
+ @sam_file = sam_file
+ @options = options
+ @command = []
+ end
+
+ # Method to run bwa aln.
+ def aln
+ @command << "bwa aln"
+ @command << "-t #{@options[:cpus]}"
+ @command << "-R #{@options[:max_hits]}"
+ @command << "-f #{@sai_file}"
+ @command << @options[:index_name]
+ @command << @fq_file
+
+ execute
+ end
+
+ # Method to run bwa samse.
+ def samse
+ @command << "bwa samse"
+ @command << "-f #{@sam_file}"
+ @command << @options[:index_name]
+ @command << @sai_file
+ @command << @fq_file
+
+ execute
+ end
+
+ private
+
+ # Method to execute a command using a system() call.
+ # The command is composed of bits from the @command variable.
+ def execute
+ @command.unshift "nice -n 19"
+ @command << "> /dev/null 2>&1" unless @options[:verbose]
+
+ command = @command.join(" ")
+ $stderr.puts "Running command: #{command}" if @options[:verbose]
+ system(command)
+ raise "Command failed: #{command}" unless $?.success?
+
+ @command = []
+ end
+end
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+ Fastq.open(tmp_fq, 'w') do |io_fq|
+ input.each_record do |record|
+ output.puts record
+
+ if record[:SEQ_NAME] and record[:SEQ] and record[:SCORES]
+ entry = Seq.new_bp(record)
+
+ io_fq.puts entry.to_fastq
+ end
+ end
+ end
+
+ bwa = BWA.new(tmp_fq, tmp_sai, tmp_sam, options)
+ bwa.aln
+ bwa.samse
+
+ Sam.open(tmp_sam, 'r') do |io_sam|
+ io_sam.each do |entry|
+ output.puts Sam.to_bp(entry) unless entry[:RNAME] == '*'
+ end
+ end
+end
-__END__
projects / biopieces.git / blobdiff