#!/usr/bin/perl
use strict;
use strict;
use warnings;
use Bio::SearchIO;
use Bio::Seq;
use Bio::SeqIO;

my($seqio);
my($genio);

if(-e $ARGV[0]) {
       $seqio  = Bio::SeqIO->new( '-format' => 'fasta' , -file => $ARGV[0]);
} else {
       die "$ARGV[0] not found\n";
}


my($seq)        = "";
my($len)		= "";
my($head)		= "";


while ( my $seqobj = $seqio->next_seq ) {
       $len    = $seqobj->length();
       $head   = $seqobj->id();
       $seq    = $seqobj->seq();

	chomp($seq);
}


my(%genetic_code) = (
   
	    'TCA' => 'S',    # Serine
	    'TCC' => 'S',    # Serine
	    'TCG' => 'S',    # Serine
	    'TCT' => 'S',    # Serine
	    'TTC' => 'F',    # Phenylalanine
	    'TTT' => 'F',    # Phenylalanine
	    'TTA' => 'L',    # Leucine
	    'TTG' => 'L',    # Leucine
	    'TAC' => 'Y',    # Tyrosine
	    'TAT' => 'Y',    # Tyrosine
	    'TAA' => '_',    # Stop
	    'TAG' => '_',    # Stop
	    'TGC' => 'C',    # Cysteine
	    'TGT' => 'C',    # Cysteine
	    'TGA' => '_',    # Stop
	    'TGG' => 'W',    # Tryptophan
	    'CTA' => 'L',    # Leucine
	    'CTC' => 'L',    # Leucine
	    'CTG' => 'L',    # Leucine
	    'CTT' => 'L',    # Leucine
	    'CCA' => 'P',    # Proline
	    'CCC' => 'P',    # Proline
	    'CCG' => 'P',    # Proline
	    'CCT' => 'P',    # Proline
	    'CAC' => 'H',    # Histidine
	    'CAT' => 'H',    # Histidine
	    'CAA' => 'Q',    # Glutamine
	    'CAG' => 'Q',    # Glutamine
	    'CGA' => 'R',    # Arginine
	    'CGC' => 'R',    # Arginine
	    'CGG' => 'R',    # Arginine
	    'CGT' => 'R',    # Arginine
	    'ATA' => 'I',    # Isoleucine
	    'ATC' => 'I',    # Isoleucine
	    'ATT' => 'I',    # Isoleucine
	    'ATG' => 'M',    # Methionine
	    'ACA' => 'T',    # Threonine
	    'ACC' => 'T',    # Threonine
	    'ACG' => 'T',    # Threonine
	    'ACT' => 'T',    # Threonine
	    'AAC' => 'N',    # Asparagine
	    'AAT' => 'N',    # Asparagine
	    'AAA' => 'K',    # Lysine
	    'AAG' => 'K',    # Lysine
	    'AGC' => 'S',    # Serine
	    'AGT' => 'S',    # Serine
	    'AGA' => 'R',    # Arginine
	    'AGG' => 'R',    # Arginine
	    'GTA' => 'V',    # Valine
	    'GTC' => 'V',    # Valine
	    'GTG' => 'V',    # Valine
	    'GTT' => 'V',    # Valine
	    'GCA' => 'A',    # Alanine
	    'GCC' => 'A',    # Alanine
	    'GCG' => 'A',    # Alanine
	    'GCT' => 'A',    # Alanine
	    'GAC' => 'D',    # Aspartic Acid
	    'GAT' => 'D',    # Aspartic Acid
	    'GAA' => 'E',    # Glutamic Acid
	    'GAG' => 'E',    # Glutamic Acid
	    'GGA' => 'G',    # Glycine
	    'GGC' => 'G',    # Glycine
	    'GGG' => 'G',    # Glycine
	    'GGT' => 'G',    # Glycine
	);
	
 my @startsRF1 =();
    my @startsRF2 =();
    my @startsRF3 =();
    my @stopsRF1 = ();
    my @stopsRF2 = ();
    my @stopsRF3 = ();
    my @arrayOfORFs = ();
    my @arrayOfTranslations = ();
    
    my $joinedAminoAcids = ();

    while ($seq =~ m/ATG|TTG|CTG|ATT|CTA|GTG|ATT/gi){
	my $matchPosition = pos($seq) - 3;
	if (($matchPosition % 3) == 0) {
	    push (@startsRF1, $matchPosition);
	    }
	    
	    
	    while ($seq =~ m/TAG|TAA|TGA/gi){
	my $matchPosition = pos($seq);
	if (($matchPosition % 3) == 0) {
	    push (@stopsRF1, $matchPosition);
	  }  
	    
	 my $codonRange = "";
    	 my $startPosition = 0;
   	 my $stopPosition = 0;

    	@startsRF1 = reverse(@startsRF1);
    	@stopsRF1 = reverse(@stopsRF1);
	while (scalar(@startsRF1) > 0) {
	$codonRange = "";
	$startPosition = pop(@startsRF1);
	if ($startPosition < $stopPosition) {
	    next;
	}
	
	
	my $ORFseq = "";
	
	while (scalar(@stopsRF1) > 0) {
	    $stopPosition = pop(@stopsRF1);
	    if ($stopPosition > $startPosition) {

		my $difF = $stopPosition - $startPosition;
		$ORFseq = substr($seq, $startPosition,(length($seq)-$difF));
		push (@arrayOfORFs, $ORFseq);
		
		
	    }
	foreach $ORFseq (@arrayOfORFs){
		
	my @growingProtein = ();
    for (my $i = 0; $i <= (length($ORFseq) - 3); $i = $i + 3) {
	my $codon = substr($ORFseq, $i, 3);
	if (exists( $genetic_code{$codon} )){
	    push (@growingProtein, $genetic_code{$codon});
	   	}
	else {
	    push (@growingProtein, "X");
	}
    }
	my $joinedAminoAcids = join("",@growingProtein);
	push (@arrayOfTranslations, $joinedAminoAcids);
}

foreach(@arrayOfTranslations) {
   print $_, "\n";
   
	}
      }

   }

  }


}