def test_allow_internal_stop_codons():
assert (minimal(
cds(
min_size=3,
allow_internal_stop_codons=False,
include_start_codon=False,
include_stop_codon=False,
allow_ambiguous=False,
),
lambda x: all(c not in
["AGA", "AGG", "TAA", "TAG", "TCA", "TGA", "TTA"]
for c in x),
) == "AAA")
def test_min_size_equal_to_max_size():
# you can't fit two codons in 3 bases
with pytest.raises(ValueError):
minimal(
cds(
min_size=3,
max_size=3,
include_start_codon=True,
include_stop_codon=True,
))
# but you can fit one
assert (minimal(
cds(
min_size=3,
max_size=3,
include_start_codon=True,
include_stop_codon=False,
)) == "ATA")
assert (minimal(
cds(
min_size=3,
max_size=3,
include_start_codon=False,
include_stop_codon=True,
)) == "AGA")
# non mod 3 specific sizes won't work
with pytest.raises(Unsatisfiable):
@given(cds(min_size=7, max_size=7))
@settings(suppress_health_check=HealthCheck.all())
def inner(x):
pass
inner()
with pytest.raises(Unsatisfiable):
@given(cds(min_size=8, max_size=8))
@settings(suppress_health_check=HealthCheck.all())
def inner(x):
pass
inner()
# if start and stop codons are included, there is no other codon in a 6-mer
assert minimal(cds(min_size=6, max_size=6)) == "ATAAGA"
def test_max_size_less_than_min_size():
with pytest.raises(InvalidArgument):
minimal(cds(min_size=10, max_size=9))
def test_size_with_codon():
assert minimal(cds(min_size=7)) == "ATAAAAAGA"
def test_total_size_mer():
assert minimal(cds(min_size=4)) == "ATAAGA"
def test_smallest_non_empty_coding_region():
assert minimal(cds(min_size=1)) == "ATAAGA"
def test_smallest_example_with_stop_codon():
assert minimal(cds(include_start_codon=False,
include_stop_codon=True)) == "AGA"
def test_smallest_example():
assert minimal(cds(include_start_codon=False,
include_stop_codon=False)) == ""
import pytest
from hypothesis import HealthCheck, given, settings
from hypothesis.errors import InvalidArgument, Unsatisfiable
from hypothesis_bio import cds
from .minimal import minimal
@given(cds())
def test_cds_type(seq):
assert type(seq) == str
def test_smallest_example():
assert minimal(cds(include_start_codon=False,
include_stop_codon=False)) == ""
def test_smallest_example_with_start_codon():
assert minimal(cds(include_start_codon=True,
include_stop_codon=False)) == "ATA"
def test_smallest_example_with_stop_codon():
assert minimal(cds(include_start_codon=False,
include_stop_codon=True)) == "AGA"
def test_smallest_non_empty_coding_region():
assert minimal(cds(min_size=1)) == "ATAAGA"