added read_fastq biopiece

git-svn-id: http://biopieces.googlecode.com/svn/trunk@572 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/bowtie_seq b/bp_bin/bowtie_seq
index 560b1c4de023cc1eb7f43209901d6a95b267d2b7..92a511869107faf713e4771833509443d8072210 100755 (executable)
--- a/bp_bin/bowtie_seq
+++ b/bp_bin/bowtie_seq
@@ -120,10 +120,10 @@ sub bowtie2biopiece
     $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->{ '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_MEAN' } = sprintf( "%.2f", Maasha::Calc::mean( [ split /;/, $record->{ 'SCORES' } ] ) );
 
     $record->{ 'REC_TYPE' } = "BOWTIE";
 

diff --git a/bp_bin/read_fastq b/bp_bin/read_fastq
new file mode 100755 (executable)
index 0000000..ce1db6d
--- /dev/null
+++ b/bp_bin/read_fastq
@@ -0,0 +1,97 @@
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Read FASTQ entries from one or more files.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Maasha::Biopieces;
+use Maasha::Filesys;
+use Maasha::Fastq;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $data_in, $num, $entry );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'data_in', short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'num',     short => 'n', type => 'uint',   mandatory => 'no', default => undef, allowed => undef, disallowed => '0' },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) {
+    Maasha::Biopieces::put_record( $record, $out );
+}
+
+if ( $options->{ 'data_in' } )
+{
+    $data_in = Maasha::Filesys::files_read_open( $options->{ 'data_in' } );
+
+    $num = 1;
+
+    while ( $entry = Maasha::Fastq::get_entry( $data_in ) ) 
+    {
+        if ( $record = Maasha::Fastq::fastq2biopiece( $entry ) ) {
+            Maasha::Biopieces::put_record( $record, $out );
+        }
+
+        last if $options->{ "num" } and $num == $options->{ "num" };
+
+        $num++;
+    }
+
+    close $data_in;
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__