def test_translate(gbkfile):
config = parsing.initial(gbkfile)
config['startBase'] = 161
config['endBase'] = 355
result = parsing.translate(config, rc=False)
assert result['seq'] == 'CTGCCTTTTGGTGTCGTTTATTTCGGCTTTTGCCATAGAAGCCAAAGCCCCCAGAAGTTCGCCTTTGTCCCATGTTGGATTGCCGGTCTTACTATCGACCAGACCGGCCAGAATAAGCAGGCCAGCAGACTGGATGAGGTTATGCGTTCTTTCCTTGTCCTTGGCGTCTCTTTCTCTCTTGGCGATTTTCGATGA'
assert result['trans'] == 'LPFGVVYFGFCHRSQSPQKFAFVPCWIAGLTIDQTGQNKQASRLDEVMRSFLVLGVSFSLGDFR*'
def test_trans_complement(gbkfile):
config = parsing.initial(gbkfile)
config['startBase'] = 116
config['endBase'] = 562
result = parsing.translate(config, rc=True)
assert result['seq'] == 'ATGGCCTCTTTTCGGATTGAAACGCATATCGCTAACCTTCGACAGCTTGAGAAGCCATCGACAGAACAGCGCATCCTGATCTTGCTCTATGACAAGACTGACAGAACGCCAAAAGAGGAAAGAGACCTCAAGGCACTCATCCGGTCGGAAAAAGCGCAGGAAGCCGTAAAAGAGGCTAAAGCCAAAGCATCCGAAGCAAAGGCCAGATCATCGAAAATCGCCAAGAGAGAAAGAGACGCCAAGGACAAGGAAAGAACGCATAACCTCATCCAGTCTGCTGGCCTGCTTATTCTGGCCGGTCTGGTCGATAGTAAGACCGGCAATCCAACATGGGACAAAGGCGAACTTCTGGGGGCTTTGGCTTCTATGGCAAAAGCCGAAATAAACGACACCAAAAGGCAGGAGTGGAAAGAAAAAGGTGATGCGTTATTAGCCGGAGAAAAATGA'
assert result['trans'] == 'MASFRIETHIANLRQLEKPSTEQRILILLYDKTDRTPKEERDLKALIRSEKAQEAVKEAKAKASEAKARSSKIAKRERDAKDKERTHNLIQSAGLLILAGLVDSKTGNPTWDKGELLGALASMAKAEINDTKRQEWKEKGDALLAGEK*'
def test_trans_myco(gbkfile):
config = parsing.initial(gbkfile)
config['startBase'] = 116
config['endBase'] = 562
config['mycoplasma'] = True
result = parsing.translate(config, rc=True)
assert result['trans'] == 'MASFRIETHIANLRQLEKPSTEQRILILLYDKTDRTPKEERDLKALIRSEKAQEAVKEAKAKASEAKARSSKIAKRERDAKDKERTHNLIQSAGLLILAGLVDSKTGNPTWDKGELLGALASMAKAEINDTKRQEWKEKGDALLAGEKW'
def translate2(path):
"Translate the known file with params"
config = build_config(path)
try:
return jsonify(
parsing.translate(config, parsing.tobool(request.args.get('rc')))
)
except Exception as e:
logger.exception('Error While Translating')
return flask.make_response(repr(e), 500)