prod_reproduction/202307-FMBY2/qc/trim_picard_hs.pl

#!/usr/bin/perl

use strict;
use warnings;
use Getopt::Std;
use File::Basename;
use File::Find;

my $usage="Usage:\n\tperl $0 outfile\n
        Options:\n
    -d  input directory. default '.' .
    -s  If Scan is required.True for YES,False for NO. default 1 (YES) .
        \n";

my ($in_dir,$scan);
my %opts = (d => '.', s=>1);
my %opts1;

unless (@ARGV){
    print $usage;
    exit;
}
getopts(':d:s:', \%opts1);
my $OUT=shift;

for my $key (keys %opts1){
    my $val=$opts1{$key};
    $opts{$key}=$val;
}

for my $key (keys %opts){
    my $val=$opts{$key};
    if($key eq 'd'){
        $in_dir=$val;
        print "Input directory: $val .\n";
    }
    if($key eq 's'){
        $scan=$val;
        print "Directory Scan is required.\n" if $scan;
        print "Sinple glob $in_dir for *_stats.\n" unless $scan;
    }
}
my @files;
if($scan){
    find(sub {
            push @files,$File::Find::name if -f and /_hs_metrics.txt$/;
        }, $in_dir);
    print "sanning...\n";
}else{
    @files=<$in_dir/*_hs_metrics.txt>;
    print "No sanning...\n";
}

my (@samples,%data);

my @keys=qw(TARGET_TERRITORY TOTAL_READS PCT_PF_UQ_READS PCT_PF_UQ_READS_ALIGNED
    PCT_SELECTED_BASES MEAN_TARGET_COVERAGE PCT_USABLE_BASES_ON_TARGET FOLD_80_BASE_PENALTY
    PCT_TARGET_BASES_1X	PCT_TARGET_BASES_2X	PCT_TARGET_BASES_10X PCT_TARGET_BASES_20X PCT_TARGET_BASES_30X 
    PCT_TARGET_BASES_40X PCT_TARGET_BASES_50X PCT_TARGET_BASES_100X AT_DROPOUT GC_DROPOUT);

for my $file (sort @files){
    open my $fh, '<', $file or die "Cannot open file:$!";
    my $sam=basename $file;
    $sam=~s/_hs_metrics.txt//;
    push @samples,$sam;
    my $flag=0;
    my @head;
    while(<$fh>){
        chomp;
        next if /^#/ or /^\s*$/;
        if(/^BAIT_SET/){
            $flag=1;
            @head=split /\t/;
            next;
        }
        next unless $flag;
        my @conts=split /\t/;
        my ($cov30,$cov1);
        for my $i (0..$#conts){
            my $key=$head[$i];
            my $val=$conts[$i];
            $cov30=$val if $key eq 'PCT_TARGET_BASES_30X';
            $cov1=$val if $key eq 'PCT_TARGET_BASES_1X';
            if($val=~/^\d+\.\d+$/ ){
                $val= $val<100? sprintf("%.3f",$val):sprintf("%.0f",$val);
            }
            $data{$sam}{$key}=$val;
        }
        my $adj30=$cov1 ? sprintf("%.4f",$cov30/$cov1) : 0;
        $data{$sam}{Con}=$adj30;
        $flag=0;
    }
}
open my $wfh,'>',$OUT or die "Cannot write file:$OUT $!\n";
print $wfh join("\t",'#Sample',@keys),"\tAdjust_30X\n";
for my $sam (sort {$data{$a}{TARGET_TERRITORY}<=> $data{$b}{TARGET_TERRITORY} } @samples){
    print $wfh $sam;
    for my $key(@keys){
        print $wfh "\t",$data{$sam}{$key};
    }
    print $wfh "\t",$data{$sam}{Con},"\n";
}