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 # Using the first sequence in the stream as reference, tile all subsequent sequences based on pairwise alignments.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 use Maasha::Biopieces;
40 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
43 my ( $options, $in, $out, $record, $first, $ref_entry, @entries );
45 $options = Maasha::Biopieces::parse_options(
47 { long => 'identity', short => 'i', type => 'uint', mandatory => 'no', default => 70, allowed => undef, disallowed => 0 },
48 { long => 'supress_indels', short => 's', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
52 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
53 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
57 while ( $record = Maasha::Biopieces::get_record( $in ) )
59 if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
63 $ref_entry = [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
69 push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
74 Maasha::Biopieces::put_record( $record, $out );
78 @entries = Maasha::Align::align_tile( $ref_entry, \@entries, $options );
80 map { Maasha::Biopieces::put_record( { SEQ_NAME => $_->[ SEQ_NAME ], SEQ => $_->[ SEQ ] }, $out ) } @entries;
82 Maasha::Biopieces::close_stream( $in );
83 Maasha::Biopieces::close_stream( $out );
86 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
91 Maasha::Biopieces::status_set();
97 Maasha::Biopieces::status_log();
101 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<