def test_get_sequence_coordinates_na(self):
seq = Seq("atgcccaagctgaatagcgtagaggggttttcatcatttgaggacgatgtataa")
a = annotate.Annotate("hobbit")
result, coordinates = get_sequence(seq,
coordinates=(0, 12),
amino_acid=False)
expected = "atgcccaagctg"
self.assertEqual(expected, result)
def test_identify_orf_coordinates(self):
ref_seq = "atgcccaagctgaatagcgtagaggggttttcatcatttgaggacgatgtataa"
query_seq = "cccatgcccaacctgaataccgtagagggttttcaacatttgaggaccgatgtataac"
a = annotate.Annotate()
result = pairwise_sw_align(ref_seq, query_seq)
(ref_begin, ref_end, read_begin,
read_end) = get_alignment_start_end(result)
self.assertEqual(3, read_begin)
self.assertEqual(read_end, 56)
def test_load_consensus_simple_case(self):
consensus_filepath = os.path.join(data_dir, 'consensus.fasta')
a = annotate.Annotate("accession")
a.load_consensus_sequence(consensus_filepath)
records = [
a.consensus_sequence[record_id]
for record_id in a.consensus_sequence
]
self.assertEqual(len(records), 10)
self.assertEqual(
records[0].seq,
"attaacgcgcatctggaaattaacacccatgaaggccgcaacgatacccatgaacgcgaactgattgtggaa"
"gatgcgcatattacctaa")
self.assertEqual(
records[1].seq,
"aacaccgcgaacgcgagcacctatgatattcgcacctattgggaaacccatctggaatttattctgctggaag"
"attggattacccatacccatgaagaaaacgatagcttttggcgcatgagctaa")
a.consensus_sequence.close()
def run(options):
if options.verbose:
log_level = logging.DEBUG
msg = "Using debug logging"
else:
log_level = logging.INFO
msg = "Using info logging"
#log_file = f"annotate.log"
#if os.path.exists(log_file):
# os.unlink(log_file)
logging.basicConfig(
#filename=log_file,
stream=sys.stdout,
level=log_level,
format="%(asctime)s\t%(levelname)s\t%(message)s",
datefmt="%d/%m/%Y %I:%M:%S",
)
logging.info(msg)
logging.info(
"Input parameters:\nReference JSON: %s\nConsensus fasta: %s\nEdit file: %s\nAccession: %s\nStop codons: %s\n"
"Min sequence length: %s\nNo stops in middle: %s\nDiscover frame shifts: %s\nFind compensating frame shifts: %s",
options.reference_file, options.consensus_file, options.edit_file,
options.accession, options.stop_codons, options.min_seq_length,
options.no_stops_in_middle, options.discover_frame_shifts,
options.find_compensating_frame_shifts)
a = annotate.Annotate(options.accession)
stop_codons = ",".split(options.stop_codons)
a.run(options.reference_file,
options.consensus_file,
options.edit_file,
stop_codons=stop_codons,
max_mismatch=3,
include_compensatory=options.find_compensating_frame_shifts,
min_seq_length=options.min_seq_length,
discover_frame_shifts=options.discover_frame_shifts,
allow_stop_codons_in_middle=not options.no_stops_in_middle)
def test_load_consensus_empty_file(self):
consensus_filepath = os.path.join(data_dir, 'empty_consensus.fasta')
a = annotate.Annotate("accession")
self.assertRaises(AssertionError, a.load_consensus_sequence,
consensus_filepath)
def test_load_reference_info_correct_accession(self):
ref_filepath = os.path.join(data_dir, 'ref.json')
a = annotate.Annotate("hobbit")
data = a.load_reference_info(ref_filepath)
self.assertIsNotNone(data)
def test_load_reference_info_locations_empty(self):
ref_filepath = os.path.join(data_dir, 'locations_empty_ref.json')
a = annotate.Annotate("test")
self.assertRaises(AssertionError, a.load_reference_info, ref_filepath)
def test_load_reference_info_no_locations(self):
ref_filepath = os.path.join(data_dir, 'missing_locations_ref.json')
a = annotate.Annotate("hobbit")
self.assertRaises(AssertionError, a.load_reference_info, ref_filepath)
def test_load_reference_info_missing_accession(self):
ref_filepath = os.path.join(data_dir, 'ref.json')
a = annotate.Annotate("accession")
self.assertRaises(AssertionError, a.load_reference_info, ref_filepath)
def test_load_reference_info_empty_file(self):
ref_filepath = os.path.join(data_dir, 'empty_ref.json')
a = annotate.Annotate("accession")
self.assertRaises(json.decoder.JSONDecodeError, a.load_reference_info,
ref_filepath)
def test_load_reference_info_no_file(self):
ref_filepath = os.path.join(data_dir, 'idontexist.json')
a = annotate.Annotate("accession")
self.assertRaises(AssertionError, a.load_reference_info, ref_filepath)
def setUp(self):
ref_filepath = os.path.join(data_dir, 'ref.json')
consensus_filepath = os.path.join(data_dir, 'consensus.fasta')
self.a = annotate.Annotate("hobbit")
self.a.load_input_files(ref_filepath, consensus_filepath)
def test_get_sequence_aa_length_remainder_2(self):
seq = Seq("atgcccaagctgaatagcgtagaggggttttcatcatttgaggacgatgtata")
a = annotate.Annotate("hobbit")
result, coordinates = get_sequence(seq)
expected = "MPKLNSVEGFSSFEDDVX"
self.assertEqual(expected, result)
def test_get_sequence_coordinates_aa(self):
seq = Seq("atgcccaagctgaatagcgtagaggggttttcatcatttgaggacgatgtataa")
a = annotate.Annotate("hobbit")
result, coordinates = get_sequence(seq, coordinates=(0, 48))
expected = "MPKLNSVEGFSSFEDD"
self.assertEqual(expected, result)
def test_get_sequence_simple_case(self):
seq = Seq("atgcccaagctgaatagcgtagaggggttttcatcatttgaggacgatgtataa")
a = annotate.Annotate("hobbit")
result, coordinates = get_sequence(seq, amino_acid=False)
self.assertEqual(seq, result)
def test_get_sequence_not_Seq(self):
seq = "atgcccaagctgaatagcgtagaggggttttcatcatttgaggacgatgtataa"
a = annotate.Annotate("hobbit")
self.assertRaises(TypeError, get_sequence, seq)
