def test_AminoAcidChange_exception(self):
aac = "YP_512823.1:p.Ser35Tyr.[Ser35Tyr]"
try:
VariantFormat.AminoAcidChange(aac)
except ValidationException as aac_error:
self.assertEqual(aac_error.errors,
"_error: YP_512823.1:p.Ser35Tyr.[Ser35Tyr]")
def test_FormatVariant_snv(self):
file_info = "sample_data.xlsx row 25"
variant_type = "SNV"
reference = 'G'
allele = 'A'
crc = "YP_512841.1:c.150G>A"
self.assertEqual(
VariantFormat.FormatVariant(file_info, variant_type, reference,
allele, crc), "G150A")
def test_FormatVariant_snv_nocrc(self):
file_info = "sample_data.xlsx row 25"
variant_type = "SNV"
reference = 'G'
allele = 'A'
crc = ''
self.assertEqual(
VariantFormat.FormatVariant(file_info, variant_type, reference,
allele, crc), "G>A")
def test_FormatVariant_insertion(self):
file_info = "sample_data.xlsx row 25"
variant_type = "Insertion"
reference = '-'
allele = 'C'
crc = "YP_512901.1:c.292_293insG"
self.assertEqual(
VariantFormat.FormatVariant(file_info, variant_type, reference,
allele, crc), "Cins293")
def test_FormatVariant_deletion(self):
file_info = "sample_data.xlsx row 25"
variant_type = "Deletion"
reference = 'A'
allele = '-'
crc = "YP_513007.1:c.907delA"
self.assertEqual(
VariantFormat.FormatVariant(file_info, variant_type, reference,
allele, crc), "Adel907")
def test_FormatVariant_unknown(self):
file_info = "-"
variant_type = "unknown"
reference = '-'
allele = '-'
crc = "-"
self.assertEqual(
VariantFormat.FormatVariant(file_info, variant_type, reference,
allele, crc), "")
def test_FormatVariant_deletion_contains_illegal(self):
file_info = "sample_data.xlsx row 25"
variant_type = "Deletion"
reference = 'A'
allele = '-'
crc = "YP_513095.1:c.[1delA];YP_513094.1:c.[590_591delAA]"
self.assertEqual(
VariantFormat.FormatVariant(file_info, variant_type, reference,
allele, crc),
"Adel_error: YP_513095.1:c.[1delA];YP_513094.1:c.[590_591delAA]")
def format(table_variant):
formatted = OrderedDict()
formatted[cfg.F_LOCATION] = table_variant[cfg.V_REFPOS]
formatted[cfg.F_VARIANT] = VariantFormat.FormatVariant(
table_variant.file_info, table_variant[cfg.V_TYPE],
table_variant[cfg.V_REF], table_variant[cfg.V_ALLELE],
table_variant[cfg.V_CRC])
formatted[cfg.F_CODONPOS] = VariantFormat.CodonPos(
formatted[cfg.F_VARIANT])
formatted[cfg.F_AAC] = "" # TODO: first change the AminoAcidChange()
formatted[cfg.F_OA] = table_variant[cfg.V_ANOT]
formatted[cfg.F_FREQ] = table_variant[cfg.V_FREQ]
return formatted
def test_AminoAcidChange_contains(self):
aac = "YP_512823.1:p.Ser35Tyr"
self.assertEqual(VariantFormat.AminoAcidChange(aac), "Ser35Tyr")
def test_GetIntFromString(self):
val = "Abgdfsb dasdasdw adsad dasd78dasdsd"
self.assertEqual(VariantFormat.GetIntFromString(val), "78")
def test_ContainsIllegal_contains(self):
crc = "YP_513095.1:c.[1delA];YP_513094.1:c.[590_591delAA]"
self.assertEqual(VariantFormat.ContainsIllegal(crc, ['[', ';']), True)
def test_CodonPos_three(self):
val = "A288C"
self.assertEqual(VariantFormat.CodonPos(val), "3")
def test_GetIntFromString_doesntcontain(self):
val = "dasdasdadsdsdad dasdasdas das dsada"
self.assertEqual(VariantFormat.GetIntFromString(val), "")
def test_CodonPos_two(self):
val = "A287C"
self.assertEqual(VariantFormat.CodonPos(val), "2")
def test_CodonPos_one(self):
val = "A286C"
self.assertEqual(VariantFormat.CodonPos(val), "1")
def test_AminoAcidChange_doesnt_contain(self):
aac = ""
self.assertEqual(VariantFormat.AminoAcidChange(aac), "")
def test_ContainsIllegal(self):
crc = "YP_513007.1:c.907delA"
self.assertEqual(VariantFormat.ContainsIllegal(crc, ['[', ';']), False)
def test_CodonPos_none(self):
val = "A>C"
self.assertEqual(VariantFormat.CodonPos(val), "")