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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########## | ||
| # Copyright (c) 2014-2016 Genome Research Ltd. | ||
| # | ||
| # Author: CancerIT <[email protected]> | ||
| # | ||
| # This file is part of AscatNGS. | ||
| # | ||
| # AscatNGS is free software: you can redistribute it and/or modify it under | ||
| # the terms of the GNU Affero 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 Affero General Public License for more | ||
| # details. | ||
| # | ||
| # You should have received a copy of the GNU Affero General Public License | ||
| # along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| ##########LICENCE########## | ||
|
|
||
| use strict; | ||
| use warnings FATAL => 'all'; | ||
| use autodie qw(:all); | ||
| use FindBin qw($Bin); | ||
| use lib "$Bin/../lib"; | ||
| use Getopt::Long; | ||
| use Pod::Usage qw(pod2usage); | ||
| use IO::Uncompress::Gunzip qw(gunzip $GunzipError) ; | ||
| use Const::Fast qw(const); | ||
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| use PCAP::Cli; | ||
| use Sanger::CGP::Ascat; | ||
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| # chr, 0-start, 1-stop, value (use string to leave precision as source) | ||
| const my $BG_FRMT => "%s\t%d\t%d\t%s\n"; | ||
| const my $DFLT_ALIAS => '23:X,24:Y'; | ||
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| my $options = setup(); | ||
| my $chr_map = chr_lookup($options->{'alias'}); | ||
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| my $z = new IO::Uncompress::Gunzip $options->{'input'}, MultiStream=>1 or die "gunzip failed: $GunzipError\n"; | ||
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| my $bg_fhs = get_output_files($options->{'outpre'}); | ||
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| my $chr_last = q{}; | ||
| my ($start_segbaf, $end_segbaf, $val_segbaf) = (0,0,'NA'); | ||
| my ($start_seglogr, $end_seglogr, $val_seglogr) = (0,0,'NA'); | ||
| my ($start_total_cn, $end_total_cn, $val_total_cn) = (0,0,'NA'); | ||
| my ($start_minor_cn, $end_minor_cn, $val_minor_cn) = (0,0,'NA'); | ||
|
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||
| while(my $line = <$z>) { | ||
| next if($line =~ /^\t/); | ||
| chomp $line; | ||
| my (undef, $chr, $pos, $logR, $segLogR, $baf, $segBaf, $total_cn, $minor_cn, $raw_cn) = split /\t/, $line; | ||
| $chr = $chr_map->{$chr} if(exists $chr_map->{$chr}); | ||
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|
||
| if($chr ne $chr_last) { | ||
| if($chr_last ne q{}) { | ||
| printf {$bg_fhs->{'segLogR'}} $BG_FRMT, $chr_last, $start_seglogr-1, $end_seglogr, $val_seglogr if($val_seglogr ne 'NA'); | ||
| printf {$bg_fhs->{'segBaf'}} $BG_FRMT, $chr_last, $start_segbaf-1, $end_segbaf, $val_segbaf if($val_segbaf ne 'NA'); | ||
| printf {$bg_fhs->{'totalCn'}} $BG_FRMT, $chr_last, $start_total_cn-1, $end_total_cn, $val_total_cn if($val_total_cn ne 'NA'); | ||
| printf {$bg_fhs->{'minorCn'}} $BG_FRMT, $chr_last, $start_minor_cn-1, $end_minor_cn, $val_minor_cn if($val_minor_cn ne 'NA'); | ||
| } | ||
| $chr_last = $chr; | ||
| ($start_segbaf, $end_segbaf, $val_segbaf) = (0,0,'NA'); | ||
| ($start_seglogr, $end_seglogr, $val_seglogr) = (0,0,'NA'); | ||
| ($start_total_cn, $end_total_cn, $val_total_cn) = (0,0,'NA'); | ||
| ($start_minor_cn, $end_minor_cn, $val_minor_cn) = (0,0,'NA'); | ||
| } | ||
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| printf {$bg_fhs->{'logR'}} $BG_FRMT, $chr, $pos-1, $pos, $logR if($logR ne 'NA'); | ||
| printf {$bg_fhs->{'baf'}} $BG_FRMT, $chr, $pos-1, $pos, $baf if($baf ne 'NA'); | ||
| printf {$bg_fhs->{'rawCn'}} $BG_FRMT, $chr, $pos-1, $pos, $raw_cn if($raw_cn ne 'NA'); | ||
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| if($segLogR ne $val_seglogr) { | ||
| printf {$bg_fhs->{'segLogR'}} $BG_FRMT, $chr_last, $start_seglogr-1, $end_seglogr, $val_seglogr if($val_seglogr ne 'NA'); | ||
| ($start_seglogr, $end_seglogr, $val_seglogr) = ($pos, $pos, $segLogR); | ||
| } | ||
| else { | ||
| $end_seglogr = $pos; | ||
| } | ||
|
|
||
| if($segBaf ne $val_segbaf) { | ||
| printf {$bg_fhs->{'segBaf'}} $BG_FRMT, $chr_last, $start_segbaf-1, $end_segbaf, $val_segbaf if($val_segbaf ne 'NA'); | ||
| ($start_segbaf, $end_segbaf, $val_segbaf) = ($pos, $pos, $segBaf); | ||
| } | ||
| else { | ||
| $end_segbaf = $pos; | ||
| } | ||
|
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| if($total_cn ne $val_total_cn) { | ||
| printf {$bg_fhs->{'totalCn'}} $BG_FRMT, $chr_last, $start_total_cn-1, $end_total_cn, $val_total_cn if($val_total_cn ne 'NA'); | ||
| ($start_total_cn, $end_total_cn, $val_total_cn) = ($pos, $pos, $total_cn); | ||
| } | ||
| else { | ||
| $end_total_cn = $pos; | ||
| } | ||
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| if($minor_cn ne $val_minor_cn) { | ||
| printf {$bg_fhs->{'minorCn'}} $BG_FRMT, $chr_last, $start_minor_cn-1, $end_minor_cn, $val_minor_cn if($val_minor_cn ne 'NA'); | ||
| ($start_minor_cn, $end_minor_cn, $val_minor_cn) = ($pos, $pos, $minor_cn); | ||
| } | ||
| else { | ||
| $end_minor_cn = $pos; | ||
| } | ||
| } | ||
| close $z; | ||
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| printf {$bg_fhs->{'segLogR'}} $BG_FRMT, $chr_last, $start_seglogr-1, $end_seglogr, $val_seglogr if($val_seglogr ne 'NA'); | ||
| printf {$bg_fhs->{'segBaf'}} $BG_FRMT, $chr_last, $start_segbaf-1, $end_segbaf, $val_segbaf if($val_segbaf ne 'NA'); | ||
| printf {$bg_fhs->{'totalCn'}} $BG_FRMT, $chr_last, $start_total_cn-1, $end_total_cn, $val_total_cn if($val_total_cn ne 'NA'); | ||
| printf {$bg_fhs->{'minorCn'}} $BG_FRMT, $chr_last, $start_minor_cn-1, $end_minor_cn, $val_minor_cn if($val_minor_cn ne 'NA'); | ||
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| close_output_files($options->{'outpre'}, $bg_fhs); | ||
| convert_bg_to_bw($options->{'outpre'}, $options->{'fai'}); | ||
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| sub chr_lookup { | ||
| my $alias_lst = shift; | ||
| my %chr_map = split /[:,]/, $alias_lst; | ||
| return \%chr_map; | ||
| } | ||
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| sub convert_bg_to_bw { | ||
| my ($outpre, $chromlst) = @_; | ||
| for (qw(logR segLogR baf segBaf totalCn minorCn rawCn)) { | ||
| my $bg_file = sprintf '%s.%s.bg', $outpre, $_; | ||
| my $bw_file = sprintf '%s.%s.bw', $outpre, $_; | ||
| my $cmd = sprintf 'bg2bw -i %s -o %s -c %s', $bg_file, $bw_file, $chromlst; | ||
| warn "Executing: $cmd\n"; | ||
| system($cmd) && die "Execution failed: $!"; | ||
| unlink $bg_file; | ||
| } | ||
| } | ||
|
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| sub get_output_files { | ||
| my $outpre = shift; | ||
| my %fhs; | ||
| for (qw(logR segLogR baf segBaf totalCn minorCn rawCn)) { | ||
| my $bg_file = sprintf '%s.%s.bg', $outpre, $_; | ||
| open my $fh, '>', $bg_file or die "Failed to create $bg_file"; | ||
| $fhs{$_} = $fh; | ||
| } | ||
| return \%fhs; | ||
| } | ||
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| sub close_output_files { | ||
| my ($outpre, $fhs) = @_; | ||
| for (keys %{$fhs}) { | ||
| my $bg_file = sprintf '%s.%s.bg', $outpre, $_; | ||
| close $fhs->{$_} or die "Failed to close $bg_file"; | ||
| } | ||
| } | ||
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| sub setup { | ||
| my %opts; | ||
| pod2usage(-msg => "\nERROR: Options must be defined.\n", -verbose => 1, -output => \*STDERR) if(scalar @ARGV == 0); | ||
| $opts{'cmd'} = join " ", $0, @ARGV; | ||
| warn "Executing: $opts{cmd}\n"; | ||
| GetOptions( 'h|help' => \$opts{'h'}, | ||
| 'm|man' => \$opts{'m'}, | ||
| 'v|version' => \$opts{'v'}, | ||
| 'i|input=s' => \$opts{'input'}, | ||
| 'o|outpre=s' => \$opts{'outpre'}, | ||
| 'f|fai=s' => \$opts{'fai'}, | ||
| 'a|alias:s' => \$opts{'alias'}, | ||
| ) or pod2usage(2); | ||
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| pod2usage(-verbose => 1, -exitval => 0) if(defined $opts{'h'}); | ||
| pod2usage(-verbose => 2, -exitval => 0) if(defined $opts{'m'}); | ||
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| if($opts{'v'}){ | ||
| print Sanger::CGP::Ascat->VERSION."\n"; | ||
| exit; | ||
| } | ||
|
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| # then check for no args: | ||
| my $defined; | ||
| for(keys %opts) { $defined++ if(defined $opts{$_}); } | ||
| pod2usage(-msg => "\nERROR: Parameters must be defined.\n", -verbose => 1, -output => \*STDERR) unless($defined); | ||
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| PCAP::Cli::file_for_reading('input', $opts{'input'}); | ||
| PCAP::Cli::file_for_reading('fai', $opts{'fai'}); | ||
| pod2usage(-msg => "\nERROR: '-o' must be defined.\n", -verbose => 1, -output => \*STDERR) unless(defined $opts{'outpre'}); | ||
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| $opts{'alias'} = $DFLT_ALIAS unless(defined $opts{'alias'}); | ||
|
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| return \%opts; | ||
| } | ||
|
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| __END__ | ||
| =head1 ascatToBigWig.pl | ||
| Converts raw data used in log and BAF plots to BigWig data files | ||
| suitable for use with JBrowse/MuiltBigWig. | ||
| =head1 SYNOPSIS | ||
| ascatToBigWig.pl [options] | ||
| Required parameters | ||
| -input -i Input *.ascat_ngs.cn.tsv[.gz] | ||
| -outpre -o File name to use in output, suffixes applied are: | ||
| - *.logR.bw | ||
| - *.segLogR.bw | ||
| - *.baf.bw | ||
| - *.segBaf.bw | ||
| -fai -f Path to chrom list or fai file | ||
| - a tsv file with first 2 columns chr, chr-length | ||
| -alias -a csv for numeric to chr mapping applied to chr column of input [23:X,24:Y] | ||
| Other | ||
| -help -h Brief help message | ||
| -man -m Full documentation. | ||
| -version -v Ascat version number |
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