def test_to_vcf_row_from_file(self):
def _split_multiallelic(rows):
for row in rows:
for alt in row.ALT.split(','):
kwds = {f:getattr(row,f) for f in VCF_FIELDS}
kwds['ALT'] = alt
kwds['INFO'] = '.'
kwds['FORMAT'] = None
kwds['SAMPLES'] = None
yield str(VCFRow(**kwds))
reader = VCFReader(pkg_file('genomvar.test','data/example1.vcf'))
variants = list(reader.iter_vrt(
parse_info=False,parse_samples=False))
rows = [str(self.writer.get_row(v)) for v in variants]
for r1, r2 in zip(
_split_multiallelic(reader.iter_rows()), rows):
if 'AG\tAGG' in r1: # stripping
continue
self.assertEqual(r1,r2)
reader.close()
def test_change_of_attributes(self):
reader = VCFReader(
pkg_file('genomvar.test','data/example1.vcf'))
vrt = list(reader.iter_vrt())[0]
self.assertEqual(str(self.writer.get_row(vrt)),
'chr24\t23\t1\tAG\tA\t100\tPASS\t.')
vrt2 = copy.deepcopy(vrt)
vrt2.attrib['id'] = '.'
vrt2.attrib['qual'] = '.'
vrt2.attrib['filter'] = '.'
self.assertEqual(str(self.writer.get_row(vrt2)),
'chr24\t23\t.\tAG\tA\t.\t.\t.')
self.assertEqual(str(self.writer.get_row(vrt2, id='.', qual='.', filter='.')),
'chr24\t23\t.\tAG\tA\t.\t.\t.')
vrt3 = copy.deepcopy(vrt)
vrt3.attrib['id'] = None
vrt3.attrib['qual'] = None
vrt3.attrib['filter'] = None
self.assertEqual(str(self.writer.get_row(vrt3)),
'chr24\t23\t.\tAG\tA\t.\t.\t.')
reader.close()
reader.close()