#!/usr/bin/perl -w
# Copyright 2013 Scott Hunicke-Smith
#
#
#given a fastq file, reverse complement the sequence and reverse the quality (quality in ASCII characters)
use strict;
my ($rfile, $line, $dna, $revcomp);
$rfile=$ARGV[0];
open RFILE, "<$rfile";
while (defined(my $line = <RFILE>)) {
chomp($line);
my $dna = <RFILE>; #read to be revcomplemented
chomp($dna);
if ( substr($dna,0,15) eq "CCTATCCCCTGTGTG") {
print "$line\n"; #read id
print STDERR "$line\n"; #read id
my $revcomp = reverse($dna);
$revcomp =~ tr/ACGTNacgtn/TGCANtgcan/;
print substr($revcomp,42), "\n";
print STDERR substr($revcomp,30,11), "\n";
$line = <RFILE>; #quality id
chomp($line);
print "$line\n";
print STDERR "$line\n";
my $qual = <RFILE>;
chomp ($qual);
my $revqual = reverse($qual);
print substr($revqual,42),"\n";
print STDERR substr($revqual,30,11), "\n";
} else {
if ( substr($dna,0,15) eq "CCATCTCATCCCTGC" ) {
print "$line\n"; #read id
print STDERR "$line\n"; #read id
print substr($dna,42), "\n";
print STDERR substr($dna,30,11), "\n";
$line = <RFILE>; #quality id
chomp($line);
print "$line\n";
print STDERR "$line\n";
my $qual = <RFILE>;
chomp ($qual);
print substr($qual,42),"\n";
print STDERR substr($qual,30,11), "\n";
}
}
}