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 # Split BED entries into overlapping windows.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
30 use Maasha::Biopieces;
33 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
36 my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $new_record, $i );
38 $options = Maasha::Biopieces::parse_options(
40 { long => 'window_size', short => 'w', type => 'uint', mandatory => 'no', default => 20, allowed => undef, disallowed => 0 },
41 { long => 'step_size', short => 's', type => 'uint', mandatory => 'no', default => 1, allowed => undef, disallowed => 0 },
45 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
46 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
48 while ( $record = Maasha::Biopieces::get_record( $in ) )
50 if ( $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "CHR_END" } )
52 $record->{ "BED_LEN" } = $record->{ "CHR_END" } - $record->{ "CHR_BEG" } + 1;
54 for ( $i = 0; $i < $record->{ "BED_LEN" } - $options->{ "window_size" }; $i += $options->{ "step_size" } )
56 $new_record->{ "REC_TYPE" } = "BED";
57 $new_record->{ "CHR" } = $record->{ "CHR" };
58 $new_record->{ "CHR_BEG" } = $record->{ "CHR_BEG" } + $i;
59 $new_record->{ "CHR_END" } = $record->{ "CHR_BEG" } + $i + $options->{ "window_size" };
60 $new_record->{ "BED_LEN" } = $options->{ "window_size" };
61 $new_record->{ "Q_ID" } = $record->{ "Q_ID" } . "_$i";
62 $new_record->{ "SCORE" } = $record->{ "SCORE" };
63 $new_record->{ "STRAND" } = $record->{ "STRAND" };
65 Maasha::Biopieces::put_record( $new_record, $out );
70 Maasha::Biopieces::put_record( $record, $out );
75 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
80 $run_time_beg = Maasha::Biopieces::run_time();
82 Maasha::Biopieces::log_biopiece();
88 Maasha::Biopieces::close_stream( $in );
89 Maasha::Biopieces::close_stream( $out );
91 $run_time_end = Maasha::Biopieces::run_time();
93 Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
97 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<