Python reserved_info_field Examples

Example #1

def main(argv):
    if len(argv) != 3:
        print('Usage: %s <input_vcf> <output_vcf>' % argv[0])
        sys.exit(-1)
    in_vcf = argv[1]
    out_vcf = argv[2]

    with vcf.VcfReader(in_vcf) as reader:
        if 'AD' in [info.id for info in reader.header.infos]:
            print('%s already contains AD field.' % in_vcf)
            sys.exit(-1)
        out_header = reader.header
        out_header.infos.extend([vcf_constants.reserved_info_field('AD')])

        with vcf.VcfWriter(out_vcf, header=out_header) as writer:
            for variant in reader:
                variant_utils.set_info(variant, 'AD', get_variant_ad(variant),
                                       writer)
                writer.write(variant)

Example #2

File: vcf_constants_test.py Project: zpeng1989/nucleus

 def test_invalid_get_reserved_info(self, field_id):
     with self.assertRaisesRegexp(ValueError, 'No reserved field with id'):
         vcf_constants.reserved_info_field(field_id)

Example #3

File: vcf_constants_test.py Project: zpeng1989/nucleus

 def test_get_reserved_info(self, field_id):
     info = vcf_constants.reserved_info_field(field_id)
     self.assertIsInstance(info, variants_pb2.VcfInfo)
     self.assertEqual(info.id, field_id)