#!/usr/bin/perl
use Bio::Seq;
use Bio::SeqIO;
use Bio::SeqUtils;  
my $counter=0;

#=================================
#Script to translate sequences in 3 or 6 frames
#briandotoakleyatarsdotusdadotgov
#k.purdy at warwick.ac dot uk
#=================================


#---define input file----
$usage = "\n\nUsage:  $0 filename\n\n";
my $input_file = $ARGV[0] or die $usage;
	
	print "\nDo you want to see 3 forward frames or all 6 frames?  \n\nEnter 3 or 6:  ";
	chomp ($frame=<STDIN>);
		
	$seqio  = Bio::SeqIO->new( '-format' => 'fasta' , -file => $input_file);

	while ($seqobj = $seqio->next_seq() )  {
	$counter++;
        my $line_counter=0;
	
	print "\n\nSequence number ",$counter,"  ",$seqobj->id,"\n", $seqobj->seq(),"\n\n";

		if ($frame==3) {@prot  = Bio::SeqUtils->translate_3frames($seqobj)};
		if ($frame==6) {@prot  = Bio::SeqUtils->translate_6frames($seqobj)};
		
		foreach $line(@prot) {
                $line_counter++;    
		print "Frame $line_counter:  ",$line->seq(),"\n";
		}

}