prod_reproduction/202307-FMBY2/script/get_chr_CR.pl

#!/usr/bin/perl

use strict;
use warnings;
my $usage="perl $0 sample.cov/sample.pcov
Chech chrX and SRY Copy Ratio. ";
die $usage unless @ARGV;
my $covf=shift;
my (%dat,$tot,$num);
open my $fhcov,'<', $covf or die "Cannot open file:$covf $!";
while(<$fhcov>){
    next if /^contig/ or $.==1;
    my ($chr,$start,$cnt)=(split /\s+/)[0,1,4];
    $chr=~s/chr//;
    next if $chr=~/Y/ and $start> 2700000;
    $dat{$chr}{CNT}++;
    $dat{$chr}{VAL}+=$cnt;
    $tot+=$cnt;
    $num++;
}
close($fhcov);
my $avg=$tot/$num;
my @chrs=(1..22,'X','Y');
print "#Chr\tCopy_Ratio\tCopy_Infer\n";
for my $chr(@chrs){
    next unless exists $dat{$chr};
    my $chr_tot=$dat{$chr}{VAL};
    my $chr_num=$dat{$chr}{CNT};
    $chr="SRY" if $chr eq 'Y';
    my $chr_avg=sprintf("%.2f",$chr_tot/($chr_num*$avg));
    my $copy=2;
    if($chr_avg<0.1){
        $copy=0;
    }elsif($chr_avg<0.75){
        $copy=1;
    }
    print $chr,"\t",$chr_avg,"\t$copy\n";
}