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from CAI import RSCU
import pytest
def test_sum():
# The sum of the RSCUs should be equal to the number of codons
assert abs(sum(RSCU(["AAC"]).values()) - len(RSCU(["AAC"]))) < 0.0001
assert abs(sum(RSCU(["AACGATACGGCACGT"]).values()) - len(RSCU(["AAC"]))) < 0.0001
def test_rscu():
assert RSCU(["AAC"]) == {
"AAA": 1.0,
"AAC": 1 / (0.5 * (1 + 0.5)),
"AAG": 1.0,
"AAT": 0.5 / (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_str_arg():
# raise an error if given a string
with pytest.raises(ValueError):
RSCU("AAA")
def test_seq():
# make sure module works on Bio.Seq objects
from Bio.Seq import Seq
assert RSCU([Seq("AGC")]) == RSCU(["AGC"])
assert RSCU([Seq("AACGATACGGCACGT")]) == RSCU(["AACGATACGGCACGT"])
def test_multiple_seqs():
# multiple sequences should be identical to their concatenation
assert RSCU(["AAC", "ATC"]) == RSCU(["AACATC"])
assert RSCU(["AAC", "ATC", "AACGATACGGCACGT"]) == RSCU(["AACATCAACGATACGGCACGT"])
def test_stop_codon():
# stop codons should be equivalent to an empty string since they don't have RSCUs
assert RSCU(["TAA"]) == RSCU(["TAG"]) == RSCU([" "])
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