Python _ExcludeMalformedRef Examples

Example #1

 def test_add_tag_value_validIndelRefEdgecaseNoFilter(self):
     record = vcf.VcfRecord("chr1",
                            "42",
                            "ACGTNacgtn",
                            "C",
                            vcf_filter="PASS")
     translate._ExcludeMalformedRef().add_tag_values(record)
     self.assertEquals("PASS", record.filter)

Example #2

File: translate_test.py Project: umich-brcf-bioinf/Jacquard

 def test_add_tag_value_invalidIndelReplacesFilter(self):
     record = vcf.VcfRecord("chr1", "42", "XYZ", "C", vcf_filter="PASS")
     translate._ExcludeMalformedRef().add_tag_values(record)
     self.assertEquals("JQ_EXCLUDE_MALFORMED_REF", record.filter)

Example #3

File: translate_test.py Project: umich-brcf-bioinf/Jacquard

 def test_add_tag_value_validIndelRefEdgecaseNoFilter(self):
     record = vcf.VcfRecord("chr1", "42", "ACGTNacgtn", "C", vcf_filter="PASS")
     translate._ExcludeMalformedRef().add_tag_values(record)
     self.assertEquals("PASS", record.filter)

Example #4

File: translate_test.py Project: umich-brcf-bioinf/Jacquard

 def test_metaheader(self):
     self.assertEquals('##FILTER=<ID=JQ_EXCLUDE_MALFORMED_REF,Description="The format of the reference value for this variant record does not comply with VCF standard.">',
                       translate._ExcludeMalformedRef().metaheader)

Example #5

 def test_add_tag_value_invalidIndelReplacesFilter(self):
     record = vcf.VcfRecord("chr1", "42", "XYZ", "C", vcf_filter="PASS")
     translate._ExcludeMalformedRef().add_tag_values(record)
     self.assertEquals("JQ_EXCLUDE_MALFORMED_REF", record.filter)

Example #6

 def test_metaheader(self):
     self.assertEquals(
         '##FILTER=<ID=JQ_EXCLUDE_MALFORMED_REF,Description="The format of the reference value for this variant record does not comply with VCF standard.">',
         translate._ExcludeMalformedRef().metaheader)