fasta-qual-to-fastq

#!/usr/bin/perl

use EA;

die "usage: $0 <fasta> <qual>\n" unless @ARGV == 2;

my ($fa, $ql) = @ARGV;

# gz compat open fasta and qual files
zopen(FA, $fa) || die;
zopen(QL, $ql) || die;

$fid = <FA>;
$qid = <QL>;

$fid =~ s/\s+$//;	# win32 compat chomp
$qid =~ s/\s+$//;

while (1) {
	$seq = '';

	if (!$fid) {
		exit 0;
	}

	while($fline = <FA>) {				# read fasta rec
		$fline =~ s/\s+$//;
		if ($fline =~ /^>/) {
			last;
		}
		$seq .= $fline;
	}

	$qual = '';
	if (!($qid eq $fid)) {
		die "Line $. : $qid not equal to $fid\n";
	}

	while($qline = <QL>) {				# read qual rec
		$qline =~ s/\s+$//;
		if ($qline =~ /^>/) {
			last;
		}
		for (split / /, $qline) {
			$qual .= chr($_+33);		# convert to fq qual
		}
	}

	$fid =~ s/^>/@/;					
	print "$fid\n$seq\n+\n$qual\n";

	$fid = $fline;						# line that stopped rec is id
	$qid = $qline;
}