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())