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added test cases for hgvs util functions
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@erikyao
erikyao committed Jan 13, 2022
1 parent 38e73e4 commit f6c8718
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Empty file removed src/tests/utils/__init__.py
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199 changes: 198 additions & 1 deletion src/tests/utils/hgvs_test.py
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import unittest
from utils.hgvs import DocEncoder
from utils.hgvs import *


class TestFunctions(unittest.TestCase):
def test_is_snp(self):
hgvs = "chrY:g.1885021C>A"
self.assertTrue(is_snp(hgvs))

hgvs = "chrY:g.21733168del"
self.assertFalse(is_snp(hgvs))

hgvs = "chrMT:m.8279_8280del"
self.assertFalse(is_snp(hgvs))

hgvs = "chrMT:m.15452_15453delinsAC"
self.assertFalse(is_snp(hgvs))

hgvs = "chrY:g.21878072_21878073insT"
self.assertFalse(is_snp(hgvs))

hgvs = "chrY:g.21724699_21724700delinsTTGTACAGAGA"
self.assertFalse(is_snp(hgvs))

def test_reverse_complement_seq(self):
pass
# TODO fix bug

def test_reverse_complement_hgvs(self):
pass
# TODO it uses the buggy `test_reverse_complement_seq`

# def test_normalized_vcf(self):
# # TODO rename `_normalized_vcf` to make it non-private
#
# input_vcf = ("X", 100, "CTTTT", "CT")
# output_vcf = ('X', 101, 'TTTT', 'T')
# self.assertEqual(output_vcf, normalized_vcf(*input_vcf))
#
# input_vcf = ("X", 100, "TC", "TG")
# output_vcf = ('X', 101, 'C', 'G')
# self.assertEqual(output_vcf, normalized_vcf(*input_vcf))
#
# input_vcf = ("X", 123, "T", "C")
# output_vcf = ('X', 123, 'T', 'C')
# self.assertEqual(output_vcf, normalized_vcf(*input_vcf))
#
# input_vcf = ("X", 123, "CC", "CCT")
# output_vcf = ('X', 124, 'C', 'CT')
# self.assertEqual(output_vcf, normalized_vcf(*input_vcf))
#
# # TODO failed
# # input_vcf = ("X", 123, "TCCCCT", "CCCCT")
# # output_vcf = ('X', 123, 'TC', 'C')
# # self.assertEqual(output_vcf, normalized_vcf(*input_vcf))
#
# input_vcf = ("X", 123, "TCCCCTA", "CCCCT")
# output_vcf = ('X', 123, 'TCCCCTA', 'CCCCT')
# self.assertEqual(output_vcf, normalized_vcf(*input_vcf))
#
# # TODO failed
# # input_vcf = ("X", 123, 'AAATCCCCTA', 'AAACCCCTA')
# # output_vcf = ('X', 125, 'AT', 'A')
# # self.assertEqual(output_vcf, normalized_vcf(*input_vcf))
#
# input_vcf = ("X", 123, 'CAAATCCCCTAG', 'AAACCCCTA')
# output_vcf = ('X', 123, 'CAAATCCCCTAG', 'AAACCCCTA')
# self.assertEqual(output_vcf, normalized_vcf(*input_vcf))

def test_get_hgvs_from_vcf(self):
input_vcf = ("X", 100, "A", "C")
output_hgvs, output_vartype = get_hgvs_from_vcf(*input_vcf, mutant_type=True)
expected_hgvs, expected_vartype = "chrX:g.100A>C", "snp"
self.assertEqual(expected_hgvs, output_hgvs)
self.assertEqual(expected_vartype, output_vartype)

input_vcf = ("X", 100, "CT", "C")
output_hgvs, output_vartype = get_hgvs_from_vcf(*input_vcf, mutant_type=True)
expected_hgvs, expected_vartype = "chrX:g.101del", "del"
self.assertEqual(expected_hgvs, output_hgvs)
self.assertEqual(expected_vartype, output_vartype)

input_vcf = ("X", 100, "CTTTT", "CT")
output_hgvs, output_vartype = get_hgvs_from_vcf(*input_vcf, mutant_type=True)
expected_hgvs, expected_vartype = "chrX:g.102_104del", "del"
self.assertEqual(expected_hgvs, output_hgvs)
self.assertEqual(expected_vartype, output_vartype)

input_vcf = ("X", 100, "CT", "A")
output_hgvs, output_vartype = get_hgvs_from_vcf(*input_vcf, mutant_type=True)
expected_hgvs, expected_vartype = "chrX:g.100_101delinsA", "delins"
self.assertEqual(expected_hgvs, output_hgvs)
self.assertEqual(expected_vartype, output_vartype)

input_vcf = ("X", 100, "A", "AT")
output_hgvs, output_vartype = get_hgvs_from_vcf(*input_vcf, mutant_type=True)
expected_hgvs, expected_vartype = "chrX:g.100_101insT", "ins"
self.assertEqual(expected_hgvs, output_hgvs)
self.assertEqual(expected_vartype, output_vartype)

input_vcf = ("X", 100, "A", "CT")
output_hgvs, output_vartype = get_hgvs_from_vcf(*input_vcf, mutant_type=True)
expected_hgvs, expected_vartype = "chrX:g.100delinsCT", "delins"
self.assertEqual(expected_hgvs, output_hgvs)
self.assertEqual(expected_vartype, output_vartype)

input_vcf = ("X", 100, "CT", "CTTTT")
output_hgvs, output_vartype = get_hgvs_from_vcf(*input_vcf, mutant_type=True)
expected_hgvs, expected_vartype = "chrX:g.101_102insTTT", "ins"
self.assertEqual(expected_hgvs, output_hgvs)
self.assertEqual(expected_vartype, output_vartype)

input_vcf = ("X", 100, "", "CTTTT")
self.assertRaises(ValueError, get_hgvs_from_vcf, *input_vcf, True)

input_vcf = ("X", 100, "GENE", "SEQ")
self.assertRaises(ValueError, get_hgvs_from_vcf, *input_vcf, True)

input_vcf = ("X", 100, "SEQ", "GENE")
self.assertRaises(ValueError, get_hgvs_from_vcf, *input_vcf, True)

def test_get_pos_start_end(self):
input_vcf = ("X", "one-hundred", "A", "C")
self.assertRaises(ValueError, get_pos_start_end, *input_vcf)

input_vcf = ("X", "100", "A", "")
self.assertRaises(ValueError, get_pos_start_end, *input_vcf)

input_vcf = ("X", "100", "", "C")
self.assertRaises(ValueError, get_pos_start_end, *input_vcf)

input_vcf = ("X", "100", "A", "C")
output_start, output_end = get_pos_start_end(*input_vcf)
expected_start, expected_end = 100, 100
self.assertEqual(expected_start, output_start)
self.assertEqual(expected_end, output_end)

input_vcf = ("X", "100", "CT", "C")
output_start, output_end = get_pos_start_end(*input_vcf)
expected_start, expected_end = 101, 102
self.assertEqual(expected_start, output_start)
self.assertEqual(expected_end, output_end)

# TODO https://github.com/biothings/myvariant.info/issues/111
# input_vcf = ("X", "100", "CT", "A")
# output_start, output_end = get_pos_start_end(*input_vcf)
# expected_start, expected_end = 100, 101
# self.assertEqual(expected_start, output_start)
# self.assertEqual(expected_end, output_end)

input_vcf = ("X", "100", "C", "CT")
output_start, output_end = get_pos_start_end(*input_vcf)
expected_start, expected_end = 100, 101
self.assertEqual(expected_start, output_start)
self.assertEqual(expected_end, output_end)

# TODO https://github.com/biothings/myvariant.info/issues/111
# input_vcf = ("X", "100", "A", "CT")
# output_start, output_end = get_pos_start_end(*input_vcf)
# expected_start, expected_end = 100, 100
# self.assertEqual(expected_start, output_start)
# self.assertEqual(expected_end, output_end)

input_vcf = ("X", "100", "AC", "GT")
self.assertRaises(ValueError, get_pos_start_end, *input_vcf)

def test_fix_hgvs_indel(self):
input_hgvs = "chr19:g.58863869C>-"
expected_hgvs = "chr19:g.58863869_58863869del"
self.assertEqual(expected_hgvs, fix_hgvs_indel(input_hgvs))

input_hgvs = "chr10:g.52596077->T"
expected_hgvs = "chr10:g.52596077insT"
self.assertEqual(expected_hgvs, fix_hgvs_indel(input_hgvs))

input_hgvs = "chr19:g.58863869A>C"
expected_hgvs = None
self.assertEqual(expected_hgvs, fix_hgvs_indel(input_hgvs))

def test_trim_delseq_from_hgvs(self):
input_hgvs = "chrX:g.100_101delinsA"
expected_prefix = "chrX:g.100_101delins"
self.assertEqual(expected_prefix, trim_delseq_from_hgvs(input_hgvs, True))

input_hgvs = "chrX:g.100_101insT"
expected_prefix = "chrX:g.100_101ins"
self.assertEqual(expected_prefix, trim_delseq_from_hgvs(input_hgvs, True))

input_hgvs = "chrX:g.102_104del"
expected_prefix = "chrX:g.102_104del"
self.assertEqual(expected_prefix, trim_delseq_from_hgvs(input_hgvs, True))

input_hgvs = "chrX:g.102_104dup"
expected_prefix = "chrX:g.102_104dup"
self.assertEqual(expected_prefix, trim_delseq_from_hgvs(input_hgvs, True))

input_hgvs = "chrX:g.102_104dup"
expected_prefix = "chrX:g.102_104dup"
self.assertEqual(expected_prefix, trim_delseq_from_hgvs(input_hgvs, True))


class TestDocEncoder(unittest.TestCase):
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