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))