def test_wrap(self, fasta_filename): chr_names = ['chrM', 'chr1', 'chr2'] chr_lengths = [100, 76, 121] fasta = test_utils.genomics_core_testdata(fasta_filename) fai = test_utils.genomics_core_testdata(fasta_filename + '.fai') with reference_fai.GenomeReferenceFai.from_file(fasta, fai) as ref: self.assertEqual(ref.n_contigs, 3) self.assertIn(fasta, ref.fasta_path) self.assertIn('GenomeReference backed by htslib FAI index', str(ref)) self.assertEqual(ref.contig_names, chr_names) self.assertEqual(ref.n_bp, sum(chr_lengths)) self.assertEqual(ref.bases(ranges.make_range('chrM', 1, 10)), 'ATCACAGGT') self.assertTrue( ref.is_valid_interval(ranges.make_range('chrM', 1, 10))) self.assertFalse( ref.is_valid_interval(ranges.make_range('chrM', 1, 100000))) self.assertEqual(len(ref.contigs), 3) self.assertEqual([c.name for c in ref.contigs], chr_names) self.assertEqual([c.n_bases for c in ref.contigs], chr_lengths) for contig in ref.contigs: self.assertEqual(ref.contig(contig.name), contig) self.assertTrue(ref.has_contig(contig.name)) self.assertFalse(ref.has_contig(contig.name + '.unknown'))
def setUp(self): self.sites_reader = genomics_io.make_vcf_reader( test_utils.genomics_core_testdata('test_sites.vcf'), use_index=False) self.samples_reader = genomics_io.make_vcf_reader( test_utils.genomics_core_testdata('test_samples.vcf.gz'), use_index=True)
def test_from_file_raises_with_missing_inputs(self, fasta_filename, fai_filename): fasta = test_utils.genomics_core_testdata(fasta_filename) fai = test_utils.genomics_core_testdata(fai_filename) with self.assertRaisesRegexp( ValueError, 'Not found: could not load fasta and/or fai for fasta ' + fasta): reference_fai.GenomeReferenceFai.from_file(fasta, fai)
def setUp(self): self.unindexed_options = core_pb2.VcfReaderOptions() self.indexed_options = core_pb2.VcfReaderOptions( index_mode=core_pb2.INDEX_BASED_ON_FILENAME) self.sites_vcf = test_utils.genomics_core_testdata('test_sites.vcf') self.samples_vcf = test_utils.genomics_core_testdata('test_samples.vcf.gz') self.sites_reader = vcf_reader.VcfReader.from_file(self.sites_vcf, self.unindexed_options) self.samples_reader = vcf_reader.VcfReader.from_file( self.samples_vcf, self.indexed_options)
def test_round_trip_vcf(self, test_datum_name): # Round-trip variants through writing and reading: # 1. Read variants v1 from VcfReader; # 2. Write v1 to vcf using our VcfWriter; # 3. Read back in using VcfReader -- v2; # 4. compare v1 and v2. in_file = test_utils.genomics_core_testdata(test_datum_name) out_file = test_utils.test_tmpfile('output_' + test_datum_name) v1_reader = genomics_io.make_vcf_reader(in_file, use_index=False) v1_records = list(v1_reader.iterate()) self.assertTrue(v1_records, 'Reader failed to find records') writer_options = core_pb2.VcfWriterOptions( contigs=v1_reader.contigs, sample_names=v1_reader.samples, filters=v1_reader.filters) with vcf_writer.VcfWriter.to_file(out_file, writer_options) as writer: for record in v1_records: writer.write(record) v2_reader = genomics_io.make_vcf_reader(out_file, use_index=False) v2_records = list(v2_reader.iterate()) self.assertEqual(v1_records, v2_records, 'Round-tripped variants not as expected')
def test_sam_iterate_raises_on_malformed_record(self): malformed = test_utils.genomics_core_testdata('malformed.sam') reader = sam_reader.SamReader.from_file(malformed, self.options) iterable = iter(reader.iterate()) self.assertIsNotNone(next(iterable)) with self.assertRaises(ValueError): list(iterable)
def test_from_regions(self, regions, expected): # For convenience we allow 'test.bed' in our regions but the actual file # path is in our testdata directory. for i in range(len(regions)): if regions[i] == 'test.bed': regions[i] = test_utils.genomics_core_testdata('test.bed') self.assertEqual(list(ranges.from_regions(regions)), expected)
def test_from_bed(self): source = test_utils.genomics_core_testdata('test.bed') self.assertCountEqual([ ranges.make_range('chr1', 1, 10), ranges.make_range('chr2', 20, 30), ranges.make_range('chr2', 40, 60), ranges.make_range('chr3', 80, 90), ], ranges.RangeSet.from_bed(source))
def test_sam_query(self): reader = genomics_io.make_sam_reader( test_utils.genomics_core_testdata('test.bam')) expected = [(ranges.parse_literal('chr20:10,000,000-10,000,100'), 106), (ranges.parse_literal('chr20:10,000,000-10,000,000'), 45)] with reader: for interval, n_expected in expected: with reader.query(interval) as iterable: self.assertEqual(test_utils.iterable_len(iterable), n_expected)
def test_bam_iterate_partially(self): """Verify that iteration provides results incrementally, not all at once.""" reader = genomics_io.make_sam_reader( test_utils.genomics_core_testdata('test.bam'), use_index=False) with reader: iterable = reader.iterate() # We expect 106 records in total. for _ in xrange(10): results = list(itertools.islice(iterable, 10)) self.assertEqual(len(results), 10) results = list(itertools.islice(iterable, 10)) self.assertEqual(len(results), 6)
def test_downsampling(self, method, maybe_range, fraction, expected_n_reads): reader = genomics_io.make_sam_reader( test_utils.genomics_core_testdata('test.bam'), downsample_fraction=fraction, random_seed=12345) with reader: if method == 'iterate': reads_iter = reader.iterate() elif method == 'query': reads_iter = reader.query(ranges.parse_literal(maybe_range)) else: self.fail('Unexpected method', method) self.assertEqual(test_utils.iterable_len(reads_iter), expected_n_reads)
def setUp(self): self.bam = test_utils.genomics_core_testdata('test.bam') self.options = core_pb2.SamReaderOptions() self.indexed_options = core_pb2.SamReaderOptions( index_mode=core_pb2.INDEX_BASED_ON_FILENAME)
def test_writing_canned_variants(self): """Tests writing all the variants that are 'canned' in our tfrecord file.""" # This file is in the TF record format tfrecord_file = test_utils.genomics_core_testdata( 'test_samples.vcf.golden.tfrecord') writer_options = core_pb2.VcfWriterOptions( contigs=[ core_pb2.ContigInfo(name='chr1', n_bases=248956422), core_pb2.ContigInfo(name='chr2', n_bases=242193529), core_pb2.ContigInfo(name='chr3', n_bases=198295559), core_pb2.ContigInfo(name='chrX', n_bases=156040895) ], sample_names=['NA12878_18_99'], filters=[ core_pb2.VcfFilterInfo(id='LowQual'), core_pb2.VcfFilterInfo(id='VQSRTrancheINDEL95.00to96.00'), core_pb2.VcfFilterInfo(id='VQSRTrancheINDEL96.00to97.00'), core_pb2.VcfFilterInfo(id='VQSRTrancheINDEL97.00to99.00'), core_pb2.VcfFilterInfo(id='VQSRTrancheINDEL99.00to99.50'), core_pb2.VcfFilterInfo(id='VQSRTrancheINDEL99.50to99.90'), core_pb2.VcfFilterInfo(id='VQSRTrancheINDEL99.90to99.95'), core_pb2.VcfFilterInfo(id='VQSRTrancheINDEL99.95to100.00+'), core_pb2.VcfFilterInfo(id='VQSRTrancheINDEL99.95to100.00'), core_pb2.VcfFilterInfo(id='VQSRTrancheSNP99.50to99.60'), core_pb2.VcfFilterInfo(id='VQSRTrancheSNP99.60to99.80'), core_pb2.VcfFilterInfo(id='VQSRTrancheSNP99.80to99.90'), core_pb2.VcfFilterInfo(id='VQSRTrancheSNP99.90to99.95'), core_pb2.VcfFilterInfo(id='VQSRTrancheSNP99.95to100.00+'), core_pb2.VcfFilterInfo(id='VQSRTrancheSNP99.95to100.00'), ]) variant_records = list( io_utils.read_tfrecords(tfrecord_file, proto=variants_pb2.Variant)) out_fname = test_utils.test_tmpfile('output.vcf') with vcf_writer.VcfWriter.to_file(out_fname, writer_options) as writer: for record in variant_records[:5]: writer.write(record) # Check: are the variants written as expected? # pylint: disable=line-too-long expected_vcf_content = [ '##fileformat=VCFv4.2\n', '##FILTER=<ID=PASS,Description="All filters passed">\n', '##FILTER=<ID=LowQual,Description="">\n', '##FILTER=<ID=VQSRTrancheINDEL95.00to96.00,Description="">\n', '##FILTER=<ID=VQSRTrancheINDEL96.00to97.00,Description="">\n', '##FILTER=<ID=VQSRTrancheINDEL97.00to99.00,Description="">\n', '##FILTER=<ID=VQSRTrancheINDEL99.00to99.50,Description="">\n', '##FILTER=<ID=VQSRTrancheINDEL99.50to99.90,Description="">\n', '##FILTER=<ID=VQSRTrancheINDEL99.90to99.95,Description="">\n', '##FILTER=<ID=VQSRTrancheINDEL99.95to100.00+,Description="">\n', '##FILTER=<ID=VQSRTrancheINDEL99.95to100.00,Description="">\n', '##FILTER=<ID=VQSRTrancheSNP99.50to99.60,Description="">\n', '##FILTER=<ID=VQSRTrancheSNP99.60to99.80,Description="">\n', '##FILTER=<ID=VQSRTrancheSNP99.80to99.90,Description="">\n', '##FILTER=<ID=VQSRTrancheSNP99.90to99.95,Description="">\n', '##FILTER=<ID=VQSRTrancheSNP99.95to100.00+,Description="">\n', '##FILTER=<ID=VQSRTrancheSNP99.95to100.00,Description="">\n', '##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n', '##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n', '##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth of all ' 'passing filters reads.">\n', '##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth of all ' 'passing filters reads for each allele.">\n', '##FORMAT=<ID=VAF,Number=A,Type=Float,Description=\"Variant allele ' 'fractions.">\n', '##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype ' 'likelihoods, log10 encoded">\n', '##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Genotype ' 'likelihoods, Phred encoded">\n', '##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of ' 'the interval">\n', '##contig=<ID=chr1,length=248956422>\n', '##contig=<ID=chr2,length=242193529>\n', '##contig=<ID=chr3,length=198295559>\n', '##contig=<ID=chrX,length=156040895>\n', '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA12878_18_99\n', 'chr1\t13613\t.\tT\tA\t39.88\tVQSRTrancheSNP99.90to99.95\t.\tGT:GQ:DP:AD:PL\t0/1:16:4:1,3:68,0,16\n', 'chr1\t13813\t.\tT\tG\t90.28\tPASS\t.\tGT:GQ:DP:AD:PL\t1/1:9:3:0,3:118,9,0\n', 'chr1\t13838\trs28428499\tC\tT\t62.74\tPASS\t.\tGT:GQ:DP:AD:PL\t1/1:6:2:0,2:90,6,0\n', 'chr1\t14397\trs756427959\tCTGT\tC\t37.73\tPASS\t.\tGT:GQ:DP:AD:PL\t0/1:75:5:3,2:75,0,152\n', 'chr1\t14522\t.\tG\tA\t49.77\tVQSRTrancheSNP99.60to99.80\t.\tGT:GQ:DP:AD:PL\t0/1:78:10:6,4:78,0,118\n' ] # pylint: enable=line-too-long with tf.gfile.GFile(out_fname, 'r') as f: self.assertEqual(f.readlines(), expected_vcf_content)
def test_make_ref_reader(self, fasta_filename): fasta_path = test_utils.genomics_core_testdata(fasta_filename) with genomics_io.make_ref_reader(fasta_path) as reader: self.assertEqual(reader.bases(ranges.make_range('chrM', 1, 6)), 'ATCAC')
def test_from_file_raises_with_missing_index(self): with self.assertRaisesRegexp(ValueError, 'Not found: No index found for'): vcf_reader.VcfReader.from_file( test_utils.genomics_core_testdata('test_sites.vcf'), self.indexed_options)
def test_bam_iterate(self): reader = genomics_io.make_sam_reader( test_utils.genomics_core_testdata('test.bam'), use_index=False) with reader: self.assertEqual(test_utils.iterable_len(reader.iterate()), 106)
def test_from_file_raises_with_missing_index(self): with self.assertRaisesRegexp(ValueError, 'Not found: No index found for'): sam_reader.SamReader.from_file( test_utils.genomics_core_testdata('unindexed.bam'), self.indexed_options)