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 # Create a residue composition weight matrix of an alignment in the stream.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 use Maasha::Biopieces;
34 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
37 my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $count, $i, $res, %freq_hash, %res_hash, $freq );
39 $options = Maasha::Biopieces::parse_options(
41 { long => 'percent', short => 'p', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
45 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
46 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
50 while ( $record = Maasha::Biopieces::get_record( $in ) )
52 if ( $record->{ "SEQ" } )
54 for ( $i = 0; $i < length $record->{ "SEQ" }; $i++ )
56 $res = substr $record->{ "SEQ" }, $i, 1;
58 $freq_hash{ $i }{ $res }++;
59 $res_hash{ $res } = 1;
66 Maasha::Biopieces::put_record( $record, $out );
70 foreach $res ( sort keys %res_hash )
74 $record->{ "V0" } = $res;
76 for ( $i = 0; $i < keys %freq_hash; $i++ )
78 $freq = $freq_hash{ $i }{ $res } || 0;
80 if ( $options->{ "percent" } ) {
81 $freq = sprintf( "%.0f", 100 * $freq / $count ) if $freq > 0;
84 $record->{ "V" . ( $i + 1 ) } = $freq;
87 Maasha::Biopieces::put_record( $record, $out );
91 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
96 $run_time_beg = Maasha::Biopieces::run_time();
98 Maasha::Biopieces::log_biopiece();
103 Maasha::Biopieces::close_stream( $in );
104 Maasha::Biopieces::close_stream( $out );
106 $run_time_end = Maasha::Biopieces::run_time();
108 Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
112 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<