def test_translate(self): '''Test translate works in each frame''' tmp = 'tmp.translated.fa' for i in range(3): tasks.translate(os.path.join(data_dir, 'sequences_test_translate.fa'), tmp, frame=i) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_translate.fa.frame' + str(i)), tmp)) os.unlink(tmp)
def run(description): parser = argparse.ArgumentParser( description = 'Translates all sequences in input file. Output is always FASTA format', usage = 'fastaq translate [options] <infile> <outfile>') parser.add_argument('--frame', type=int, choices=[0,1,2], help='Frame to translate [%(default)s]', default=0) parser.add_argument('infile', help='Name of file to be translated') parser.add_argument('outfile', help='Name of output FASTA file') options = parser.parse_args() tasks.translate(options.infile, options.outfile, frame=options.frame)
def run(description): parser = argparse.ArgumentParser( description="Translates all sequences in input file. Output is always FASTA format", usage="fastaq translate [options] <infile> <outfile>", ) parser.add_argument("--frame", type=int, choices=[0, 1, 2], help="Frame to translate [%(default)s]", default=0) parser.add_argument("infile", help="Name of file to be translated") parser.add_argument("outfile", help="Name of output FASTA file") options = parser.parse_args() tasks.translate(options.infile, options.outfile, frame=options.frame)