def test_extract_sample_name_from_reads_single_sample(self): mock_sample_reader = mock.Mock() mock_sample_reader.header = reads_pb2.SamHeader( read_groups=[reads_pb2.ReadGroup(sample_id='sample_name')]) self.assertEqual( make_examples_core.extract_sample_name_from_sam_reader( mock_sample_reader), 'sample_name')
def test_extract_sample_name_from_reads_uses_default_when_necessary( self, samples, expected_sample_name): mock_sample_reader = mock.Mock() mock_sample_reader.header = reads_pb2.SamHeader(read_groups=[ reads_pb2.ReadGroup(sample_id=sample) for sample in samples ]) self.assertEqual( expected_sample_name, make_examples_core.extract_sample_name_from_sam_reader( mock_sample_reader))
def setUp(self): self.read1 = test_utils.make_read(bases='ACCGT', chrom='chr1', start=10, cigar='5M', mapq=50, quals=range(30, 35), name='read1') self.read2 = test_utils.make_read(bases='AACCTT', chrom='chr2', start=15, cigar='7M', mapq=40, quals=range(20, 26), name='read2') self.contigs = [ reference_pb2.ContigInfo(name='chr1'), reference_pb2.ContigInfo(name='chr2'), ] self.header = reads_pb2.SamHeader()