def test_dna_wt_length(self):
wtseq = "TGGACC"
valid_seqids = ["3-D", "0,3-L,D", "0,3,12-L,D,N", "3-*"]
for seqid in valid_seqids:
with self.subTest(seqid=seqid, wtseq=wtseq):
with self.assertRaises(ValueError):
seqid_to_variant(seqid, wtseq)
def test_wt_type(self):
invalid_wtseqs = [
"AGCT", # partial codon
"BAGTC", # invalid bases
"XATG", # invalid bases
"3-D", # invalid characters
"TGU", # rna
"acgtga", # rna
]
for wtseq in invalid_wtseqs:
with self.subTest(wtseq=wtseq):
with self.assertRaises(ValueError):
seqid_to_variant("0-L", wtseq)
def test_invalid_seqids(self):
invalid_seqids = [
"MGLYTAKLVEN*",
"0,3-L",
"-L",
"-1-D",
"3-L,D",
"0,3;L,D",
"0;3-L;D",
"0,3-L,B",
"0-X",
]
for seqid in invalid_seqids:
with self.subTest(seqid=seqid):
with self.assertRaises(ValueError):
seqid_to_variant(seqid, "AAA")
def test_protein_wt(self):
wtseq = "MGLYTAKLVEN*"
seqid_tuples = [
("p.Met1Leu", "0-L"),
("p.Tyr4Asp", "3-D"),
("p.[Met1Leu;Tyr4Asp]", "0,3-L,D"),
("p.[Met1Leu;Tyr4Asp;Ter12Asn]", "0,3,11-L,D,N"),
("p.Tyr4Ter", "3-*"),
]
for hgvs, seqid in seqid_tuples:
with self.subTest(hgvs=hgvs, seqid=seqid, wtseq=wtseq):
self.assertEqual(Variant(hgvs), seqid_to_variant(seqid, wtseq))
def test_dna_wt(self):
wtseq = "ATGGGCCTGTATACCGCGAAACTGGTGGAAAACTAA"
seqid_tuples = [
("p.Met1Leu", "0-L"),
("p.Tyr4Asp", "3-D"),
("p.[Met1Leu;Tyr4Asp]", "0,3-L,D"),
("p.[Met1Leu;Tyr4Asp;Ter12Asn]", "0,3,11-L,D,N"),
("p.Tyr4Ter", "3-*"),
]
for hgvs, seqid in seqid_tuples:
with self.subTest(hgvs=hgvs, seqid=seqid, wtseq=wtseq):
self.assertEqual(Variant(hgvs), seqid_to_variant(seqid, wtseq))