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| Original file line number | Diff line number | Diff line change |
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| #!/usr/bin/perl | ||
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| ##########LICENCE########## | ||
| # PCAP - NGS reference implementations and helper code for the ICGC/TCGA Pan-Cancer Analysis Project | ||
| # Copyright (C) 2014-2016 ICGC PanCancer Project | ||
| # | ||
| # 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 see: | ||
| # http://www.gnu.org/licenses/gpl-2.0.html | ||
| ##########LICENCE########## | ||
|
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| use Cwd qw(abs_path); | ||
| use strict; | ||
| use English qw( -no_match_vars ); | ||
| use warnings FATAL => 'all'; | ||
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| use File::Basename; | ||
| use Carp; | ||
| use Getopt::Long; | ||
| use Pod::Usage; | ||
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| use PCAP; | ||
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| use Bio::DB::BigWig 'binMean','binStdev'; | ||
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| my %chr_stats; | ||
| my @chr_order; | ||
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| { | ||
| my $options = option_builder(); | ||
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| my $wig = Bio::DB::BigWig->new(-bigwig=>$options->{'b'}); | ||
| my @chroms = $wig->features(-type=>'summary'); | ||
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| for my $c (@chroms) { | ||
| my $seqid = $c->seq_id; | ||
| next if(defined $options->{'r'} && $options->{'r'} ne $seqid && 'chr'.$options->{'r'} ne $seqid); | ||
| my $start = $c->start; | ||
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| my $stats = $c->statistical_summary(1); | ||
| my $bin_width = $c->length/@$stats; | ||
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| my $s = shift @{$stats}; | ||
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| my $mean = binMean($s); | ||
| my $stdev = binStdev($s); | ||
| my $end = $start + $bin_width-1; | ||
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| push @chr_order, $seqid; | ||
| $chr_stats{$seqid} = {'mean' => binMean($s), | ||
| 'stdev' => binStdev($s)}; | ||
| warn sprintf "%s: mean %.2f, stdev %.2f\n", $seqid, $chr_stats{$seqid}{'mean'}, $chr_stats{$seqid}{'stdev'}; | ||
| } | ||
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| open my $OFH, '>', $options->{'o'} or die "Failed to create $options->{o}: $!\n"; | ||
| for my $chr(@chr_order) { | ||
| my $max_val = $chr_stats{$chr}{'mean'} + ($chr_stats{$chr}{'stdev'} * $options->{'s'}); | ||
| warn sprintf "%s: Max depth permitted = %d\n", $chr, $max_val; | ||
| my $iterator = $wig->get_seq_stream(-seq_id=> $chr); | ||
| while (my $p = $iterator->next_seq) { | ||
| next if($p->score <= $max_val); | ||
| printf $OFH "%s\t%d\t%d\t%d\n", $chr, $p->start-1, $p->end, $p->score; | ||
| } | ||
| } | ||
| close $OFH; | ||
| } | ||
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| sub option_builder { | ||
| my ($factory) = @_; | ||
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| my %opts; | ||
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| &GetOptions ( | ||
| 'h|help' => \$opts{'h'}, | ||
| 'b|bigwig=s' => \$opts{'b'}, | ||
| 'o|output=s' => \$opts{'o'}, | ||
| 'r|ref=s' => \$opts{'r'}, | ||
| 'd|decode=s@' => \$opts{'d'}, | ||
| 's|sd=n' => \$opts{'s'}, | ||
| 'v|version' => \$opts{'v'}, | ||
| ); | ||
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| if(defined $opts{'v'}) { | ||
| print PCAP->VERSION,"\n"; | ||
| exit 0; | ||
| } | ||
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| pod2usage(0) if($opts{'h'}); | ||
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| pod2usage(1) if(!$opts{'b'} || !$opts{'o'}); | ||
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| croak $opts{'b'}.' was not found or is empty' if(!-e $opts{'b'} || !-s $opts{'b'}); | ||
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| if($opts{'d'}) { | ||
| if(!$opts{'r'}) { | ||
| croak '-d should not be defined without -r'; | ||
| } | ||
| my %decode; | ||
| foreach my $d_str(@{$opts{'d'}}) { | ||
| if($d_str =~ m/^(\d+)\:(.*)$/) { | ||
| my $num = $1; | ||
| my $chr = $2; | ||
| $decode{$num} = $chr; | ||
| } | ||
| else { | ||
| croak "Decode string of $d_str is invalid see --help"; | ||
| } | ||
| } | ||
| if(defined $decode{$opts{'r'}}) { | ||
| $opts{'r'} = $decode{$opts{'r'}}; | ||
| } | ||
| } | ||
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| my $fn = fileparse($opts{'b'}); | ||
| $fn =~ s/\.bw$//; | ||
| $opts{'o'} .= '/' if($opts{'o'} !~ m/\/$/); | ||
| $opts{'o'} .= $fn; | ||
| if($opts{'r'}) { | ||
| $opts{'o'} .= '.'.$opts{'r'}; | ||
| } | ||
| $opts{'o'} .= '.bed'; | ||
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| if(!$opts{'s'}) { | ||
| $opts{'s'} = 12; | ||
| } | ||
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| return \%opts; | ||
| } | ||
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| __END__ | ||
| =head1 NAME | ||
| detectExtremeDepth.pl - Generate profile of BigWig file and identify regions outside the normal range | ||
| =head1 SYNOPSIS | ||
| General Options (list OR project must be defined): | ||
| --bigwig (-b) FILE BigWig file path | ||
| --output (-o) DIR Folder to send output to | ||
| - named as input file with '.tab' extension | ||
| - if '-r' defined '.{val}' will prefix '.bed' | ||
| Optional: | ||
| --ref (-r) STR Restrict to this reference (mainly for testing) | ||
| - without 'chr' prefix, will test with and without the 'chr' for you. | ||
| --decode (-d) STR Decode -r to chromosome names (do not include 'chr') | ||
| e.g. -d 23:X -d 24:Y -d 25:MT | ||
| --sd (-s) INT Number of standard deviations above mean for group to be included [12] | ||
| --help (-h) This message | ||
| --version (-v) Version | ||
| Examples: | ||
| perl ~/detectExtremeDepth.pl -o someplace -b sample.bw | ||
| =cut |
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