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from CAI import CAI, RSCU, relative_adaptiveness
import pytest
import math
def test_bad_args():
# make sure bad arguments raise errors
with pytest.raises(TypeError):
CAI("AAC") # no reference data
with pytest.raises(TypeError):
CAI("AAC", reference=["AAC"], RSCUs=RSCU(["AAC"]))
def test_cai():
# first, make sure all arguments get the same result
assert (
CAI("AAC", reference=["AAC"])
== CAI("AAC", RSCUs=RSCU(["AAC"]))
== CAI("AAC", weights=relative_adaptiveness(sequences=["AAC"]))
== 1.0
)
# check other sequences
assert CAI("AAT", reference=["AAC"]) == 0.5
assert CAI("AATAAT", reference=["AAC"]) == 0.5
assert CAI("AAT" * 100, reference=["AAC"]) == 0.5
def test_only_non_synonymous():
assert math.isnan(CAI("ATG", reference=["AAC"]))
def test_stop_codon():
# stop codons don't count for CAI
assert (
CAI("AAT", reference=["AAC"])
== CAI("AATTAA", reference=["AAC"])
== CAI("TAAAAT", reference=["AAC"])
)
def test_alternate_genetic_code():
# the differing stop codon
assert CAI("AATTGA", reference=["AAC"]) != CAI(
"AATTGA", reference=["AAC"], genetic_code=10
)
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