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 # Translate peptide sequences in the stream.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 use Maasha::Biopieces;
35 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
38 my ( $options, $in, $out, $record, $frame, %new_record );
40 $options = Maasha::Biopieces::parse_options(
42 { long => 'frames', short => 'f', type => 'list', mandatory => 'no', default => '1,2,3,-1,-2,-3', allowed => '1,2,3,-1,-2,-3', disallowed => undef },
46 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
47 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
49 while ( $record = Maasha::Biopieces::get_record( $in ) )
51 if ( $record->{ "SEQ" } )
53 if ( Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) eq "DNA" )
55 foreach $frame ( @{ $options->{ "frames" } } )
57 %new_record = %{ $record };
59 $new_record{ "SEQ" } = Maasha::Seq::translate( $record->{ "SEQ" }, $frame );
60 $new_record{ "SEQ_LEN" } = length $new_record{ "SEQ" };
61 $new_record{ "FRAME" } = $frame;
63 Maasha::Biopieces::put_record( \%new_record, $out );
69 Maasha::Biopieces::put_record( $record, $out );
73 Maasha::Biopieces::close_stream( $in );
74 Maasha::Biopieces::close_stream( $out );
77 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
82 Maasha::Biopieces::status_set();
88 Maasha::Biopieces::status_log();
92 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<