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 # Fold sequences in stream.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
30 use Maasha::Biopieces;
33 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
36 my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $type, $struct, $index );
38 $options = Maasha::Biopieces::parse_options();
40 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
41 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
43 while ( $record = Maasha::Biopieces::get_record( $in ) )
45 if ( $record->{ "SEQ" } )
48 $type = Maasha::Seq::seq_guess_type( $record->{ "SEQ" } );
51 if ( $type ne "protein" )
53 ( $struct, $index ) = Maasha::Seq::fold_struct_rnafold( $record->{ "SEQ" } );
54 $record->{ "SEC_STRUCT" } = $struct;
55 $record->{ "FREE_ENERGY" } = $index;
56 $record->{ "SCORE" } = abs int $index;
57 $record->{ "SIZE" } = length $struct;
58 $record->{ "CONF" } = "1," x $record->{ "SIZE" };
62 Maasha::Biopieces::put_record( $record, $out );
66 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
71 $run_time_beg = Maasha::Biopieces::run_time();
73 Maasha::Biopieces::log_biopiece();
78 Maasha::Biopieces::close_stream( $in );
79 Maasha::Biopieces::close_stream( $out );
81 $run_time_end = Maasha::Biopieces::run_time();
83 Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
87 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<