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scripts/bam_uniq.pl

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+#!/usr/bin/env perl
+# -*-CPerl-*-
+# Last changed Time-stamp: <2014-11-27 14:21:53 mtw>
+#
+# ***********************************************************************
+# *  Copyright notice
+# *
+# *  Copyright 2014 Michael T. Wolfinger <michael@wolfinger.eu>
+# *  All rights reserved
+# *
+# *  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 3 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, see <http://www.gnu.org/licenses/>.
+# *
+# *  This copyright notice MUST APPEAR in all copies of the script!
+# ***********************************************************************
+
+use strict;
+use warnings;
+use Getopt::Long qw( :config posix_default bundling no_ignore_case );
+use Pod::Usage;
+use Path::Class;
+use Bio::ViennaNGS qw(uniquify_bam);
+
+#^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#
+#^^^^^^^^^^ Variables ^^^^^^^^^^^#
+#^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#
+
+my $bam_in;
+my $logfile = "bam_uniq.log";
+my $outdir = "./";
+my @result = ();
+
+#^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#
+#^^^^^^^^^^^^^^ Main ^^^^^^^^^^^^^#
+#^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#
+
+Getopt::Long::config('no_ignore_case');
+pod2usage(-verbose => 1) unless GetOptions("bam=s"   => \$bam_in,
+					   "o=s"     => \$outdir,
+					   "man"     => sub{pod2usage(-verbose => 2)},
+					   "help|h"  => sub{pod2usage(1)}
+					  );
+
+
+unless ($bam_in =~ /^\//) {$bam_in = "./".$bam_in;}
+unless (-f $bam_in){
+  warn "Could not find input file $bam_in given via -bam option";
+  pod2usage(-verbose => 0);
+}
+
+#TODO check if we are allowed to write to $outdir
+unless ($outdir =~ /\/$/){$outdir .= "/";}
+unless (-d $outdir){mkdir $outdir or die $!;}
+
+# Make BED12 line from each splice junction
+@result = uniquify_bam($bam_in,$outdir,$logfile);
+
+__END__
+
+
+=head1 NAME
+
+bam_uniq.pl - Deconvolute BAM files into unique and multi mappers
+
+=head1 SYNOPSIS
+
+bam_uniq.pl [-bam I<FILE>] [-o I<DIR>]
+[options]
+
+=head1 DESCRIPTION
+
+This program extracts uniquely and multiply mapping reads from BAM
+files acoording to the NH:i SAM attribute and creates separate BAM
+files for unique and multi mappers, respectively.
+
+=head1 OPTIONS
+
+=over
+
+=item B<--bam>
+
+BAM file to extract unique and multi mappers from
+
+=item B<-o>
+
+Output path
+
+=item B<--help -h>
+
+Print short help
+
+=item B<--man>
+
+Prints the manual page and exits
+
+=back
+
+=head1 AUTHOR
+
+Michael T. Wolfinger E<lt>michael@wolfinger.euE<gt>
+
+=cut
+