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 # Introduce indels into sequences in the stream.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
32 use Maasha::Biopieces;
36 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
39 my ( $options, $in, $out, $insertions, $deletions, $seq_len, $record );
41 $options = Maasha::Biopieces::parse_options(
43 { long => 'insertions', short => 'i', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef },
44 { long => 'insertions_percent', short => 'P', type => 'float', mandatory => 'no', default => 0, allowed => undef, disallowed => undef },
45 { long => 'deletions', short => 'd', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef },
46 { long => 'deletions_percent', short => 'D', type => 'float', mandatory => 'no', default => 0, allowed => undef, disallowed => undef },
50 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
51 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
53 while ( $record = Maasha::Biopieces::get_record( $in ) )
55 if ( $record->{ "SEQ" } )
57 $seq_len = length $record->{ "SEQ" };
59 $insertions = $options->{ "insertions" } || int( $seq_len * ( $options->{ "insertions_percent" } / 100 ) );
60 $deletions = $options->{ "deletions" } || int( $seq_len * ( $options->{ "deletions_percent" } / 100 ) );
62 Maasha::Common::error( qq(insertions > sequence length: $insertions > $seq_len) ) if $insertions > $seq_len;
63 Maasha::Common::error( qq(deletions > sequence length: $deletions > $seq_len) ) if $deletions > $seq_len;
65 $record->{ "SEQ" } = Maasha::Seq::seq_insert( $record->{ "SEQ" }, $insertions );
66 $record->{ "SEQ" } = Maasha::Seq::seq_delete( $record->{ "SEQ" }, $deletions );
68 $record->{ "SEQ_LEN" } = length $record->{ "SEQ" };
71 Maasha::Biopieces::put_record( $record, $out );
74 Maasha::Biopieces::close_stream( $in );
75 Maasha::Biopieces::close_stream( $out );
78 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
83 Maasha::Biopieces::status_set();
89 Maasha::Biopieces::status_log();
93 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<