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 # Assemble tag contigs from overlapping BED type records in the stream.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 use Maasha::Biopieces;
33 use Maasha::UCSC::BED;
36 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
39 my ( $options, $in, $out, $tmp_dir, $bed_file, $tag_file, $fh_in, $fh_out,
40 $cols, $record, $bed_entry, $file_hash, $chr, $strand );
42 $options = Maasha::Biopieces::parse_options(
44 { long => 'check', short => 'C', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
48 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
49 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
51 `cd "$ENV{ BP_C }/Maasha/src" && make`; # FIXME OMG this is crufty!
53 $tmp_dir = Maasha::Biopieces::get_tmpdir();
55 $bed_file = "$tmp_dir/assemble_tag_contigs.bed";
56 $fh_out = Maasha::Filesys::file_write_open( $bed_file );
57 $cols = 6; # we only need the first 6 BED columns
59 while ( $record = Maasha::Biopieces::get_record( $in ) )
61 if ( $bed_entry = Maasha::UCSC::BED::biopiece2bed( $record, $cols ) )
63 $strand = $record->{ 'STRAND' } || '+';
65 Maasha::UCSC::BED::bed_entry_put( $bed_entry, $fh_out, $cols, $options->{ 'check' } );
71 $file_hash = Maasha::UCSC::BED::bed_file_split_on_chr( $bed_file, $tmp_dir, $cols );
75 foreach $chr ( sort keys %{ $file_hash } )
77 $bed_file = $file_hash->{ $chr };
78 $tag_file = "$bed_file.tc";
80 Maasha::Common::run( "bed2tag_contigs", "< $bed_file > $tag_file" );
82 $fh_in = Maasha::Filesys::file_read_open( $tag_file );
84 while ( $bed_entry = Maasha::UCSC::BED::bed_entry_get( $fh_in, $cols, $options->{ 'check' } ) )
86 if ( $record = Maasha::UCSC::BED::bed2biopiece( $bed_entry ) ) {
87 Maasha::Biopieces::put_record( $record, $out );
97 Maasha::Biopieces::close_stream( $in );
98 Maasha::Biopieces::close_stream( $out );
101 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
106 Maasha::Biopieces::status_set();
112 Maasha::Biopieces::status_log();
116 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<