added bowtie_seq biopiece

git-svn-id: http://biopieces.googlecode.com/svn/trunk@570 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/bowtie_seq b/bp_bin/bowtie_seq
new file mode 100755 (executable)
index 0000000..560b1c4
--- /dev/null
+++ b/bp_bin/bowtie_seq
@@ -0,0 +1,152 @@
+#!/usr/bin/env perl
+
+# Copyright (C) 2007-2009 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
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Use bowtie to map sequences in the stream against a specified genome.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Maasha::Biopieces;
+use Maasha::Common;
+use Maasha::Fasta;
+use Maasha::Calc;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $index, $tmp_dir, $tmp_in, $tmp_out, $fh_in, $fh_out, $record, $entry, $line, @fields );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'genome', short => 'g', type => 'genome', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$index = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/bowtie/$options->{ 'genome' }";
+
+$tmp_dir = Maasha::Biopieces::get_tmpdir();
+$tmp_in  = "$tmp_dir/bowtie.seq";
+$tmp_out = "$tmp_dir/bowtie.out";
+
+$fh_out = Maasha::Filesys::file_write_open( $tmp_in );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) ) {
+        Maasha::Fasta::put_entry( $entry, $fh_out );
+    }
+
+    Maasha::Biopieces::put_record( $record, $out );
+}
+
+close $fh_out;
+
+if ( $options->{ 'verbose' } ) {
+    Maasha::Common::run( "bowtie", "-f $index $tmp_in $tmp_out" );
+} else {
+    Maasha::Common::run( "bowtie", "-f $index $tmp_in $tmp_out > /dev/null 2>&1" );
+}
+
+unlink $tmp_in;
+
+$fh_in = Maasha::Filesys::file_read_open( $tmp_out );
+
+while ( $line = <$fh_in> )
+{
+    chomp $line;
+
+    @fields = split /\t/, $line;
+
+    $record = bowtie2biopiece( \@fields );
+
+    Maasha::Biopieces::put_record( $record, $out );
+}
+
+close $fh_out;
+
+unlink $tmp_out;
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+sub bowtie2biopiece
+{
+    # Martin A. Hansen, July 2009
+
+    # Convert a bowtie entry to a Biopiece record.
+
+    my ( $entry,   # bowtie entry
+       ) = @_;
+
+    # Returns a hash.
+
+    my ( $record, @scores );
+
+    $record->{ 'Q_ID' }     = $entry->[ 0 ];
+    $record->{ 'STRAND' }   = $entry->[ 1 ];
+    $record->{ 'S_ID' }     = $entry->[ 2 ];
+    $record->{ 'S_BEG' }    = $entry->[ 3 ];
+    $record->{ 'SEQ' }      = $entry->[ 4 ];
+    $record->{ 'SCORES' }   = $entry->[ 5 ];
+    $record->{ 'MISMATCH' } = $entry->[ 6 ];
+
+    $record->{ 'SEQ_LEN' }  = length $entry->[ 4 ];
+    $record->{ 'S_END' }    = $record->{ 'S_BEG' } + $record->{ 'SEQ_LEN' } - 1;
+    $record->{ 'SCORES' }   =~ s/(.)/ord( $1 ) - 33 . ";"/ge; # http://maq.sourceforge.net/fastq.shtml
+    $record->{ 'SCORE' }    = Maasha::Calc::mean( [ split /;/, $record->{ 'SCORES' } ] );
+
+    $record->{ 'REC_TYPE' } = "BOWTIE";
+
+    return wantarray ? %{ $record } : $record; 
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__

diff --git a/bp_bin/format_genome b/bp_bin/format_genome
index 71e1d21e2bc179ce9cde2e9af3e7614025dc0089..9fbdcb859d7e1f93be37fd1ca9a6a5aff2b9b026 100755 (executable)
--- a/bp_bin/format_genome
+++ b/bp_bin/format_genome
@@ -113,7 +113,7 @@ foreach $format ( @{ $options->{ 'formats' } } )
     elsif ( $format =~ /^blast$/i )     { Maasha::NCBI::blast_index( "$genome.fna", $fasta_dir, "$dir/genomes/$genome/blast", "dna", $genome ) }
     elsif ( $format =~ /^blat$/i )      { warn "BLAT FORMAT NOT IMPLEMENTED" }
     elsif ( $format =~ /^vmatch$/i )    { Maasha::Match::vmatch_index( "$genome.fna", $fasta_dir, "$dir/genomes/$genome/vmatch", $tmp_dir ) }
-    elsif ( $format =~ /^bowtie$/i )    { bowtie_index( "$fasta_dir/$genome.fna", "$dir/genomes/$genome/bowtie", $genome, $option->{ 'verbose' } ) }
+    elsif ( $format =~ /^bowtie$/i )    { bowtie_index( "$fasta_dir/$genome.fna", "$dir/genomes/$genome/bowtie", $genome, $options->{ 'verbose' } ) }
     elsif ( $format =~ /^phastcons$/i ) { Maasha::UCSC::phastcons_index( "$genome.pp", $phastcons_dir ) }
 }
 

diff --git a/code_perl/Maasha/Solexa.pm b/code_perl/Maasha/Solexa.pm
index f5396584248c044310ef73887f1378e87ac90c9d..a26b0ceb5d88c28b6b7e61cf9284f18763a1e478 100644 (file)
--- a/code_perl/Maasha/Solexa.pm
+++ b/code_perl/Maasha/Solexa.pm
@@ -65,7 +65,7 @@ sub solexa_get_entry_octal
 
     # Returns a list.
 
-    my ( $seq_header, $seq, $score_head, $score, @scores );
+    my ( $seq_header, $seq, $score_head, $score );
 
     $seq_header   = <$fh>;
     $seq          = <$fh>;
@@ -79,13 +79,8 @@ sub solexa_get_entry_octal
     chomp $score_header;
     chomp $score;
 
-    @scores = split //, $score;
-
-    map { $_ = int( score_oct2dec( $_ ) ) } @scores;
-
     $seq_header =~ s/^@//;
-
-    $score = join( ";", @scores );
+    $score      =~ s/(.)/int( score_oct2dec( $1 ) ) . ";"/ge;
 
     return wantarray ? ( $seq_header, $seq, $score ) : [ $seq_header, $seq, $score ];
 }