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 # Analyze sequence tags in sequence or BED records from the stream.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
30 use Maasha::Biopieces;
34 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
37 my ( $options, $in, $out, $record, %len_hash, %clone_hash, $clones, $key, $tag_record );
39 $options = Maasha::Biopieces::parse_options();
41 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
42 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
44 while ( $record = Maasha::Biopieces::get_record( $in ) )
46 if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
48 if ( $record->{ "SEQ_NAME" } =~ /_(\d+)$/ )
52 $len_hash{ length( $record->{ "SEQ" } ) }++;
53 $clone_hash{ length( $record->{ "SEQ" } ) } += $clones;
56 elsif ( $record->{ "Q_ID" } and $record->{ "BED_LEN" } )
58 if ( $record->{ "Q_ID" } =~ /_(\d+)$/ )
62 $len_hash{ $record->{ "BED_LEN" } }++;
63 $clone_hash{ $record->{ "BED_LEN" } } += $clones;
68 foreach $key ( sort { $a <=> $b } keys %len_hash )
70 $tag_record->{ "TAG_LEN" } = $key;
71 $tag_record->{ "TAG_COUNT" } = $len_hash{ $key };
72 $tag_record->{ "TAG_CLONES" } = $clone_hash{ $key };
74 Maasha::Biopieces::put_record( $tag_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 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<