#!/usr/bin/perl
use Bio::Seq;
use Bio::SeqIO;
use Getopt::Long;
use FindBin qw($Bin);

use strict;
use warnings;

if(@ARGV < 1) { die "fasta-file codon_table codon_file\n"; }
&main;
####################################################################################################
#main program
sub main {
	my($seqio);
        my($line)       			= "";
        my($seq)        			= "";
       	my($revcomp)				= "";
	my($head)       			= "null";
        my($len)        			= "";
	my($frame_seq)				= "";
	my($codonfile)				= "";
	my($codon)				= "";
	my($codontab)				= 11;

	my(%frame)      			= ();
	my(%result)				= ();
	my(@temptable)				= ();
	my(%codontable)				= ();
	my(%results)				= ();
	my $L= 50;
	GetOptions('L=i' => \$L);
	####################################################################################################
	#read the given codon table from file
        if(defined($ARGV[1])) {
                $codontab = $ARGV[1];
        }

	if(defined($ARGV[2])) {
		$codonfile = $ARGV[2];
	} else {
		$codonfile = "$Bin/codon_tables_ncbi.txt";
	}

	if(-e $codonfile) {
		open(TABLE, $codonfile) or die "$codonfile not opened\n";
		while($line = <TABLE>) {
			if($line =~ m/\#$codontab\./) {
				for(my($i) = 0; $i < 7; ++$i) {
					$line 		= <TABLE>;
					$line 		=~ s/^.*=\s*//g;
					$line		=~ s/\s+$//g;
					if(length($line) > 0) {
						#print "$line\n";
						push(@temptable, $line);
					}
				}
			}
		}
		close TABLE;
		if(scalar(@temptable) > 0) {
			for(my($i) = 0; $i < length($temptable[0]); ++$i) {
				$codon = substr($temptable[2], $i, 1)."".substr($temptable[3], $i, 1)."".substr($temptable[4], $i, 1);
				$codontable{$codon}{'aa'} = substr($temptable[0], $i, 1);
				$codontable{$codon}{'start'} = substr($temptable[1], $i, 1);

				#print "$codon\t".substr($temptable[1], $i, 1)."\t".substr($temptable[0], $i, 1)."\n";
			}
		}
	} else {
		die "$codonfile not found\n";
	}

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

	while ( my $seqobj = $seqio->next_seq ) {
        	$len    	= $seqobj->length();
        	$head   	= $seqobj->id();
        	$seq    	= uc($seqobj->seq());
		$revcomp	= reverse($seq);
		$revcomp	=~ tr/ACGT/TGCA/;
		%results	= ();

		for(my($i) = 0; $i < 3; ++$i) {
			$frame_seq 	= substr($seq, $i);
			&translate($frame_seq, \%codontable, \%result, $head, ($i+1), \%results, $L);
			$frame_seq 	= substr($revcomp, $i);
			&translate($frame_seq, \%codontable, \%result, $head, (($i+1)*-1), \%results, $L);
		}

		for my $key (sort { $a <=> $b; } (keys(%results))) {
			print "$results{$key}{'header'}";
			print "$results{$key}{'seq'}";
		}
	}
	####################################################################################################
};
####################################################################################################
#finds always the longest AA-sequence
sub translate {
	my($seq, $conv_table, $result, $name, $frame, $res, $L)	= @_;
	my($piece)						= "";
	my($aa_seq)						= "";
	my($last)						= "";
	my($orf)						= "";
	my($pos)						= 0;
	my($end_char)						= "";
	my($start_end_string)					= "";
	my($len)						= length($seq);


	##################################################################################################
	#convert to aa (for Emmanuel, start codons must be stored into another hash as otherwise
	#all start are assumed to encode M, that is not true

	$aa_seq				= "X";
	$start_end_string               = "M";

	for(my($i) = 0; $i < length($seq); $i = $i + 3) {
		$piece          = substr($seq, $i, 3);
		if(length($piece) == 3 ) {
			if(exists(${$conv_table}{$piece})) {
				$aa_seq			.= ${$conv_table}{$piece}{'aa'};

				if((${$conv_table}{$piece}{'start'} eq 'M')) {
					$start_end_string 		.= "M";
				} elsif(${$conv_table}{$piece}{'aa'} eq '*') {
					$start_end_string		.= "*";
				} else {
					$start_end_string		.= "-";
				}
			} else {
				$aa_seq 		.= "X";
				$start_end_string	.= "-";
			}
		}
	}
	$aa_seq 			.= "*";
	$start_end_string               .= "*";

	###################################################################################################
	#get all orf longer than $L aa (gives the longest possible orf-always!!!)

	#print "$aa_seq\n\n";
	#print "$start_end_string\n\n";

	my($temp_aa)		= "";
	my($start_map)		= "";
	my($start_coord)	= "";
	my($alt_start)		= "";
	my($sub_seq)		= 0;
	my($namecounter)	= 0;
	while($start_end_string =~ m/M.*?\*/g) {
		if(length($&) >= $L) {
			$start_map		= $&;
			if($frame <= 0) {
				$start_coord	= ($len+abs($frame)) - ((pos($start_end_string)*3)+abs($frame)) + 4 #extra codon;
			} else {
				$start_coord	= (pos($start_end_string)*3)-(length($&)*3)+abs($frame) - 3;
			}

			$temp_aa		= substr($aa_seq, pos($start_end_string)-length($&), length($&));
			$temp_aa		=~ s/^./M/;
			$temp_aa		=~ s/.{60}/$&\n/g;
			$temp_aa		=~ s/^\s+|\s+$//g;

			if(!(exists(${$res}{"$start_coord.0"}))) {
				${$res}{"$start_coord.0"}{'header'} 	= ">$name\_orf_frame:$frame\_pos:$start_coord\_len:".length($start_map)." X ".length($aa_seq)."\n";
				${$res}{"$start_coord.0"}{'seq'}	= "$temp_aa\n";
				#print "NON: $name\_orf_frame:$frame\_pos:$start_coord\_len:".length($start_map)."\n";
			} else {
				$namecounter = 0;
				while((exists(${$res}{$start_coord.".".$namecounter}))) {
					++$namecounter;
				}
				${$res}{$start_coord.".".$namecounter}{'header'}	= ">$name\_orf_frame:$frame\_pos:$start_coord\_len:".length($start_map)."\n";
				${$res}{$start_coord.".".$namecounter}{'seq'}		= "$temp_aa\n";
				#print STDERR "DUBLICATED: $namecounter $name\_orf_frame:$frame\_pos:$start_coord\_len:".length($start_map)."\n";
			}
		}
	}
};
#####################################################################################################
#