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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
25 # Analyze GC content in sequences in the stream.
28 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
33 use Maasha::Biopieces;
36 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
39 my ( $options, $in, $out, $record, $gc_count, $gc_percent );
41 $options = Maasha::Biopieces::parse_options();
43 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
44 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
46 while ( $record = Maasha::Biopieces::get_record( $in ) )
48 if ( $record->{ "SEQ" } )
50 $gc_count = $record->{ "SEQ" } =~ tr/GgCc//;
51 $gc_percent = ( $gc_count / length $record->{ "SEQ" } ) * 100;
52 $record->{ 'GC%' } = sprintf( "%.2f", $gc_percent );
53 # $record->{ 'GC%' } = int $gc_percent;
56 Maasha::Biopieces::put_record( $record, $out );
59 Maasha::Biopieces::close_stream( $in );
60 Maasha::Biopieces::close_stream( $out );
63 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
68 Maasha::Biopieces::status_set();
74 Maasha::Biopieces::status_log();
78 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<