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_CodonPos_none(self):
val = "A>C"
self.assertEqual(VariantFormat.CodonPos(val), "")
def test_CodonPos_one(self):
val = "A286C"
self.assertEqual(VariantFormat.CodonPos(val), "1")
def test_CodonPos_two(self):
val = "A287C"
self.assertEqual(VariantFormat.CodonPos(val), "2")
def test_CodonPos_three(self):
val = "A288C"
self.assertEqual(VariantFormat.CodonPos(val), "3")