def get_scheme(fasta, config=None):
if not config:
config = get_config()
references = process_fasta(fasta)
scheme = MultiplexScheme(
references,
config.get("primer3"),
config.get("target_overlap"),
config.get("step_distance"),
config.get("min_unique"),
config.get("prefix"),
)
scheme.design_scheme()
return scheme
def get_scheme(fasta, **kwargs):
references = process_fasta(fasta)
scheme = MultiplexScheme(references, **kwargs)
scheme.design_scheme()
return scheme
def test_scheme_runs_with_single_reference(chikv_input):
references = process_fasta(chikv_input)[:1]
scheme = MultiplexScheme(references)
scheme.design_scheme()
assert len(scheme.regions) > 30
def test_process_fasta_too_short_input(input_fasta_short_500):
with pytest.raises(ValueError, match="too short"):
process_fasta(input_fasta_short_500, min_ref_size=900)
def test_process_fasta_gaps_removed(input_fasta_valid_with_gaps):
references = process_fasta(input_fasta_valid_with_gaps)
assert "-" not in references[0]
def test_process_fasta_chikv_demo(chikv_input):
references = process_fasta(chikv_input)
assert len(references) == 2
def test_process_fasta_returns_list_of_seq_records(input_fasta_5_random_valid):
references = process_fasta(input_fasta_5_random_valid)
assert len(references) == 5
assert all(isinstance(r, SeqRecord) for r in references)
def test_process_fasta_size_difference_over_500(
input_fasta_size_difference_over_500, ):
with pytest.raises(ValueError, match="too different in size"):
process_fasta(input_fasta_size_difference_over_500)
def test_process_fasta_too_many_records(input_fasta_101_random_valid):
with pytest.raises(ValueError, match="A maximum of 100"):
process_fasta(input_fasta_101_random_valid)
def test_process_fasta_invalid_alphabet(input_fasta_invalid_alphabet):
with pytest.raises(ValueError, match="invalid nucleotide codes"):
process_fasta(input_fasta_invalid_alphabet)
def test_process_fasta_empty_input(input_fasta_empty):
with pytest.raises(ValueError,
match="does not contain any valid references"):
process_fasta(input_fasta_empty)
def test_process_fasta_chikv_demo(chikv_input):
"""Does process_fasta return 2 SeqRecord objects for demo CHIKV input?"""
references = process_fasta(chikv_input)
assert len(references) == 2
def test_process_fasta_size_difference_over_500(
input_fasta_size_difference_over_500, ):
"""Does process_fasta raise for size difference over 500?"""
with pytest.raises(ValueError, match="too different in size"):
process_fasta(input_fasta_size_difference_over_500)
def test_process_fasta_too_many_records(input_fasta_101_random_valid):
"""Does process_fasta raise for too many references?"""
with pytest.raises(ValueError, match="A maximum of 100"):
process_fasta(input_fasta_101_random_valid)
def test_process_fasta_maintains_gaps(input_fasta_valid_with_gaps):
"""Does process_fasta remove gaps?"""
references = process_fasta(input_fasta_valid_with_gaps)
assert "-" not in references[0]
def test_process_fasta_too_many_records(input_fasta_too_many_refs_random_valid):
"""Does process_fasta raise for too many references?"""
with pytest.raises(ValueError, match=f"A maximum of {config.MAX_REFERENCES}"):
process_fasta(input_fasta_too_many_refs_random_valid)
