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 # Align sequences in the stream.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 use Maasha::Biopieces;
40 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
43 my ( $options, $in, $out, $record, @entries, $entry );
45 $options = Maasha::Biopieces::parse_options();
47 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
48 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
50 while ( $record = Maasha::Biopieces::get_record( $in ) )
52 if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) { # TODO use biopieces2fasta() instead
53 push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
54 } elsif ( $record->{ "Q_ID" } and $record->{ "SEQ" } ) {
55 push @entries, [ $record->{ "Q_ID" }, $record->{ "SEQ" } ];
57 Maasha::Biopieces::put_record( $record, $out );
61 @entries = Maasha::Align::align( \@entries );
63 foreach $entry ( @entries )
65 if ( $entry->[ SEQ_NAME ] and $entry->[ SEQ ] )
68 SEQ_NAME => $entry->[ SEQ_NAME ],
69 SEQ => $entry->[ SEQ ],
70 SEQ_LEN => length $entry->[ SEQ ],
73 Maasha::Biopieces::put_record( $record, $out );
77 Maasha::Biopieces::close_stream( $in );
78 Maasha::Biopieces::close_stream( $out );
81 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
86 Maasha::Biopieces::status_set();
92 Maasha::Biopieces::status_log();
96 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<