--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qseq2fastq/qseq2fastq.pl	Tue Jun 07 17:42:46 2011 -0400
@@ -0,0 +1,51 @@
+#!/usr/bin/perl -w
+use strict;
+use Carp;
+
+my $usage = q(
+qseq2fastq.pl  - a script to convert all qseq files in a directory into a single fastq file with sanger-style ASCII q-score encoding
+USAGE: qseq2fastq.pl <qseq.txt file> <output file>
+);
+
+if (scalar(@ARGV) != 2) {
+    print $usage;
+    exit;
+}
+
+my $in_file = $ARGV[0];
+my $output_fastq_file = $ARGV[1];
+
+my $qfilter = "";
+open(OUTFASTAQFILE, "> $output_fastq_file");
+
+open INFILE, "< $in_file" || die "Error: Couldn't open $in_file\n";
+while(<INFILE>)
+{
+	chomp;
+	my @this_line = split/\t/, $_;
+	croak("Error: invalid column number in $in_file\n") unless(scalar(@this_line) == 11);
+	if($this_line[10] == 1) {
+	$qfilter = "Y";
+	} else {
+		$qfilter = "N";
+	}
+    # Convert quality scores
+	my @quality_array = split(//, $this_line[9]);
+	my $phred_quality_string = "";
+    # convert each char to Phred quality score
+	foreach my $this_char (@quality_array){
+	    my $phred_quality = ord($this_char) - 64; # convert illumina scaled phred char to phred quality score
+		my $phred_char = chr($phred_quality + 33); # convert phred quality score into phred char (sanger style)
+		$phred_quality_string = $phred_quality_string . $phred_char;
+	}
+    # replace "." gaps with N
+	$this_line[8] =~ s/\./N/g;
+	# output line
+	print OUTFASTAQFILE "@" . $this_line[2] . ":" . $this_line[3] . ":" . $this_line[4] . ":" . $this_line[5] . ":" . $qfilter . "\n" .  #header line
+					$this_line[8] . "\n" . # output sequence
+					"+" . $this_line[2] . ":" . $this_line[3] . ":" . $this_line[4] . ":" . $this_line[5] . ":" .  $qfilter . "\n" . # header line
+					$phred_quality_string . "\n"; # output quality string
+}
+close INFILE;
+close OUTFASTAQFILE;
+exit;