#!usr/bin/perl 

use strict;
use library;

my $filename = usrquery ("Please enter multiple FASTA filename: \n");
my %MULTIFAS = parseMULTIFAS ($filename);
my @keys = keys %MULTIFAS;
my ($key, $dna, $size) = '';

open_outfile;

foreach $key (@keys)
	{if (length $key>0)
	{
	$dna = $MULTIFAS{"$key"};
	$size = length($dna);
	my ($start, $stop, $j, $translated_frame, $frame) = '';
	my (@all_orfs) = ();

	$j = 1;
	while ($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;
			my $tag = "$key, $size bp, frame $frame, positions $nt_start to $nt_stop, $aa residues";
			print OUTFILE "$tag\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;
			my $tag = "$key, $size bp, frame -$frame, positions $rc_nt_start to $rc_nt_stop, $aa residues.";
			print OUTFILE "$tag\n";
			print OUTFILE "$ORF\n";
			}
		++$j;
		}

	}} # end of original foreach and if loops #

close (OUTFILE);

exit;