Python VcfRecord.add_or_replace_filter Examples

Example #1

 def test_add_or_replace_filter_filtersOnlyAppendsUnique(self):
     record = VcfRecord("chr1", "42", "XYZ", "C", vcf_filter="indelError")
     record.add_or_replace_filter("JQ_EXCLUDE")
     record.add_or_replace_filter("JQ_EXCLUDE")
     self.assertEquals("indelError;JQ_EXCLUDE", record.filter)

Example #2

 def test_add_or_replace_filter_duplicateFilterNotAdded(self):
     record = VcfRecord("chr1", "42", "XYZ", "C", vcf_filter="JQ_EXCLUDE")
     record.add_or_replace_filter("JQ_EXCLUDE")
     self.assertEquals("JQ_EXCLUDE", record.filter)

Example #3

 def test_add_or_replace_filter_filterReplacesEmptyFilter(self):
     record = VcfRecord("chr1", "42", "X", "C", vcf_filter="")
     record.add_or_replace_filter("JQ_EXCLUDE")
     self.assertEquals("JQ_EXCLUDE", record.filter)

Example #4

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

 def test_add_or_replace_filter_filtersOnlyAppendsUnique(self):
     record = VcfRecord("chr1", "42", "XYZ", "C", vcf_filter="indelError")
     record.add_or_replace_filter("JQ_EXCLUDE")
     record.add_or_replace_filter("JQ_EXCLUDE")
     self.assertEquals("indelError;JQ_EXCLUDE", record.filter)

Example #5

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

 def test_add_or_replace_filter_duplicateFilterNotAdded(self):
     record = VcfRecord("chr1", "42", "XYZ", "C", vcf_filter="JQ_EXCLUDE")
     record.add_or_replace_filter("JQ_EXCLUDE")
     self.assertEquals("JQ_EXCLUDE", record.filter)

Example #6

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

 def test_add_or_replace_filter_filterReplacesEmptyFilter(self):
     record = VcfRecord("chr1", "42", "X", "C", vcf_filter="")
     record.add_or_replace_filter("JQ_EXCLUDE")
     self.assertEquals("JQ_EXCLUDE", record.filter)