#!/usr/bin/env python import sys from Bio import SeqIO from os.path import exists from dark.aa import CODONS START_CODON = 'ATG' STOP_CODONS = {'TAA', 'TAG', 'TGA'} CODON_TO_AA = {} START_AA = 'M' STOP_AA = '*' for aa, codons in CODONS.items(): for codon in codons: CODON_TO_AA[codon] = aa for codon in STOP_CODONS: CODON_TO_AA[codon] = STOP_AA _rcTable = str.maketrans('ACGT', 'TGCA') def revcomp(s): """ Reverse complement a nucleotide string. """ return s.translate(_rcTable)[::-1]