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from CAI import RSCU, relative_adaptiveness
import pytest
def test_bad_args():
# make sure bad arguments raise errors
with pytest.raises(TypeError):
relative_adaptiveness()
with pytest.raises(TypeError):
relative_adaptiveness(sequences=["AAC"], RSCUs=RSCU(["AAC"]))
def test_arg_equivalence():
# should be able to take either reference sequences or an RSCU dict
assert relative_adaptiveness(sequences=["AAC"]) == relative_adaptiveness(
RSCUs=RSCU(["AAC"])
)
def test_weights():
assert relative_adaptiveness(sequences=["AAC"]) == {
"AAA": 1.0,
"AAC": 1.0,
"AAG": 1.0,
"AAT": (0.5 / (0.5 * (1 + 0.5))) / (1 / (0.5 * (1 + 0.5))),
"ACA": 1.0,
"ACC": 1.0,
"ACG": 1.0,
"ACT": 1.0,
"AGA": 1.0,
"AGC": 1.0,
"AGG": 1.0,
"AGT": 1.0,
"ATA": 1.0,
"ATC": 1.0,
"ATG": 1.0,
"ATT": 1.0,
"CAA": 1.0,
"CAC": 1.0,
"CAG": 1.0,
"CAT": 1.0,
"CCA": 1.0,
"CCC": 1.0,
"CCG": 1.0,
"CCT": 1.0,
"CGA": 1.0,
"CGC": 1.0,
"CGG": 1.0,
"CGT": 1.0,
"CTA": 1.0,
"CTC": 1.0,
"CTG": 1.0,
"CTT": 1.0,
"GAA": 1.0,
"GAC": 1.0,
"GAG": 1.0,
"GAT": 1.0,
"GCA": 1.0,
"GCC": 1.0,
"GCG": 1.0,
"GCT": 1.0,
"GGA": 1.0,
"GGC": 1.0,
"GGG": 1.0,
"GGT": 1.0,
"GTA": 1.0,
"GTC": 1.0,
"GTG": 1.0,
"GTT": 1.0,
"TAC": 1.0,
"TAT": 1.0,
"TCA": 1.0,
"TCC": 1.0,
"TCG": 1.0,
"TCT": 1.0,
"TGC": 1.0,
"TGG": 1.0,
"TGT": 1.0,
"TTA": 1.0,
"TTC": 1.0,
"TTG": 1.0,
"TTT": 1.0,
}
def test_alternate_genetic_code():
assert relative_adaptiveness(sequences=["AAC"], genetic_code=10) == {
"AAA": 1.0,
"AAC": 1.0,
"AAG": 1.0,
"AAT": (0.5 / (0.5 * (1 + 0.5))) / (1 / (0.5 * (1 + 0.5))),
"ACA": 1.0,
"ACC": 1.0,
"ACG": 1.0,
"ACT": 1.0,
"AGA": 1.0,
"AGC": 1.0,
"AGG": 1.0,
"AGT": 1.0,
"ATA": 1.0,
"ATC": 1.0,
"ATG": 1.0,
"ATT": 1.0,
"CAA": 1.0,
"CAC": 1.0,
"CAG": 1.0,
"CAT": 1.0,
"CCA": 1.0,
"CCC": 1.0,
"CCG": 1.0,
"CCT": 1.0,
"CGA": 1.0,
"CGC": 1.0,
"CGG": 1.0,
"CGT": 1.0,
"CTA": 1.0,
"CTC": 1.0,
"CTG": 1.0,
"CTT": 1.0,
"GAA": 1.0,
"GAC": 1.0,
"GAG": 1.0,
"GAT": 1.0,
"GCA": 1.0,
"GCC": 1.0,
"GCG": 1.0,
"GCT": 1.0,
"GGA": 1.0,
"GGC": 1.0,
"GGG": 1.0,
"GGT": 1.0,
"GTA": 1.0,
"GTC": 1.0,
"GTG": 1.0,
"GTT": 1.0,
"TAC": 1.0,
"TAT": 1.0,
"TCA": 1.0,
"TCC": 1.0,
"TCG": 1.0,
"TCT": 1.0,
"TGA": 1.0, # this is not a stop codon in genetic code 10
"TGC": 1.0,
"TGG": 1.0,
"TGT": 1.0,
"TTA": 1.0,
"TTC": 1.0,
"TTG": 1.0,
"TTT": 1.0,
}
|
