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 # Transliterate chars from sequences in stream.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 use Maasha::Biopieces;
34 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
37 my ( $options, $in, $out, $record, $search, $replace, $delete );
39 $options = Maasha::Biopieces::parse_options(
41 { long => 'search', short => 's', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
42 { long => 'replace', short => 'r', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
43 { long => 'delete', short => 'd', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
47 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
48 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
50 $search = $options->{ "search" } || "";
51 $replace = $options->{ "replace" } || "";
52 $delete = $options->{ "delete" } || "";
54 while ( $record = Maasha::Biopieces::get_record( $in ) )
56 if ( $record->{ "SEQ" } )
58 if ( $search and $replace ) {
59 eval "\$record->{ 'SEQ' } =~ tr/$search/$replace/";
61 eval "\$record->{ 'SEQ' } =~ tr/$delete//d";
63 $record->{ "SEQ_LEN" } = length $record->{ "SEQ" };
67 Maasha::Biopieces::put_record( $record, $out );
70 Maasha::Biopieces::close_stream( $in );
71 Maasha::Biopieces::close_stream( $out );
74 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
79 Maasha::Biopieces::status_set();
85 Maasha::Biopieces::status_log();
89 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<