3 # Copyright (C) 2007-2010 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 # Create a lineplot from quality scores in the stream.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 use Maasha::Biopieces;
37 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
40 my ( $options, $in, $out, $default, $terminals, $formats, $record, %count_hash, %sum_hash, $i, @scores, @data_list, $result, $fh, $tmp_dir );
42 $default = "Quality Scores";
43 $terminals = "dumb,x11,aqua,post,svg";
44 $formats = "solexa,phred,decimal";
46 $options = Maasha::Biopieces::parse_options(
48 { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
49 { long => 'format' , short => 'f', type => 'string', mandatory => 'no', default => "solexa", allowed => $formats, disallowed => undef },
50 { long => 'terminal', short => 't', type => 'string', mandatory => 'no', default => 'dumb', allowed => $terminals, disallowed => undef },
51 { long => 'title', short => 'T', type => 'string', mandatory => 'no', default => $default, allowed => undef, disallowed => undef },
52 { long => 'xlabel', short => 'X', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
53 { long => 'ylabel', short => 'Y', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
57 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
58 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
60 while ( $record = Maasha::Biopieces::get_record( $in ) )
62 if ( $record->{ 'SCORES' } )
64 if ( $options->{ 'format' } eq "solexa" )
66 for ( $i = 0; $i < length $record->{ 'SCORES' }; $i++ )
69 $sum_hash{ $i } += Maasha::Fastq::solexa2dec( substr $record->{ "SCORES" }, $i, 1 );
72 elsif ( $options->{ 'format' } eq "phred" )
74 for ( $i = 0; $i < length $record->{ 'SCORES' }; $i++ )
77 $sum_hash{ $i } += Maasha::Fastq::phred2dec( substr $record->{ "SCORES" }, $i, 1 );
82 @scores = split ";", $record->{ 'SCORES' };
84 for ( $i = 0; $i < @scores; $i++ )
87 $sum_hash{ $i } += $scores[ $i ];
92 Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
95 for ( $i = 0; $i < keys %count_hash; $i++ ) {
96 push @data_list, [ $sum_hash{ $i } / $count_hash{ $i } ];
99 $tmp_dir = Maasha::Biopieces::get_tmpdir();
101 $result = Maasha::Plot::lineplot_simple( \@data_list, $options, $tmp_dir );
103 $fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
105 print $fh "$_\n" foreach @{ $result };
109 Maasha::Biopieces::close_stream( $in );
110 Maasha::Biopieces::close_stream( $out );
113 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
118 Maasha::Biopieces::status_set();
124 Maasha::Biopieces::status_log();
128 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<