def test_small_seqs(self):
"""Test sequences smaller than the probe length.
"""
with self.assertRaises(ValueError):
candidate_probes.make_candidate_probes_from_sequences(
['ATCGATCGATCG', 'CCGG'],
probe_length=6,
probe_stride=3,
min_n_string_length=2)
with self.assertRaises(ValueError):
candidate_probes.make_candidate_probes_from_sequences(
['ATCGATCGATCG', 'CCGG'],
probe_length=6,
probe_stride=3,
allow_small_seqs=5,
min_n_string_length=2)
with self.assertRaises(ValueError):
candidate_probes.make_candidate_probes_from_sequences(
['ATCGATCGATCG', 'CNNN'],
probe_length=6,
probe_stride=3,
allow_small_seqs=4,
min_n_string_length=2)
p = candidate_probes.make_candidate_probes_from_sequences(
['ATCGATCGATCG', 'CCGG'],
probe_length=6,
probe_stride=3,
allow_small_seqs=4,
min_n_string_length=2)
p = [''.join(x.seq) for x in p]
self.assertCountEqual(p, ['ATCGAT', 'GATCGA', 'CGATCG'] + ['CCGG'])
def setUp(self):
"""Read the dataset's genomes and create candidate probes.
Only process the first 100 genomes to avoid using too much memory
with the candidate probes.
"""
# Disable logging
logging.disable(logging.WARNING)
seqs = [
gnm.seqs[0]
for gnm in seq_io.read_dataset_genomes(zaire_ebolavirus)
]
seqs = seqs[:100]
self.probes_100 = candidate_probes.make_candidate_probes_from_sequences(
seqs, probe_length=100, probe_stride=50, min_n_string_length=2)
self.probes_75 = candidate_probes.make_candidate_probes_from_sequences(
seqs, probe_length=75, probe_stride=25, min_n_string_length=2)
def test_multiple_seqs(self):
p = candidate_probes.make_candidate_probes_from_sequences(
['ATCGNCGNNTCG', 'ATCGNCGNNTCGATAT'],
probe_length=6,
probe_stride=3,
min_n_string_length=2)
p = [''.join(x.seq) for x in p]
self.assertCountEqual(
p, ['ATCGNC', 'TCGNCG'] + ['ATCGNC', 'TCGNCG', 'TCGATA', 'TCGATA',
'CGATAT'])
def test_one_genome(self):
target_genomes = [['ABCDEFGHIJKLMNOPQRSTUVWXYZ']]
target_genomes = self.convert_target_genomes(target_genomes)
# Create probes of length 6 bp with a stride of 3 bp
input = []
for genomes_from_group in target_genomes:
for g in genomes_from_group:
input += cp.make_candidate_probes_from_sequences(
g.seqs, probe_length=6, probe_stride=3)
f, output = self.get_filter_and_output(6, 0, target_genomes, input, 3,
10)
desired_output = self.make_probes_with_adapters(
['ABCDEF', 'GHIJKL', 'MNOPQR', 'STUVWX'],
['DEFGHI', 'JKLMNO', 'PQRSTU', 'UVWXYZ'])
self.assertCountEqual(output, desired_output)
