def test_alt_combinations_no_het_alt(self, ref, alts, expected): options = pileup_image.default_options() options.multi_allelic_mode = ( deepvariant_pb2.PileupImageOptions.NO_HET_ALT_IMAGES) pic = pileup_image.PileupImageCreator(options, self.mock_ref_reader, self.mock_sam_reader) variant = variants_pb2.Variant(reference_bases=ref, alternate_bases=alts) self.assertEqual(expected, list(pic._alt_allele_combinations(variant)))
def setUp(self): self.options = pileup_image.default_options() self.options.width = 5 self.mock_ref_reader = mock.MagicMock(spec=fasta.RefFastaReader) self.mock_ref_reader.query.return_value = 'ACGT' self.mock_ref_reader.is_valid.return_value = True self.mock_sam_reader = mock.MagicMock() self.mock_sam_reader.query.return_value = ['read1', 'read2'] self.dv_call = _make_dv_call() self.variant = self.dv_call.variant self.pic = self._make_pic()
def setUp(self): self.options = pileup_image.default_options() self.options.width = 5 self.mock_ref_reader = mock.MagicMock( spec=reference_fai.GenomeReferenceFai) self.mock_ref_reader.bases.return_value = 'ACGT' self.mock_ref_reader.is_valid_interval.return_value = True self.mock_sam_reader = mock.MagicMock() self.mock_sam_reader.query.return_value = ['read1', 'read2'] self.dv_call = _make_dv_call() self.variant = self.dv_call.variant self.pic = self._make_pic()
def shared_flags_to_options( add_flags, flags_obj, samples_in_order, sample_role_to_train, main_sample_index) -> deepvariant_pb2.MakeExamplesOptions: """Creates options from flags that are shared, along with given samples.""" read_reqs = reads_pb2.ReadRequirements( keep_duplicates=flags_obj.keep_duplicates, keep_supplementary_alignments=flags_obj.keep_supplementary_alignments, keep_secondary_alignments=flags_obj.keep_secondary_alignments, min_base_quality=flags_obj.min_base_quality, min_mapping_quality=flags_obj.min_mapping_quality, min_base_quality_mode=reads_pb2.ReadRequirements.ENFORCED_BY_CLIENT) logging.vlog(3, 'ReadRequirements are: %s', read_reqs) pic_options = pileup_image.default_options(read_requirements=read_reqs) allele_counter_options = deepvariant_pb2.AlleleCounterOptions( partition_size=flags_obj.partition_size, read_requirements=read_reqs, track_ref_reads=flags_obj.track_ref_reads, normalize_reads=flags_obj.normalize_reads, keep_legacy_behavior=flags_obj.keep_legacy_allele_counter_behavior) options = deepvariant_pb2.MakeExamplesOptions( exclude_contigs=exclude_contigs.EXCLUDED_HUMAN_CONTIGS, # Fixed random seed produced with 'od -vAn -N4 -tu4 < /dev/urandom'. random_seed=609314161, # # Not specified by default: calling_regions = 3; read_requirements=read_reqs, allele_counter_options=allele_counter_options, pic_options=pic_options, n_cores=1, task_id=0, num_shards=0, min_shared_contigs_basepairs=0.9, sample_options=samples_in_order, main_sample_index=main_sample_index, sample_role_to_train=sample_role_to_train) if add_flags: options.mode = make_examples_core.parse_proto_enum_flag( deepvariant_pb2.MakeExamplesOptions.Mode, flags_obj.mode.upper()) options.labeler_algorithm = make_examples_core.parse_proto_enum_flag( deepvariant_pb2.MakeExamplesOptions.LabelerAlgorithm, flags_obj.labeler_algorithm.upper()) options.variant_caller = make_examples_core.parse_proto_enum_flag( deepvariant_pb2.MakeExamplesOptions.VariantCaller, flags_obj.variant_caller.upper()) if flags_obj.ref: options.reference_filename = flags_obj.ref if flags_obj.confident_regions: options.confident_regions_filename = flags_obj.confident_regions if flags_obj.truth_variants: options.truth_variants_filename = flags_obj.truth_variants if flags_obj.sequencing_type: options.pic_options.sequencing_type = make_examples_core.parse_proto_enum_flag( deepvariant_pb2.PileupImageOptions.SequencingType, flags_obj.sequencing_type) if flags_obj.channels: channel_set = flags_obj.channels.split(',') for channel in channel_set: if channel and channel not in dv_constants.OPT_CHANNELS: err_msg = 'Channel "{}" is not one of the available opt channels: {}'.format( channel, ', '.join(dv_constants.OPT_CHANNELS)) errors.log_and_raise(err_msg, errors.CommandLineError) options.pic_options.channels[:] = channel_set options.pic_options.num_channels += len(channel_set) if flags_obj.multi_allelic_mode: multi_allelic_enum = { 'include_het_alt_images': deepvariant_pb2.PileupImageOptions.ADD_HET_ALT_IMAGES, 'exclude_het_alt_images': deepvariant_pb2.PileupImageOptions.NO_HET_ALT_IMAGES, }[flags_obj.multi_allelic_mode] options.pic_options.multi_allelic_mode = multi_allelic_enum if flags_obj.pileup_image_width: options.pic_options.width = flags_obj.pileup_image_width options.pic_options.alt_aligned_pileup = flags_obj.alt_aligned_pileup options.pic_options.types_to_alt_align = flags_obj.types_to_alt_align if flags_obj.add_supporting_other_alt_color: options.pic_options.other_allele_supporting_read_alpha = 0.3 if flags_obj.select_variant_types: options.select_variant_types[:] = flags_obj.select_variant_types.split( ) for svt in options.select_variant_types: if svt not in make_examples_core.VARIANT_TYPE_SELECTORS: errors.log_and_raise( 'Select variant type {} not recognized. Allowed values are {}' .format( svt, ', '.join( make_examples_core.VARIANT_TYPE_SELECTORS)), errors.CommandLineError) num_shards, examples, candidates, gvcf, runtime_by_region = ( sharded_file_utils.resolve_filespecs( flags_obj.task, flags_obj.examples or '', flags_obj.candidates or '', flags_obj.gvcf or '', flags_obj.runtime_by_region or '')) options.examples_filename = examples options.candidates_filename = candidates options.gvcf_filename = gvcf options.include_med_dp = flags_obj.include_med_dp options.task_id = flags_obj.task options.num_shards = num_shards options.runtime_by_region = runtime_by_region options.parse_sam_aux_fields = make_examples_core.resolve_sam_aux_fields( flags_obj=flags_obj) if flags_obj.aux_fields_to_keep: options.aux_fields_to_keep[:] = flags_obj.aux_fields_to_keep.split( ',') else: options.aux_fields_to_keep = None options.use_original_quality_scores = flags_obj.use_original_quality_scores if flags_obj.add_hp_channel: options.pic_options.num_channels += 1 options.pic_options.add_hp_channel = True if flags_obj.hp_tag_for_assembly_polishing < 0: errors.log_and_raise( '--hp_tag_for_assembly_polishing has to be set to a positive int.', errors.CommandLineError) if (flags_obj.hp_tag_for_assembly_polishing > 0 and not flags_obj.sort_by_haplotypes): errors.log_and_raise( '--hp_tag_for_assembly_polishing requires --sort_by_haplotypes to be ' 'set ', errors.CommandLineError) options.pic_options.sort_by_haplotypes = flags_obj.sort_by_haplotypes options.pic_options.hp_tag_for_assembly_polishing = flags_obj.hp_tag_for_assembly_polishing if flags_obj.write_run_info: options.run_info_filename = examples + _RUN_INFO_FILE_EXTENSION options.calling_regions.extend( make_examples_core.parse_regions_flag(flags_obj.regions)) options.exclude_calling_regions.extend( make_examples_core.parse_regions_flag(flags_obj.exclude_regions)) options.realigner_enabled = flags_obj.realign_reads options.realigner_options.CopyFrom( realigner.realigner_config(flags_obj)) if (options.mode == deepvariant_pb2.MakeExamplesOptions.TRAINING and flags_obj.training_random_emit_ref_sites != NO_RANDOM_REF): options.sample_options[ main_sample_index].variant_caller_options.fraction_reference_sites_to_emit = ( flags_obj.training_random_emit_ref_sites) if (flags_obj.use_allele_frequency and not flags_obj.population_vcfs): errors.log_and_raise( 'If use_allele_frequency is set then population_vcfs ' 'must be provided.', errors.CommandLineError) if flags_obj.use_allele_frequency: options.use_allele_frequency = flags_obj.use_allele_frequency options.pic_options.num_channels += 1 options.pic_options.use_allele_frequency = True if flags_obj.population_vcfs: options.population_vcf_filenames.extend( re.split(',| ', flags_obj.population_vcfs)) options.max_reads_per_partition = flags_obj.max_reads_per_partition options.use_ref_for_cram = flags_obj.use_ref_for_cram options.hts_block_size = flags_obj.hts_block_size options.logging_every_n_candidates = flags_obj.logging_every_n_candidates options.customized_classes_labeler_classes_list = flags_obj.customized_classes_labeler_classes_list options.customized_classes_labeler_info_field_name = flags_obj.customized_classes_labeler_info_field_name return options
def default_options(add_flags=True, flags_obj=None): """Creates a DeepVariantOptions proto populated with reasonable defaults. Args: add_flags: bool. defaults to True. If True, we will push the value of certain FLAGS into our options. If False, those option fields are left uninitialized. flags_obj: object. If not None, use as the source of flags, else use global FLAGS. Returns: deepvariant_pb2.DeepVariantOptions protobuf. Raises: ValueError: If we observe invalid flag values. """ if not flags_obj: flags_obj = FLAGS read_reqs = reads_pb2.ReadRequirements( min_base_quality=10, min_mapping_quality=10, min_base_quality_mode=reads_pb2.ReadRequirements.ENFORCED_BY_CLIENT) pic_options = pileup_image.default_options(read_requirements=read_reqs) allele_counter_options = deepvariant_pb2.AlleleCounterOptions( partition_size=flags_obj.partition_size, read_requirements=read_reqs) if flags_obj.sample_name: sample_name = flags_obj.sample_name elif flags_obj.reads: with sam.SamReader(flags_obj.reads) as sam_reader: sample_name = extract_sample_name_from_sam_reader(sam_reader) else: sample_name = _UNKNOWN_SAMPLE variant_caller_options = deepvariant_pb2.VariantCallerOptions( min_count_snps=flags_obj.vsc_min_count_snps, min_count_indels=flags_obj.vsc_min_count_indels, min_fraction_snps=flags_obj.vsc_min_fraction_snps, min_fraction_indels=flags_obj.vsc_min_fraction_indels, # Not specified by default: fraction_reference_sites_to_emit, # Fixed random seed produced with 'od -vAn -N4 -tu4 < /dev/urandom'. random_seed=1400605801, sample_name=sample_name, p_error=0.001, max_gq=50, gq_resolution=flags_obj.gvcf_gq_binsize, ploidy=2) options = deepvariant_pb2.DeepVariantOptions( exclude_contigs=exclude_contigs.EXCLUDED_HUMAN_CONTIGS, # Fixed random seed produced with 'od -vAn -N4 -tu4 < /dev/urandom'. random_seed=609314161, # # Not specified by default: calling_regions = 3; read_requirements=read_reqs, allele_counter_options=allele_counter_options, variant_caller_options=variant_caller_options, pic_options=pic_options, n_cores=1, task_id=0, num_shards=0, min_shared_contigs_basepairs=0.9, ) if add_flags: options.mode = parse_proto_enum_flag( deepvariant_pb2.DeepVariantOptions.Mode, flags_obj.mode.upper()) options.labeler_algorithm = parse_proto_enum_flag( deepvariant_pb2.DeepVariantOptions.LabelerAlgorithm, flags_obj.labeler_algorithm.upper()) if flags_obj.ref: options.reference_filename = flags_obj.ref if flags_obj.reads: options.reads_filename = flags_obj.reads if flags_obj.confident_regions: options.confident_regions_filename = flags_obj.confident_regions if flags_obj.truth_variants: options.truth_variants_filename = flags_obj.truth_variants if flags_obj.downsample_fraction != NO_DOWNSAMPLING: options.downsample_fraction = flags_obj.downsample_fraction if flags_obj.multi_allelic_mode: multi_allelic_enum = { 'include_het_alt_images': deepvariant_pb2.PileupImageOptions.ADD_HET_ALT_IMAGES, 'exclude_het_alt_images': deepvariant_pb2.PileupImageOptions.NO_HET_ALT_IMAGES, }[flags_obj.multi_allelic_mode] options.pic_options.multi_allelic_mode = multi_allelic_enum if flags_obj.pileup_image_height: options.pic_options.height = flags_obj.pileup_image_height if flags_obj.pileup_image_width: options.pic_options.width = flags_obj.pileup_image_width num_shards, examples, candidates, gvcf = io_utils.resolve_filespecs( flags_obj.task, flags_obj.examples or '', flags_obj.candidates or '', flags_obj.gvcf or '') options.examples_filename = examples options.candidates_filename = candidates options.gvcf_filename = gvcf options.calling_regions.extend(parse_regions_flag(flags_obj.regions)) options.exclude_calling_regions.extend( parse_regions_flag(flags_obj.exclude_regions)) options.task_id = flags_obj.task options.num_shards = 0 if num_shards is None else num_shards options.realigner_enabled = flags_obj.realign_reads if options.realigner_enabled: options.realigner_options.CopyFrom(realigner.realigner_config(flags_obj)) options.max_reads_per_partition = flags_obj.max_reads_per_partition if (options.mode == deepvariant_pb2.DeepVariantOptions.TRAINING and flags_obj.training_random_emit_ref_sites != NO_RANDOM_REF): options.variant_caller_options.fraction_reference_sites_to_emit = ( flags_obj.training_random_emit_ref_sites) return options
def _make_image_creator(ref_reader, sam_reader_obj, **kwargs): options = pileup_image.default_options() options.MergeFrom(deepvariant_pb2.PileupImageOptions(**kwargs)) return pileup_image.PileupImageCreator(options, ref_reader, sam_reader_obj)
def _make_encoder(**kwargs): """Make a PileupImageEncoderNative with overrideable default options.""" options = pileup_image.default_options() options.MergeFrom(deepvariant_pb2.PileupImageOptions(**kwargs)) return pileup_image_native.PileupImageEncoderNative(options)
def default_options(add_flags=True, flags=None): """Creates a DeepVariantOptions proto populated with reasonable defaults. Args: add_flags: bool. defaults to True. If True, we will push the value of certain FLAGS into our options. If False, those option fields are left uninitialized. flags: object. If not None, use as the source of flags, else use global FLAGS. Returns: deepvariant_pb2.DeepVariantOptions protobuf. Raises: ValueError: If we observe invalid flag values. """ if not flags: flags = FLAGS read_reqs = core_pb2.ReadRequirements( min_base_quality=10, min_mapping_quality=10, min_base_quality_mode=core_pb2.ReadRequirements.ENFORCED_BY_CLIENT) pic_options = pileup_image.default_options(read_requirements=read_reqs) allele_counter_options = deepvariant_pb2.AlleleCounterOptions( partition_size=flags.partition_size, read_requirements=read_reqs) if flags.sample_name: sample_name = flags.sample_name elif flags.reads: sample_name = extract_sample_name_from_reads(flags.reads) else: sample_name = _UNKNOWN_SAMPLE variant_caller_options = deepvariant_pb2.VariantCallerOptions( min_count_snps=flags.vsc_min_count_snps, min_count_indels=flags.vsc_min_count_indels, min_fraction_snps=flags.vsc_min_fraction_snps, min_fraction_indels=flags.vsc_min_fraction_indels, # Not specified by default: fraction_reference_sites_to_emit, # Fixed random seed produced with 'od -vAn -N4 -tu4 < /dev/urandom'. random_seed=1400605801, sample_name=sample_name, p_error=0.001, max_gq=50, gq_resolution=1, ploidy=2) options = deepvariant_pb2.DeepVariantOptions( exclude_contigs=[ # The two canonical names for the contig representing the human # mitochondrial sequence. 'chrM', 'MT', # From hs37d5. # (ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/README_human_reference_20110707) # pylint:disable=line-too-long 'GL000207.1', 'GL000226.1', 'GL000229.1', 'GL000231.1', 'GL000210.1', 'GL000239.1', 'GL000235.1', 'GL000201.1', 'GL000247.1', 'GL000245.1', 'GL000197.1', 'GL000203.1', 'GL000246.1', 'GL000249.1', 'GL000196.1', 'GL000248.1', 'GL000244.1', 'GL000238.1', 'GL000202.1', 'GL000234.1', 'GL000232.1', 'GL000206.1', 'GL000240.1', 'GL000236.1', 'GL000241.1', 'GL000243.1', 'GL000242.1', 'GL000230.1', 'GL000237.1', 'GL000233.1', 'GL000204.1', 'GL000198.1', 'GL000208.1', 'GL000191.1', 'GL000227.1', 'GL000228.1', 'GL000214.1', 'GL000221.1', 'GL000209.1', 'GL000218.1', 'GL000220.1', 'GL000213.1', 'GL000211.1', 'GL000199.1', 'GL000217.1', 'GL000216.1', 'GL000215.1', 'GL000205.1', 'GL000219.1', 'GL000224.1', 'GL000223.1', 'GL000195.1', 'GL000212.1', 'GL000222.1', 'GL000200.1', 'GL000193.1', 'GL000194.1', 'GL000225.1', 'GL000192.1', 'NC_007605', 'hs37d5', ], # Fixed random seed produced with 'od -vAn -N4 -tu4 < /dev/urandom'. random_seed=609314161, # # Not specified by default: calling_regions = 3; read_requirements=read_reqs, allele_counter_options=allele_counter_options, variant_caller_options=variant_caller_options, pic_options=pic_options, n_cores=1, task_id=0, num_shards=0, min_shared_contigs_basepairs=0.9, ) if add_flags: if flags.mode == 'training': options.mode = deepvariant_pb2.DeepVariantOptions.TRAINING elif flags.mode == 'calling': options.mode = deepvariant_pb2.DeepVariantOptions.CALLING else: raise ValueError('Unexpected mode', flags.mode) if flags.ref: options.reference_filename = flags.ref if flags.reads: options.reads_filename = flags.reads if flags.confident_regions: options.confident_regions_filename = flags.confident_regions if flags.truth_variants: options.truth_variants_filename = flags.truth_variants if flags.downsample_fraction != NO_DOWNSAMPLING: options.downsample_fraction = flags.downsample_fraction if flags.multi_allelic_mode: multi_allelic_enum = { 'include_het_alt_images': deepvariant_pb2.PileupImageOptions.ADD_HET_ALT_IMAGES, 'exclude_het_alt_images': deepvariant_pb2.PileupImageOptions.NO_HET_ALT_IMAGES, }[flags.multi_allelic_mode] options.pic_options.multi_allelic_mode = multi_allelic_enum if flags.pileup_image_height: options.pic_options.height = flags.pileup_image_height if flags.pileup_image_width: options.pic_options.width = flags.pileup_image_width num_shards, examples, candidates, gvcf = io_utils.resolve_filespecs( flags.task, flags.examples or '', flags.candidates or '', flags.gvcf or '') options.examples_filename = examples options.candidates_filename = candidates options.gvcf_filename = gvcf # redacted regions_flag = flags.regions if isinstance(regions_flag, str): regions_flag = regions_flag.split() options.calling_regions.extend(regions_flag) options.task_id = flags.task options.num_shards = 0 if num_shards is None else num_shards if flags.realign_reads: options.realigner_enabled = True options.realigner_options.CopyFrom( realigner.realigner_config(flags)) options.max_reads_per_partition = flags.max_reads_per_partition if (options.mode == deepvariant_pb2.DeepVariantOptions.TRAINING and flags.training_random_emit_ref_sites != NO_RANDOM_REF): options.variant_caller_options.fraction_reference_sites_to_emit = ( flags.training_random_emit_ref_sites) return options
def setUp(self): self.options = pileup_image.default_options()