Python VariantFormat.CodonPos Examples

Example #1

File: table_formatter.py Project: redpixr/clc-vtable

    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

Example #2

File: tests.py Project: redpixr/clc-vtable

 def test_CodonPos_none(self):
     val = "A>C"
     self.assertEqual(VariantFormat.CodonPos(val), "")

Example #3

File: tests.py Project: redpixr/clc-vtable

 def test_CodonPos_one(self):
     val = "A286C"
     self.assertEqual(VariantFormat.CodonPos(val), "1")

Example #4

File: tests.py Project: redpixr/clc-vtable

 def test_CodonPos_two(self):
     val = "A287C"
     self.assertEqual(VariantFormat.CodonPos(val), "2")

Example #5

File: tests.py Project: redpixr/clc-vtable

 def test_CodonPos_three(self):
     val = "A288C"
     self.assertEqual(VariantFormat.CodonPos(val), "3")