removed dir check from create_bowtie_index

[biopieces.git] / bp_bin / read_solexa

diff --git a/bp_bin/read_solexa b/bp_bin/read_solexa
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..f594d8079427432e644f1e2674cbe39461a20ca8 100755 (executable)
--- a/bp_bin/read_solexa
+++ b/bp_bin/read_solexa
@@ -1,6 +1,106 @@
 #!/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 Solexa entries from one or more files.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
 use warnings;
 use strict;
+use Data::Dumper;
+use Maasha::Biopieces;
+use Maasha::Filesys;
+use Maasha::Solexa;
+use Maasha::Fastq;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $data_in, $num, $entry, @seqs, @scores, $i );
+
+$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' },
+        { long => 'convert2dec', short => 'c', type => 'flag',   mandatory => 'no', default => undef,   allowed => undef, disallowed => undef },
+        { long => 'cutoff',      short => 'C', type => 'int',    mandatory => 'no', default => 20,      allowed => undef, disallowed => undef },
+        { long => 'soft_mask',   short => 's', type => 'flag',   mandatory => 'no', default => undef,   allowed => undef, disallowed => undef },
+    ]   
+);
+
+$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::Fastq::softmask_solexa_str( $record->{ 'SEQ' }, $record->{ 'SCORES' }, $options->{ 'cutoff' } ) if $options->{ 'soft_mask' };
+            $record->{ 'SCORES' } = Maasha::Fastq::solexa_str2dec_str( $record->{ 'SCORES' } ) if $options->{ 'convert2dec' };
+
+            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();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
 
-use Maasha::BioRun;
+__END__