3 # Copyright (C) 2007-2009 Martin A. Hansen.
5 # This program is free software; you can redistribute it and/or
6 # modify it under the terms of the GNU General Public License
7 # as published by the Free Software Foundation; either version 2
8 # of the License, or (at your option) any later version.
10 # This program is distributed in the hope that it will be useful,
11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 # GNU General Public License for more details.
15 # You should have received a copy of the GNU General Public License
16 # along with this program; if not, write to the Free Software
17 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
19 # http://www.gnu.org/copyleft/gpl.html
22 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
24 # Read FASTQ entries from one or more files.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 use Maasha::Biopieces;
36 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
39 my ( $options, $in, $out, $record, $data_in, $num, $entry );
41 $options = Maasha::Biopieces::parse_options(
43 { long => 'data_in', short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
44 { long => 'num', short => 'n', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 },
45 { long => 'convert2dec', short => 'c', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
46 { long => 'cutoff', short => 'C', type => 'int', mandatory => 'no', default => 20, allowed => undef, disallowed => undef },
47 { long => 'soft_mask', short => 's', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
51 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
52 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
54 while ( $record = Maasha::Biopieces::get_record( $in ) ) {
55 Maasha::Biopieces::put_record( $record, $out );
58 if ( $options->{ 'data_in' } )
60 $data_in = Maasha::Filesys::files_read_open( $options->{ 'data_in' } );
64 while ( $entry = Maasha::Fastq::get_entry( $data_in ) )
66 if ( $record = Maasha::Fastq::fastq2biopiece( $entry ) )
68 Maasha::Fastq::softmask_phred_str( $record->{ 'SEQ' }, $record->{ 'SCORES' }, $options->{ 'cutoff' } ) if $options->{ 'soft_mask' };
69 $record->{ 'SCORES' } = Maasha::Fastq::phred_str2dec_str( $record->{ 'SCORES' } ) if $options->{ 'convert2dec' };
71 Maasha::Biopieces::put_record( $record, $out );
74 last if $options->{ "num" } and $num == $options->{ "num" };
82 Maasha::Biopieces::close_stream( $in );
83 Maasha::Biopieces::close_stream( $out );
86 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
91 Maasha::Biopieces::status_set();
97 Maasha::Biopieces::status_log();
101 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<