#!/usr/bin/env perl # Copyright (C) 2007-2009 Martin A. Hansen. # This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License # as published by the Free Software Foundation; either version 2 # of the License, or (at your option) any later version. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. # http://www.gnu.org/copyleft/gpl.html # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< # Assemble tag contigs from overlapping BED type records in the stream. # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< use warnings; use strict; use Maasha::Biopieces; use Maasha::Filesys; use Maasha::UCSC::BED; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< my ( $options, $in, $out, $tmp_dir, $bed_file, $tag_file, $fh_in, $fh_out, $cols, $record, $bed_entry, $file_hash, $chr, $strand ); $options = Maasha::Biopieces::parse_options( [ { long => 'check', short => 'C', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, ] ); $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } ); $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } ); `cd "$ENV{ BP_C }/Maasha/src" && make`; # FIXME OMG this is crufty! $tmp_dir = Maasha::Biopieces::get_tmpdir(); $bed_file = "$tmp_dir/assemble_tag_contigs.bed"; $fh_out = Maasha::Filesys::file_write_open( $bed_file ); $cols = 6; # we only need the first 6 BED columns while ( $record = Maasha::Biopieces::get_record( $in ) ) { if ( $bed_entry = Maasha::UCSC::BED::biopiece2bed( $record, $cols ) ) { $strand = $record->{ 'STRAND' } || '+'; Maasha::UCSC::BED::bed_entry_put( $bed_entry, $fh_out, $cols, $options->{ 'check' } ); } } close $fh_out; $file_hash = Maasha::UCSC::BED::bed_file_split_on_chr( $bed_file, $tmp_dir, $cols ); unlink $bed_file; foreach $chr ( sort keys %{ $file_hash } ) { $bed_file = $file_hash->{ $chr }; $tag_file = "$bed_file.tc"; Maasha::Common::run( "bed2tag_contigs", "< $bed_file > $tag_file" ); $fh_in = Maasha::Filesys::file_read_open( $tag_file ); while ( $bed_entry = Maasha::UCSC::BED::bed_entry_get( $fh_in, $cols, $options->{ 'check' } ) ) { if ( $record = Maasha::UCSC::BED::bed2biopiece( $bed_entry ) ) { Maasha::Biopieces::put_record( $record, $out ); } } close $fh_in; unlink $bed_file; unlink $tag_file; } Maasha::Biopieces::close_stream( $in ); Maasha::Biopieces::close_stream( $out ); # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< BEGIN { Maasha::Biopieces::status_set(); } END { Maasha::Biopieces::status_log(); } # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< __END__