#!usr/bin/perl -w

use library;
use strict;

### Translates a sequence in all 6 frames.
# Cutoff value for sizes of ORFs returned can be altered within the subroutine 
# 'split_sequence'. ###

my $filename = usrquery ("Please enter filename: \n");
my @filedata = read_file_data ($filename);
my $tag = extract_tag (@filedata);
my $dna = extract_sequence (@filedata);
$dna =~ tr/actg/ACTG/;
my $size = length($dna);
my ($start, $stop, $j, $translated_frame, $frame) = '';
my (@all_orfs) = ();

my $outputfile = '';
# Remember to 'close OUTFILE' at end #
open_outfile;

$j = 1;
while ($j < 4)
{$frame = $j;
@all_orfs = ();
$translated_frame = '';
for (my $i=($frame-1);$i < (length($dna)-2);$i +=3)
	{my $codon = substr ($dna, $i, 3);
	$translated_frame .= trans ($codon);}
	@all_orfs = split_sequence ($translated_frame);
foreach my $ORF (@all_orfs)
	{$translated_frame =~ /$ORF/ig;
	$stop = pos ($translated_frame);
	$start = ($stop - (length $ORF))+1;
	my ($nt_start, $nt_stop) = counting ($start, $stop, $frame);
	my $aa = length $ORF;
	print OUTFILE "$tag, $size bp, frame $frame, positions $nt_start to $nt_stop, $aa residues.\n";
	print OUTFILE "$ORF\n";
	}
	++$j;}

my $rc = revcomp ($dna);

$j = 1;
while ($j < 4)
{$frame = $j;
@all_orfs = ();
$translated_frame = '';
for (my $i=($frame-1);$i < (length($dna)-2);$i +=3)
	{my $codon = substr ($rc, $i, 3);
	$translated_frame .= trans ($codon);}
	@all_orfs = split_sequence ($translated_frame);
foreach my $ORF (@all_orfs)
	{$translated_frame =~ /$ORF/ig;
	$stop = pos ($translated_frame);
	$start = ($stop - (length $ORF))+1;
	my ($nt_start, $nt_stop) = counting ($start, $stop, $frame);
	my $rc_nt_start = (($size - $nt_start)+1);
	my $rc_nt_stop = (($size - $nt_stop)+1);
	my $aa = length $ORF;
	print OUTFILE "$tag, $size bp, frame -$frame, positions $rc_nt_start to $rc_nt_stop, $aa residues.\n";
	print OUTFILE "$ORF\n";
	}++$j;}

close OUTFILE;
exit;