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 # Write BED entries from stream.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
30 use Maasha::Biopieces;
31 use Maasha::UCSC::BED;
34 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
37 my ( $run_time_beg, $run_time_end, $options, $in, $out, $fh, $record, $bed_entry, $new_record );
39 $options = Maasha::Biopieces::parse_options(
41 { long => 'cols', short => 'c', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => '0' },
42 { long => 'check', short => 'C', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
43 { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
44 { long => 'data_out', short => 'o', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
45 { long => 'compress', short => 'Z', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
49 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
50 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
52 $fh = Maasha::Biopieces::write_stream( $options->{ 'data_out' }, $options->{ 'compress' } );
54 while ( $record = Maasha::Biopieces::get_record( $in ) )
56 $record = Maasha::UCSC::psl2record( $record ) if $record->{ 'tBaseInsert' }; # Dirty addition to allow Affy data from MySQL to be dumped
58 if ( $bed_entry = Maasha::UCSC::BED::biopiece2bed( $record, $options->{ 'cols' } ) ) {
59 Maasha::UCSC::BED::bed_entry_put( $bed_entry, $fh, $options->{ 'cols' }, $options->{ 'check' } );
62 Maasha::Biopieces::put_record( $record, $out ) if not $options->{ 'no_stream' };
68 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
73 $run_time_beg = Maasha::Biopieces::run_time();
75 Maasha::Biopieces::log_biopiece();
80 Maasha::Biopieces::close_stream( $in );
81 Maasha::Biopieces::close_stream( $out );
83 $run_time_end = Maasha::Biopieces::run_time();
85 Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
89 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<