facstont

#!/usr/bin/perl
# Convert colour-space sequence to nucleotides
# Copyright 2012 Shaun Jackman

use strict;

my %table = (
	'A' => ['A', 'C', 'G', 'T'],
	'C' => ['C', 'A', 'T', 'G'],
	'G' => ['G', 'T', 'A', 'C'],
	'T' => ['T', 'G', 'C', 'A']
);

sub cs_to_base($)
{
	my $read = shift;
	my $seed = substr($read, 0, 1);
	for (my $i = 1; $i < length $read; $i++) {
		my $p = \substr($read, $i, 1);
		$$p = $seed = $table{$seed}[$$p];
	}
	return $read;
}

while (<>) {
	if (/^[ACGT]/) {
		chomp;
		print substr cs_to_base($_), 1;
		print "\n";
	} else {
		print;
	}
}