synonymy.pl

#!/usr/bin/perl
## Pombert Lab, 2017-2018 Illinois Tech
my $version = '0.4'; ## Now compatible with NCBI GenBank GBFF and GFF files
my $name = 'synonymy.pl';

use strict; use warnings; use Getopt::Long qw(GetOptions);

## Usage definition
my $hint = "Type synonymy.pl -h (--help) for list of options\n";
my $usage = <<"OPTIONS";
NAME		$name
VERSION		$version
SYNOPSIS	Sort SNPs per type (CDS, tRNA, rRNA or intergenic) and synonymous or non-synonymous, if applicable
		## Does not work with introns yet
		
USAGE		synonymy.pl -gcode 1 -fa reference.fasta -ref reference.gff -format gb -vcf *.vcf -o table_name
OPTIONS
die "$usage\n$hint\n" unless@ARGV;

my $options = <<'END_OPTIONS';
OPTIONS:
-h (--help)	Display this list of options
-v (--version)	Display script version
-fa (--fasta)	Reference genome in fasta format
-r (--ref)	Reference genome annotation in GBK or GFF format
-f (--format)	Reference file format; gb or gff [default: gff]
-vcf (--vcf)	SNPs in Variant Calling Format (VCF)
-o (--output)	Table prefix [Default: synonymy] The .features/.intergenic suffixes and .tsv file extension will be added automatically.
-gc (--gcode)	NCBI genetic code; e.g.:
		1  - The Standard Code
		2  - The Vertebrate Mitochondrial Code
		3  - The Yeast Mitochondrial Code
		4  - The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code
		11 - The Bacterial, Archaeal and Plant Plastid Code
		NOTE - For complete list; see https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
END_OPTIONS

## GetOptions
my $help;
my $vn;
my $fasta;
my $ref;
my $format = 'gff';
my @vcf;
my $output = 'synonymy';
my $gc = '01';
GetOptions(
	'h|help' => \$help,
	'v|version' => \$vn,
	'fa|fasta=s' => \$fasta,
	'r|ref=s' => \$ref,
	'f|format=s' => \$format,
	'vcf=s@{1,}' => \@vcf,
	'o|output=s' => \$output,
	'gc|gcode=i' => \$gc
);
if ($help){die "$usage\n$options\n";} if ($vn){die "\nversion $version\n\n";}

## Building hash of sequences
open FASTA, "<$fasta";
my %sequences; my $contig;
while (my $line = <FASTA>){
	chomp $line;
	if ($line =~ /^>(\S+)/){$contig = $1;}
	else{$sequences{$contig} .= $line;}
}

## Building hashes of features + Init tables
open REF, "<$ref";
open TABLE, ">$output.features.tsv";
open INTER, ">$output.intergenic.tsv";
print TABLE "Locus_tag\tReference Contig\tVCF file\tType\tStart\tEnd\tStrandedness\tProduct\tVariant Position\tReference\tVariant\tSynonymy\tGenetic Code\tRefCodon\tVarCodon\tFrequency\tE-value\n";
print INTER "Reference Contig\tVCF file\tType\tVariant Position\tReference\tVariant\tFrequency\tE-value\n";

## Must simplify the data structure to one hash of features. Will be easier to adapt for input files. Working multiline would do it.
my %genes, my %features; my %hashes; ## hash of hashes for contigs and their feature locations
my $type; my $start; my $end; my $strand; my $id; my $locus_tag; my $parent; my $product; my $key;
if ($format eq 'gff'){
	while (my $line = <REF>){
		chomp $line;
		## Looking at GFF files
		if ($line =~ /^#/){next;}
		elsif ($line =~ /^ID=/){next;}
		elsif ($line =~ /^(\S+)\t.*\t(gene|pseudogene)\t(\d+)\t(\d+)\t\.\t([+-])\t[.012]\tID=(\w+).*\;locus_tag=([A-Za-z0-9 _]+)/){ ## Working on locus_tags
			$contig = $1; $type = $2; $start = $3; $end = $4; $strand = $5; $id = $6; $locus_tag = $7;
			$genes{$id}[0] = $contig;
			$genes{$id}[1] = $start;
			$genes{$id}[2] = $end;
			$genes{$id}[3] = $strand;
			$genes{$id}[4] = $locus_tag;
		}
		elsif ($line =~ /^(\S+)\t.*\t(tRNA|rRNA|CDS|)\t(\d+)\t(\d+)\t\.\t([+-])\t[.012]\tID=(\w+).*Parent=([A-Za-z0-9_]+).*product=([A-Za-z0-9 -]+)/){	## Working on features
			$contig = $1; $type = $2; $start = $3; $end = $4; $strand = $5; $id = $6; $parent = $7; $product = $8;
			$features{$id}[0] = $type;
			$features{$id}[1] = $start;
			$features{$id}[2] = $end;
			$features{$id}[3] = $strand;
			$features{$id}[4] = $parent;
			$features{$id}[5] = $product;
			print "$contig\t$type\t$strand\t$locus_tag\t$product\n";
			for ($start..$end){
				push (@{$hashes{$contig}{$_}}, $id);
			}
		}
	}
}
elsif ($format eq 'gb'){
	my $gbk; while (my $line = <REF>){$gbk .= $line;}
	my @contigs = split ("\/\/\n", $gbk);
	while (my $cg = shift @contigs){
	my @data = split ("ORIGIN.*?\n", $cg); ## $data[0] => annotations, $data[1] => sequences
	my $sequence = $data[1]; $sequence =~ s/[0-9\s\n]//g;
	my $locus; ($locus) = ($data[0] =~ /LOCUS\s+(\S+)/);
	my $contig; ($contig) = ($data[0] =~ /VERSION\s+(\S+)/);
	print "Working on $locus version $contig\n";
	my $feat;	($feat) = ($data[0] =~ /FEATURES(.*)/s);
	my @features = split("     gene            ", $feat);
		while (my $line = shift@features){
			if ($line =~ /\s+(CDS|rRNA|tRNA)\s+.*?(\d+)\.\.(\d+)/m){
				$type = $1; $start = $2; $end = $3;
				if ($line =~ /complement/){$strand = '-';}
				else{$strand = '+';}
				($locus_tag) = ($line =~ /\/locus_tag="(.*?)"/s); $locus_tag =~ s/\s{2,}/ /g; $locus_tag =~ s/\n//g; ## removing new lines, if any
				($product) = ($line =~ /\/product="(.*?)"/s); $product =~ s/\s{2,}/ /g; $product =~ s/\n//g; ## removing new lines, if any
				print "$contig\t$type\t$strand\t$locus_tag\t$product\n";
				$genes{$locus_tag}[0] = $contig;
				$genes{$locus_tag}[1] = $start; $features{$locus_tag}[1] = $start;
				$genes{$locus_tag}[2] = $end; $features{$locus_tag}[2] = $end;
				$genes{$locus_tag}[3] = $strand; $features{$locus_tag}[3] = $strand;
				$genes{$locus_tag}[4] = $locus_tag; $features{$locus_tag}[4] = $locus_tag;
				$features{$locus_tag}[0] = $type;
				$features{$locus_tag}[5] = $product;
				for ($start..$end){
					push (@{$hashes{$contig}{$_}}, $locus_tag);
				}
			}
		}
	}
}
## Working on VCF files
my $codon; my $snp; my $revcodon; my $revsnp; my $locus;
my %gcodes; gcodes();
while (my $vcf = shift@vcf){
	open VCF, "<$vcf";
	while (my $line = <VCF>){
		chomp $line;
		if ($line =~ /^#/){next;}
		else{
			my @vcf = split("\t", $line); my @params = split(":", $vcf[9]); my $freq = $params[6]; my $evalue = $params[7];
			$contig = $vcf[0]; my $position = $vcf[1]; my $ref = $vcf[3]; my $alt = $vcf[4];
			if (exists $hashes{$contig}{$position}){
				for (0..$#{$hashes{$contig}{$position}}){
					$locus = $hashes{$contig}{$position}[$_];
					$type = $features{$hashes{$contig}{$position}[$_]}[0];
					$start = $features{$hashes{$contig}{$position}[$_]}[1];
					$end = $features{$hashes{$contig}{$position}[$_]}[2];
					$strand = $features{$hashes{$contig}{$position}[$_]}[3];
					$parent = $features{$hashes{$contig}{$position}[$_]}[4];
					$product = $features{$hashes{$contig}{$position}[$_]}[5];
					print TABLE "$genes{$parent}[4]\t$contig\t$vcf\t$type\t$start\t$end\t$strand\t$product\t$position\t$ref\t$alt\t";
					if ($type eq 'tRNA'){print TABLE "N\/A\tN\/A\tN\/A\tN\/A\t";}
					elsif ($type eq 'rRNA'){print TABLE "N\/A\tN\/A\tN\/A\tN\/A\t";}
					elsif ($type eq 'CDS'){
						if (($strand  eq '+') || ($strand  eq 'plus')){
							if (($position - $start) == 0){
								$codon = substr($sequences{$contig}, $position-1, 3);
								$snp = $codon; $snp =~ substr($snp, 0, 1, $alt);
								translation();
							}
							elsif (($position - $start) == 1){
								$codon = substr($sequences{$contig}, $position-2, 3);
								$snp = $codon; $snp =~ substr($snp, 1, 1, $alt);
								translation();
							}
							elsif (($position - $start) > 1){
								my $location = $position - $start + 1;
								if (($location % 3) == 0){ ## Third codon position
									$codon = substr($sequences{$contig}, $position-3, 3); ## this is OK
									$snp = $codon; $snp =~ substr($snp, 2, 1, $alt);
									translation();
								}
								elsif (($location % 3) == 1){ ## First codon position
									$codon = substr($sequences{$contig}, $position-1, 3);
									$snp = $codon; $snp =~ substr($snp, 0, 1, $alt);
									translation();
								}
								elsif (($location % 3) == 2){ ## Second codon position
									$codon = substr($sequences{$contig}, $position-2, 3);
									$snp = $codon; $snp =~ substr($snp, 1, 1, $alt);
									translation();
								}
							}
						}
						elsif (($strand  eq '-') || ($strand  eq 'minus')){
							if (($end - $position) == 0){
								$revcodon = substr($sequences{$contig}, $position-3, 3);
								$revsnp = $revcodon; $revsnp =~ substr($revsnp, 2, 1, $alt);
								rev(); translation();
							}
							elsif (($end - $position) == 1){
								$revcodon  = substr($sequences{$contig}, $position-2, 3);
								$revsnp = $revcodon; $revsnp =~ substr($revsnp, 1, 1, $alt);
								rev(); translation();
							}
							elsif (($end - $position) > 1){
								my $location = $end - $position + 1;
								if (($location % 3) == 0){ ## Third codon position
									$revcodon = substr($sequences{$contig}, $position-1, 3);
									$revsnp = $revcodon; $revsnp =~ substr($revsnp, 0, 1, $alt);
									rev(); translation();
								}
								elsif (($location % 3) == 1){ ## First codon position
									$revcodon = substr($sequences{$contig}, $position-3, 3);
									$revsnp = $revcodon; $revsnp =~ substr($revsnp, 2, 1, $alt);
									rev(); translation();
								}
								elsif (($location % 3) == 2){ ## Second codon position
									$revcodon = substr($sequences{$contig}, $position-2, 3);
									$revsnp = $revcodon; $revsnp =~ substr($revsnp, 1, 1, $alt);
									rev(); translation();
								}
							}
						}
					}
					print TABLE "$freq\t$evalue\n";
				}
			}
			else {print INTER "$contig\t$vcf\tintergenic\t$position\t$ref\t$alt\t$freq\t$evalue\n"}
		}
	}
}

## Subroutines
sub rev{
	$codon = reverse($revcodon); $codon=~ tr/ATGCNatgcn/TACGNtacgn/;
	$snp = reverse($revsnp); $snp=~ tr/ATGCNatgcn/TACGNtacgn/;	
}
sub translation{
	$codon = uc($codon); $snp = uc($snp);
	if ($codon =~ /[^ATGCatgc]/){print TABLE "ambiguous bases\t$gc\t$codon\t$snp\t";}
	elsif ($gcodes{$gc}{$codon} eq $gcodes{$gc}{$snp}){print TABLE "synonym\t$gc\t$codon\t$snp\t";}
	elsif ($gcodes{$gc}{$codon} ne $gcodes{$gc}{$snp}){print TABLE "non-syn\t$gc\t$codon\t$snp\t";}
}
sub gcodes{ ## NCBI Genetic codes
	%gcodes = (
		1 => { ## The Standard Code (transl_table=1)
			'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
			'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
			'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => '*',   
			'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',
			'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
			'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
			'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
			'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
			'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
			'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
			'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',
			'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',
			'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
			'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
			'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
			'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
		},
		2 => { ## The Vertebrate Mitochondrial Code (transl_table=2)
			'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',  
			'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
			'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => 'W',
			'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',
			'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
			'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
			'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
			'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
			'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
			'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
			'ATA' => 'M', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => '*',
			'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => '*',
			'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
			'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
			'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
			'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
		},
		3 => { ## The Yeast Mitochondrial Code (transl_table=3)
			'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
			'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
			'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => 'W',
			'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',
			'CTT' => 'T', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
			'CTC' => 'T', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
			'CTA' => 'T', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
			'CTG' => 'T', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
			'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
			'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
			'ATA' => 'M', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',
			'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',
			'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
			'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
			'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
			'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
		},
		4 => { ## The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code (transl_table=4)
			'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',  
			'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',  
			'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => 'W',  
			'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',  
			'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',  
			'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',  
			'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',  
			'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',  
			'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',  
			'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',  
			'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',  
			'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',  
			'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',  
			'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',  
			'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',  
			'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G' 
		},
		5 => { ## The Invertebrate Mitochondrial Code (transl_table=5)
			'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',  
			'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',  
			'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => 'W',  
			'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',  
			'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',  
			'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',  
			'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',  
			'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',  
			'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',  
			'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',  
			'ATA' => 'M', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'S',  
			'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'S',  
			'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',  
			'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',  
			'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',  
			'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'  
		},
		6 => { ## The Ciliate, Dasycladacean and Hexamita Nuclear Code (transl_table=6)
			'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C', 
			'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C', 
			'TTA' => 'L', 'TCA' => 'S', 'TAA' => 'Q', 'TGA' => '*', 
			'TTG' => 'L', 'TCG' => 'S', 'TAG' => 'Q', 'TGG' => 'W', 
			'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R', 
			'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R', 
			'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R', 
			'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R', 
			'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S', 
			'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S', 
			'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R', 
			'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R', 
			'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G', 
			'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G', 
			'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G', 
			'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G' 
		},
		9 => { ## The Echinoderm and Flatworm Mitochondrial Code (transl_table=9)
			'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',  
			'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',  
			'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => 'W',  
			'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',  
			'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',  
			'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',  
			'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',  
			'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',  
			'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',  
			'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',  
			'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'N', 'AGA' => 'S',  
			'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'S',  
			'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',  
			'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
			'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',  
			'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'  
		},
		10 => { ## The Euplotid Nuclear Code (transl_table=10)
			'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
			'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
			'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => 'C',
			'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',
			'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
			'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
			'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
			'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
			'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
			'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
			'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',
			'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',
			'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
			'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
			'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
			'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
		},
		11 => { ## The Bacterial, Archaeal and Plant Plastid Code (transl_table=11)
			'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',  
			'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',  
			'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => '*',  
			'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',  
			'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',  
			'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',  
			'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',  
			'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',  
			'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',  
			'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',  
			'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',  
			'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',  
			'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',  
			'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',  
			'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',  
			'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'  
		},
		12 => { ## The Alternative Yeast Nuclear Code (transl_table=12)
			'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
			'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
			'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => '*',
			'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',
			'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
			'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
			'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
			'CTG' => 'S', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
			'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
			'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
			'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',
			'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',
			'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
			'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
			'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
			'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
		},
		13 => { ## The Ascidian Mitochondrial Code (transl_table=13)
			'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
			'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
			'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => 'W',
			'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',
			'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
			'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
			'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
			'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
			'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
			'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
			'ATA' => 'M', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'G',
			'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'G',
			'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
			'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
			'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
			'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G',
		},
		14 => { ## The Alternative Flatworm Mitochondrial Code (transl_table=14)
			'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
			'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
			'TTA' => 'L', 'TCA' => 'S', 'TAA' => 'Y', 'TGA' => 'W',
			'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',
			'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
			'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
			'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
			'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
			'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
			'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
			'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'N', 'AGA' => 'S',
			'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'S',
			'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
			'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
			'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
			'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G',
		},
		16 => { ## Chlorophycean Mitochondrial Code (transl_table=16)
			'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
			'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
			'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => '*',
			'TTG' => 'L', 'TCG' => 'S', 'TAG' => 'L', 'TGG' => 'W',
			'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
			'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
			'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
			'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
			'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
			'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
			'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',
			'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',
			'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
			'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
			'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
			'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
		},
		21 => { ## Trematode Mitochondrial Code (transl_table=21)
			'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',  
			'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',  
			'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => 'W',  
			'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',  
			'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',  
			'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',  
			'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',  
			'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',  
			'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',  
			'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',  
			'ATA' => 'M', 'ACA' => 'T', 'AAA' => 'N', 'AGA' => 'S',  
			'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'S',  
			'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',  
			'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',  
			'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',  
			'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'  
		},
		22 => { ## Scenedesmus obliquus Mitochondrial Code (transl_table=22)
			'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',  
			'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',  
			'TTA' => 'L', 'TCA' => '*', 'TAA' => '*', 'TGA' => '*',  
			'TTG' => 'L', 'TCG' => 'S', 'TAG' => 'L', 'TGG' => 'W',  
			'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',  
			'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',  
			'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',  
			'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',  
			'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',  
			'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',  
			'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',  
			'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',  
			'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',  
			'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',  
			'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',  
			'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'  
		},
		23 => { ## Thraustochytrium Mitochondrial Code (transl_table=23)
			'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
			'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
			'TTA' => '*', 'TCA' => 'S', 'TAA' => '*', 'TGA' => '*',
			'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',
			'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
			'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
			'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
			'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
			'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
			'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
			'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',
			'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',
			'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
			'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
			'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
			'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
		},
		24 => { ## Pterobranchia Mitochondrial Code (transl_table=24)
			'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
			'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
			'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => 'W',
			'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',
			'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
			'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
			'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
			'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
			'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
			'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
			'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'S',
			'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'K',
			'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
			'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
			'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
			'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
		},
		25 => { ## Candidate Division SR1 and Gracilibacteria Code (transl_table=25)
			'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
			'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
			'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => 'G',
			'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',
			'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
			'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
			'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
			'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
			'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
			'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
			'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',
			'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',
			'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
			'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
			'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
			'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
		},
		26 => { ## Pachysolen tannophilus Nuclear Code (transl_table=26)
			'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
			'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
			'TTA' => 'L', 'TCA' => 'S', 'TAA' => '*', 'TGA' => '*',
			'TTG' => 'L', 'TCG' => 'S', 'TAG' => '*', 'TGG' => 'W',
			'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
			'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
			'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
			'CTG' => 'A', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
			'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
			'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
			'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',
			'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',
			'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
			'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
			'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
			'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
		},
		27 => { ## Karyorelict Nuclear (transl_table=27)
			'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
			'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
			'TTA' => 'L', 'TCA' => 'S', 'TAA' => 'Q', 'TGA' => 'W',
			'TTG' => 'L', 'TCG' => 'S', 'TAG' => 'Q', 'TGG' => 'W',
			'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
			'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
			'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
			'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
			'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
			'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
			'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',
			'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',
			'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
			'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
			'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
			'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
		},
		28 => { ## Condylostoma Nuclear (transl_table=28)
			'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
			'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
			'TTA' => 'L', 'TCA' => 'S', 'TAA' => 'Q', 'TGA' => 'W',
			'TTG' => 'L', 'TCG' => 'S', 'TAG' => 'Q', 'TGG' => 'W',
			'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
			'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
			'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
			'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
			'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
			'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
			'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',
			'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',
			'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
			'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
			'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
			'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
		},
		29 => { ## Mesodinium Nuclear (transl_table=29)
			'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
			'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
			'TTA' => 'L', 'TCA' => 'S', 'TAA' => 'Y', 'TGA' => '*',
			'TTG' => 'L', 'TCG' => 'S', 'TAG' => 'Y', 'TGG' => 'W',
			'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
			'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
			'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
			'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
			'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
			'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
			'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',
			'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',
			'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
			'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
			'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
			'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
		},
		30 => { ## Peritrich Nuclear (transl_table=30)
			'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
			'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
			'TTA' => 'L', 'TCA' => 'S', 'TAA' => 'E', 'TGA' => '*',
			'TTG' => 'L', 'TCG' => 'S', 'TAG' => 'E', 'TGG' => 'W',
			'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
			'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
			'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
			'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
			'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
			'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
			'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',
			'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',
			'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
			'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
			'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
			'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
		},
		31 => { ## Blastocrithidia Nuclear (transl_table=31)
			'TTT' => 'F', 'TCT' => 'S', 'TAT' => 'Y', 'TGT' => 'C',
			'TTC' => 'F', 'TCC' => 'S', 'TAC' => 'Y', 'TGC' => 'C',
			'TTA' => 'L', 'TCA' => 'S', 'TAA' => 'E', 'TGA' => 'W',
			'TTG' => 'L', 'TCG' => 'S', 'TAG' => 'E', 'TGG' => 'W',
			'CTT' => 'L', 'CCT' => 'P', 'CAT' => 'H', 'CGT' => 'R',
			'CTC' => 'L', 'CCC' => 'P', 'CAC' => 'H', 'CGC' => 'R',
			'CTA' => 'L', 'CCA' => 'P', 'CAA' => 'Q', 'CGA' => 'R',
			'CTG' => 'L', 'CCG' => 'P', 'CAG' => 'Q', 'CGG' => 'R',
			'ATT' => 'I', 'ACT' => 'T', 'AAT' => 'N', 'AGT' => 'S',
			'ATC' => 'I', 'ACC' => 'T', 'AAC' => 'N', 'AGC' => 'S',
			'ATA' => 'I', 'ACA' => 'T', 'AAA' => 'K', 'AGA' => 'R',
			'ATG' => 'M', 'ACG' => 'T', 'AAG' => 'K', 'AGG' => 'R',
			'GTT' => 'V', 'GCT' => 'A', 'GAT' => 'D', 'GGT' => 'G',
			'GTC' => 'V', 'GCC' => 'A', 'GAC' => 'D', 'GGC' => 'G',
			'GTA' => 'V', 'GCA' => 'A', 'GAA' => 'E', 'GGA' => 'G',
			'GTG' => 'V', 'GCG' => 'A', 'GAG' => 'E', 'GGG' => 'G'
		},
	);
}