def test_compare_then_get_letter_recursively():
host = "AACCGCGGTGAGCATTTCAAGGGTACAACGGTTCAA"
parasite = "CGCGGTGAGCATTTCAAGGGTACAACGGTTCAA"
host_triplets = ga.convert_seq_to_codons(host)
parasite_triplets = ga.convert_seq_to_codons(parasite)
codon_to_codon_extended = ga.generate_swaptable(ga.codon_to_aa,
ga.aa_to_codon_extended)
host_tuplelist = ga.convert_codonlist_to_tuplelist(
host_triplets, codon_to_codon_extended)
parasite_tuplelist = ga.convert_codonlist_to_tuplelist(
parasite_triplets, codon_to_codon_extended)
host_letter = ("C", [1, 0, 0])
parasite_letter = ("C", [0, 0, 0])
result = ga.compare_then_get_letter_recursively(host_tuplelist,
parasite_tuplelist,
host_letter,
parasite_letter)
expected = (
"Finished parasite sequence, match found! Ending host position:[11, 0, 2]"
)
assert result == expected
no_result = ga.compare_then_get_letter_recursively(host_tuplelist,
(["CAA"], ["CCC"]),
host_letter,
parasite_letter)
assert no_result == "No match for this starting codon position"
def test_convert_codonlist_to_tuplelist():
codon_to_codon_extended = ga.generate_swaptable(ga.codon_to_aa,
ga.aa_to_codon_extended)
result = ga.convert_codonlist_to_tuplelist(["GTA", "CCC", "GCT", "GCG"],
codon_to_codon_extended)
assert result == [("GTX", ), ("CCX", ), ("GCX", ), ("GCX", )]
def test_find_partial_overlaps():
records = list(SeqIO.parse("tests/data/example.fa", "fasta"))
swaptable = ga.generate_swaptable(ga.codon_to_aa, ga.aa_to_codon_extended)
host = str(records[0].seq)
parasite = str(records[7].seq)
result = ga.find_partial_overlaps(host, parasite, swaptable, verbose=True)
assert result["f_0"] == [0, 4, 387]
def test_make_genealloy():
records = list(SeqIO.parse("tests/data/example.fa", "fasta"))
swaptable = ga.generate_swaptable(ga.codon_to_aa, ga.aa_to_codon_extended)
host = str(records[0].seq)
parasite = str(records[2].seq)
result = ga.make_genealloy(host, parasite, swaptable, verbose=True)
assert result["f_0"] == [55, 155]
parasite = str(records[3].seq)
result = ga.make_genealloy(host, parasite, swaptable, verbose=True)
assert result["f_0"] == []
parasite = str(records[5].seq)
result = ga.make_genealloy(host, parasite, swaptable, verbose=True)
assert result["f_1"] == [0]
parasite = str(records[6].seq)
result = ga.make_genealloy(host, parasite, swaptable, verbose=True)
assert result["f_2"] == [1, 92, 133, 281]
def test_generate_swaptable():
codon_to_codon_extended = ga.generate_swaptable(ga.codon_to_aa,
ga.aa_to_codon_extended)
assert codon_to_codon_extended["TTA"] == ("TTR", "CTX", "YTR")