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 # Calculate the bit score for each position based on an alignment in the stream.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 use Maasha::Biopieces;
35 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
38 my ( $options, $in, $out, $record, $count, $i, $res, $type, $bit_max, %freq_hash, $bit_height, $bit_diff );
40 $options = Maasha::Biopieces::parse_options();
42 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
43 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
47 while ( $record = Maasha::Biopieces::get_record( $in ) )
49 if ( $record->{ "SEQ" } )
51 $type = Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $type;
53 for ( $i = 0; $i < length $record->{ "SEQ" }; $i++ )
55 $res = substr $record->{ "SEQ" }, $i, 1;
57 next if $res =~ /-|_|~|\./;
59 $freq_hash{ $i }{ $res }++;
66 Maasha::Biopieces::put_record( $record, $out );
72 if ( $type eq "PROTEIN" ) {
78 for ( $i = 0; $i < keys %freq_hash; $i++ )
80 $bit_height = Maasha::Seq::seqlogo_calc_bit_height( $freq_hash{ $i }, $count );
82 $bit_diff = $bit_max - $bit_height;
84 $record->{ "V" . ( $i ) } = sprintf( "%.2f", $bit_diff );
87 Maasha::Biopieces::put_record( $record, $out );
89 Maasha::Biopieces::close_stream( $in );
90 Maasha::Biopieces::close_stream( $out );
93 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
98 Maasha::Biopieces::status_set();
104 Maasha::Biopieces::status_log();
108 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<