def test_raises_for_unlabeled_examples(self):
FLAGS.ref = testdata.CHR20_FASTA
FLAGS.examples = testdata.GOLDEN_CALLING_EXAMPLES
FLAGS.output_vcf = test_utils.test_tmpfile('unlabeled.vcf')
with self.assertRaisesRegexp(
ValueError,
('Variant .* does not have any genotypes. This tool only works with '
'variants that have been labeled')):
labeled_examples_to_vcf.main(0)
def test_sample_name_flag(self):
FLAGS.ref = testdata.CHR20_FASTA
FLAGS.examples = testdata.GOLDEN_TRAINING_EXAMPLES
FLAGS.sample_name = 'sample_name'
FLAGS.output_vcf = test_utils.test_tmpfile('no_sample_name.vcf')
labeled_examples_to_vcf.main(0)
with vcf.VcfReader(FLAGS.output_vcf) as vcf_reader:
self.assertEqual(list(vcf_reader.header.sample_names),
[FLAGS.sample_name])
def test_end2end(self):
FLAGS.ref = testdata.CHR20_FASTA
FLAGS.examples = testdata.GOLDEN_TRAINING_EXAMPLES + '@3' # Sharded.
FLAGS.output_vcf = test_utils.test_tmpfile('examples_to_vcf.vcf')
labeled_examples_to_vcf.main(0)
self.assertEqual(
open(FLAGS.output_vcf).readlines(),
open(testdata.deepvariant_testdata(
'golden.training_examples.vcf')).readlines())