public static void main(String[] args) throws Exception {
try {
File fastaFile = new File(args[0]);
File translationTableFile = new File(args[1]);
int direction = "+".equals(args[2]) ? 1 : -1;
FastaParser parser = new FastaParserImpl(fastaFile);
nucleotides = new GenomeNucleotides(parser.readCode(FilenameUtils.getBaseName(fastaFile.getName())));
translationTable = CodonTranslationTable
.parseTableFile(translationTableFile);
if (args.length == 4) {
int codonPosition = Integer.parseInt(args[3]);