#!/usr/bin/perl -w

#=================================
#Script to reverse complement sequences w/ plain old perl
#briandotoakleyatarsdotusdadotgov
#k.purdy at warwick.ac dot uk
#=================================

my $usage = "\nusage: $0 filename\n\n";
my $input_file = $ARGV[0] or die $usage;

open (INPUT, $input_file);

@data=<INPUT>;
$test = "@data";
@dna_sequence = split(/>/, $test);
shift @dna_sequence;

foreach $entry (@dna_sequence) {
	@lines = split(/\n/,$entry);
	$header = shift(@lines);
	$dna_sequence = "@lines";
	$dna_sequence=~s/\n|\t|\s//gi;



	$rev_com = reverse $dna_sequence;
	$rev_com =~ tr/ACGTNacgtn/TGCANtgcan/;
	print (">$header\n$rev_com\n");
}