prod_reproduction/202307-FeBY2/script/stats_chrs.pl

#!/usr/bin/perl

use strict;
use warnings;

my (@samples,%data,%total,@chrs);
my $outf=shift;
for ('X','Y',1..22){
	push @chrs, $_;
}

my @files=<*.idxstats>;
for my $file (@files){
	open my $fh, '<', $file or die "Cannot open file: $file $!";
	my $sample=$file;
	$sample=~s/.idxstats//;
	push @samples,$sample;
	while(<$fh>){
		my ($chr,$map)=(split /\t/)[0,2];
        $chr=~s/^chr//;
		next if $chr =~/_/;
		next if $chr eq '*';
        $chr='MT' if $chr eq 'M';
		$total{$sample}+=$map unless $chr eq 'MT' or $chr eq 'M';
		$data{$sample}{$chr}=$map;
	}
	close($fh);
}

open my $wfh, '>' , $outf or die "Cannot write file:$!";
print $wfh join("\t",'#Sample',@chrs,'MT (%)','Total'),"\n";
for my $sample(@samples){
	print $wfh $sample;
	my $tot=$total{$sample};
	my $nchrm=$data{$sample}{'MT'};
	for my $chr(@chrs){
		print $wfh "\t",int($data{$sample}{$chr}/$tot*10000+0.5);
		}
	print $wfh "\t",sprintf("%.2f",$nchrm/($nchrm+$tot)),"\t",$tot+$nchrm,"\n";
}