#!/usr/bin/perl -w
###############INPUT####################
#input sequence; chomp every line, and concatenate into one big scalar called $seq
	unless(@ARGV==1) {die "please provide name of the file in the command line!!\n";}
	$filename=$ARGV[0];
	open(IN, "< $filename") or die "cannot open $filename:$!";

	$seq='';
	while(defined($line=<IN>)){

        	chomp($line);
        	$seq .= $line ;
		}
# print "input sequence is  \n $seq\n"; #make sure sequence is read accurately
########### END INPUT#########################

####Program: call sub and print output
$invcomp=&RevComp($seq);#call subroutine, hand over content of $seq as parameter
# the result of the suroutines operation will be assigned to $invcomp

print "\n\n\ninverse complement is \n$invcomp\n"; #print output
########End Program###############
#### Sub: 
sub RevComp {
	my  ($DNAseq, $rev, $rev_comp);# 'local' variables
#	print "subroutine RevComp was called\n"; #make sure sub is called
	$DNAseq=$_[0];
#	print "subroutine is working on \n $DNAseq\n";# make sure sub got the right sequence
	$rev = reverse $DNAseq;	
        $rev_comp=$rev;
	$rev_comp =~ tr/atgcATGC/TACGTACG/;
        $rev_comp; # returns contents of this variable to the main program - might be superfluous- NOT else the result is the number of tranlations made
	};