Perl script to check fastq reads qualities !

Abhimanyu Singh — Tue, 12 Jun 2018 04:42:20 -0500

#!/usr/bin/env perl

use strict;
use warnings;

sub readfq {
	my ($fh, $aux) = @_;
	@$aux = [undef, 0] if (!defined(@$aux));
	return if ($aux->[1]);
	if (!defined($aux->[0])) {
		while (<$fh>) {
			chomp;
			if (substr($_, 0, 1) eq '>' || substr($_, 0, 1) eq '@') {
				$aux->[0] = $_;
				last;
			}
		}
		if (!defined($aux->[0])) {
			$aux->[1] = 1;
			return;
		}
	}
	my $name = /^.(\S+)/? $1 : '';
	my $seq = '';
	my $c;
	$aux->[0] = undef;
	while (<$fh>) {
		chomp;
		$c = substr($_, 0, 1);
		last if ($c eq '>' || $c eq '@' || $c eq '+');
		$seq .= $_;
	}
	$aux->[0] = $_;
	$aux->[1] = 1 if (!defined($aux->[0]));
	return ($name, $seq) if ($c ne '+');
	my $qual = '';
	while (<$fh>) {
		chomp;
		$qual .= $_;
		if (length($qual) >= length($seq)) {
			$aux->[0] = undef;
			return ($name, $seq, $qual);
		}
	}
	$aux->[1] = 1;
	return ($name, $seq);
}

my @aux = undef;
my ($name, $seq, $qual);
my ($n, $slen, $qlen) = (0, 0, 0);
while (($name, $seq, $qual) = readfq(\*STDIN, \@aux)) {
	++$n;
	$slen += length($seq);
	$qlen += length($qual) if ($qual);
print join("\t", $n, $slen, $qlen), "\n";
}
#print join("\t", $n, $slen, $qlen), "\n";

__END__
 my @aux = undef; # this is for keeping intermediate data
  while (my ($name, $seq, $qual) = readfq(\*STDIN, \@aux)) { 
     if( (length($seq) >= 21) && (length($seq) <= 25) ) { 
         print "@$name\n";
         print "$seq\n"; 
         print "+\n";
         print "$qual\n";
     }
  }

BOL: Perl script to check fastq reads qualities !

Perl script to check fastq reads qualities !