def create_struct_model(self, problem, args, use_cuda):
sbi_mappers_configuration = configure_mappers(
ploidy=args.struct_ploidy,
extra_genotypes=args.struct_extra_genotypes,
num_samples=1,
count_dim=args.struct_count_dim,
sample_dim=args.struct_sample_dim,
use_cuda=use_cuda)
sbi_mapper = BatchOfInstances(*sbi_mappers_configuration)
# determine feature size:
import ujson
record = ujson.loads(sbi_json_string)
if self.use_cuda:
sbi_mapper.cuda()
mapped_features_size = sbi_mapper([record],
tensor_cache=NoCache(),
cuda=self.use_cuda).size(1)
output_size = problem.output_size("softmaxGenotype")
model = StructGenotypingModel(args, sbi_mapper, mapped_features_size,
output_size, self.use_cuda,
args.use_batching)
print(model)
return model
def test_map_samples_with_model(self):
sbi_mappers_configuration = configure_mappers(ploidy=2,
extra_genotypes=2,
num_samples=1,
count_dim=16,
sample_dim=32)
sbi_mapper = BatchOfInstances(*sbi_mappers_configuration)
json_string = '{"type":"BaseInformation","referenceBase":"A","genomicSequenceContext":"GCAGATATACTTCACAGCCCACGCTGACTCTGCCAAGCACA","samples":[{"type":"SampleInfo","counts":[{"type":"CountInfo","matchesReference":true,"isCalled":true,"isIndel":false,"fromSequence":"A","toSequence":"A","genotypeCountForwardStrand":7,"genotypeCountReverseStrand":32,"gobyGenotypeIndex":0},{"type":"CountInfo","matchesReference":false,"isCalled":false,"isIndel":false,"fromSequence":"A","toSequence":"C","genotypeCountForwardStrand":0,"genotypeCountReverseStrand":1,"gobyGenotypeIndex":2},{"type":"CountInfo","matchesReference":false,"isCalled":false,"isIndel":false,"fromSequence":"A","toSequence":"T","genotypeCountForwardStrand":0,"genotypeCountReverseStrand":0,"gobyGenotypeIndex":1},{"type":"CountInfo","matchesReference":false,"isCalled":false,"isIndel":false,"fromSequence":"A","toSequence":"G","genotypeCountForwardStrand":0,"genotypeCountReverseStrand":0,"gobyGenotypeIndex":3},{"type":"CountInfo","matchesReference":false,"isCalled":false,"isIndel":false,"fromSequence":"A","toSequence":"N","genotypeCountForwardStrand":0,"genotypeCountReverseStrand":0,"gobyGenotypeIndex":4}]}]}'
# determine feature size:
import ujson
record = ujson.loads(json_string)
mapped_features_size = sbi_mapper([record, record],
tensor_cache=NoCache(),
cuda=False).size(1)
problem = StructuredSbiGenotypingProblem(
mini_batch_size=2,
code="struct_genotyping:/data/struct/CNG-NA12878-softmax-indels")
output_size = problem.output_size("softmaxGenotype")
parser = define_train_auto_encoder_parser()
args = parser.parse_args()
model = StructGenotypingModel(args,
sbi_mapper,
mapped_features_size,
output_size,
use_cuda=False,
use_batching=True)
print(model.map_sbi_messages(sbi_records=[record] * 2, cuda=True))
def test_serialize_mapper(self):
json_string = '{"type":"BaseInformation","referenceBase":"A","genomicSequenceContext":"GCAGATATACTTCACAGCCCACGCTGACTCTGCCAAGCACA","samples":[{"type":"SampleInfo","counts":[{"type":"CountInfo","matchesReference":true,"isCalled":true,"isIndel":false,"fromSequence":"A","toSequence":"A","genotypeCountForwardStrand":7,"genotypeCountReverseStrand":32,"gobyGenotypeIndex":0},{"type":"CountInfo","matchesReference":false,"isCalled":false,"isIndel":false,"fromSequence":"A","toSequence":"C","genotypeCountForwardStrand":0,"genotypeCountReverseStrand":1,"gobyGenotypeIndex":2},{"type":"CountInfo","matchesReference":false,"isCalled":false,"isIndel":false,"fromSequence":"A","toSequence":"T","genotypeCountForwardStrand":0,"genotypeCountReverseStrand":0,"gobyGenotypeIndex":1},{"type":"CountInfo","matchesReference":false,"isCalled":false,"isIndel":false,"fromSequence":"A","toSequence":"G","genotypeCountForwardStrand":0,"genotypeCountReverseStrand":0,"gobyGenotypeIndex":3},{"type":"CountInfo","matchesReference":false,"isCalled":false,"isIndel":false,"fromSequence":"A","toSequence":"N","genotypeCountForwardStrand":0,"genotypeCountReverseStrand":0,"gobyGenotypeIndex":4}]}]}'
import ujson
record = ujson.loads(json_string)
print(record)
mappers, all_modules = configure_mappers(ploidy=2,
extra_genotypes=3,
num_samples=1)
mapper = BatchOfInstances(mappers=mappers, all_modules=all_modules)
with open('testing.pickle', 'wb') as f:
pickle.dump(mapper, f)
def test_train_mapper_on_cuda(self):
json_string = '{"type":"BaseInformation","referenceBase":"A","genomicSequenceContext":"GCAGATATACTTCACAGCCCACGCTGACTCTGCCAAGCACA","samples":[{"type":"SampleInfo","counts":[{"type":"CountInfo","matchesReference":true,"isCalled":true,"isIndel":false,"fromSequence":"A","toSequence":"A","genotypeCountForwardStrand":7,"genotypeCountReverseStrand":32,"gobyGenotypeIndex":0},{"type":"CountInfo","matchesReference":false,"isCalled":false,"isIndel":false,"fromSequence":"A","toSequence":"C","genotypeCountForwardStrand":0,"genotypeCountReverseStrand":1,"gobyGenotypeIndex":2},{"type":"CountInfo","matchesReference":false,"isCalled":false,"isIndel":false,"fromSequence":"A","toSequence":"T","genotypeCountForwardStrand":0,"genotypeCountReverseStrand":0,"gobyGenotypeIndex":1},{"type":"CountInfo","matchesReference":false,"isCalled":false,"isIndel":false,"fromSequence":"A","toSequence":"G","genotypeCountForwardStrand":0,"genotypeCountReverseStrand":0,"gobyGenotypeIndex":3},{"type":"CountInfo","matchesReference":false,"isCalled":false,"isIndel":false,"fromSequence":"A","toSequence":"N","genotypeCountForwardStrand":0,"genotypeCountReverseStrand":0,"gobyGenotypeIndex":4}]}]}'
import ujson
record = ujson.loads(json_string)
print(record)
mappers, all_modules = configure_mappers(ploidy=2,
extra_genotypes=3,
num_samples=1)
mapper = BatchOfInstances(mappers=mappers, all_modules=all_modules)
mapper = mapper.to(torch.device("cuda"))
mapper([record], tensor_cache=NoCache(), cuda=True)
def test_mapper_number_freqs(self):
json_string='{"type":"BaseInformation","referenceBase":"A","genomicSequenceContext":"GCAGATATACTTCACAGCCCACGCTGACTCTGCCAAGCACA","samples":[{"type":"SampleInfo","counts":[{"type":"CountInfo","matchesReference":true,"isCalled":true,"isIndel":false,"fromSequence":"A","toSequence":"A","genotypeCountForwardStrand":7,"genotypeCountReverseStrand":32,"gobyGenotypeIndex":0,"qualityScoresForwardStrand":[{"type":"NumberWithFrequency","frequency":7,"number":40}],"qualityScoresReverseStrand":[{"type":"NumberWithFrequency","frequency":32,"number":40}],"readIndicesForwardStrand":[{"type":"NumberWithFrequency","frequency":1,"number":23},{"type":"NumberWithFrequency","frequency":1,"number":30},{"type":"NumberWithFrequency","frequency":5,"number":34}],"readIndicesReverseStrand":[{"type":"NumberWithFrequency","frequency":1,"number":6},{"type":"NumberWithFrequency","frequency":1,"number":22},{"type":"NumberWithFrequency","frequency":1,"number":28},{"type":"NumberWithFrequency","frequency":1,"number":31},{"type":"NumberWithFrequency","frequency":1,"number":34},{"type":"NumberWithFrequency","frequency":1,"number":35},{"type":"NumberWithFrequency","frequency":1,"number":44},{"type":"NumberWithFrequency","frequency":1,"number":145},{"type":"NumberWithFrequency","frequency":1,"number":150},{"type":"NumberWithFrequency","frequency":5,"number":151},{"type":"NumberWithFrequency","frequency":2,"number":171},{"type":"NumberWithFrequency","frequency":4,"number":172}],"queryPositions":[{"type":"NumberWithFrequency","frequency":39,"number":0}],"pairFlags":[{"type":"NumberWithFrequency","frequency":6,"number":16},{"type":"NumberWithFrequency","frequency":14,"number":83},{"type":"NumberWithFrequency","frequency":6,"number":99},{"type":"NumberWithFrequency","frequency":12,"number":147},{"type":"NumberWithFrequency","frequency":1,"number":163}],"distancesToReadVariationsForwardStrand":[{"type":"NumberWithFrequency","frequency":2,"number":-70},{"type":"NumberWithFrequency","frequency":4,"number":-29}],"distancesToReadVariationsReverseStrand":[{"type":"NumberWithFrequency","frequency":2,"number":-24},{"type":"NumberWithFrequency","frequency":1,"number":-15},{"type":"NumberWithFrequency","frequency":1,"number":-2},{"type":"NumberWithFrequency","frequency":1,"number":12},{"type":"NumberWithFrequency","frequency":1,"number":13},{"type":"NumberWithFrequency","frequency":1,"number":15},{"type":"NumberWithFrequency","frequency":13,"number":29},{"type":"NumberWithFrequency","frequency":1,"number":49},{"type":"NumberWithFrequency","frequency":3,"number":62},{"type":"NumberWithFrequency","frequency":9,"number":70},{"type":"NumberWithFrequency","frequency":1,"number":73}],"distanceToStartOfRead":[{"type":"NumberWithFrequency","frequency":1,"number":18},{"type":"NumberWithFrequency","frequency":1,"number":23},{"type":"NumberWithFrequency","frequency":1,"number":26},{"type":"NumberWithFrequency","frequency":1,"number":30},{"type":"NumberWithFrequency","frequency":30,"number":33},{"type":"NumberWithFrequency","frequency":5,"number":34}],"distanceToEndOfRead":[{"type":"NumberWithFrequency","frequency":1,"number":6},{"type":"NumberWithFrequency","frequency":1,"number":22},{"type":"NumberWithFrequency","frequency":1,"number":28},{"type":"NumberWithFrequency","frequency":1,"number":31},{"type":"NumberWithFrequency","frequency":1,"number":34},{"type":"NumberWithFrequency","frequency":2,"number":35},{"type":"NumberWithFrequency","frequency":1,"number":44},{"type":"NumberWithFrequency","frequency":1,"number":48},{"type":"NumberWithFrequency","frequency":1,"number":49},{"type":"NumberWithFrequency","frequency":1,"number":50},{"type":"NumberWithFrequency","frequency":1,"number":52},{"type":"NumberWithFrequency","frequency":1,"number":62},{"type":"NumberWithFrequency","frequency":1,"number":63},{"type":"NumberWithFrequency","frequency":1,"number":68},{"type":"NumberWithFrequency","frequency":2,"number":75},{"type":"NumberWithFrequency","frequency":2,"number":76},{"type":"NumberWithFrequency","frequency":1,"number":81},{"type":"NumberWithFrequency","frequency":1,"number":83},{"type":"NumberWithFrequency","frequency":1,"number":88},{"type":"NumberWithFrequency","frequency":1,"number":89},{"type":"NumberWithFrequency","frequency":1,"number":100},{"type":"NumberWithFrequency","frequency":1,"number":104},{"type":"NumberWithFrequency","frequency":1,"number":109},{"type":"NumberWithFrequency","frequency":1,"number":111},{"type":"NumberWithFrequency","frequency":1,"number":117},{"type":"NumberWithFrequency","frequency":1,"number":118},{"type":"NumberWithFrequency","frequency":1,"number":121},{"type":"NumberWithFrequency","frequency":1,"number":125},{"type":"NumberWithFrequency","frequency":1,"number":128},{"type":"NumberWithFrequency","frequency":1,"number":133},{"type":"NumberWithFrequency","frequency":2,"number":138},{"type":"NumberWithFrequency","frequency":4,"number":139}]},{"type":"CountInfo","matchesReference":false,"isCalled":false,"isIndel":false,"fromSequence":"A","toSequence":"C","genotypeCountForwardStrand":0,"genotypeCountReverseStrand":1,"gobyGenotypeIndex":2,"qualityScoresForwardStrand":[],"qualityScoresReverseStrand":[{"type":"NumberWithFrequency","frequency":1,"number":7}],"readIndicesForwardStrand":[],"readIndicesReverseStrand":[{"type":"NumberWithFrequency","frequency":1,"number":115}],"readMappingQualityForwardStrand":[],"readMappingQualityReverseStrand":[{"type":"NumberWithFrequency","frequency":1,"number":60}],"numVariationsInReads":[{"type":"NumberWithFrequency","frequency":1,"number":2}],"insertSizes":[{"type":"NumberWithFrequency","frequency":1,"number":-301}],"targetAlignedLengths":[{"type":"NumberWithFrequency","frequency":2,"number":148}],"queryAlignedLengths":[{"type":"NumberWithFrequency","frequency":1,"number":148}],"queryPositions":[{"type":"NumberWithFrequency","frequency":1,"number":0}],"pairFlags":[{"type":"NumberWithFrequency","frequency":1,"number":147}],"distancesToReadVariationsForwardStrand":[],"distancesToReadVariationsReverseStrand":[{"type":"NumberWithFrequency","frequency":1,"number":-29},{"type":"NumberWithFrequency","frequency":1,"number":0}],"distanceToStartOfRead":[{"type":"NumberWithFrequency","frequency":1,"number":33}],"distanceToEndOfRead":[{"type":"NumberWithFrequency","frequency":1,"number":115}]},{"type":"CountInfo","matchesReference":false,"isCalled":false,"isIndel":false,"fromSequence":"A","toSequence":"T","genotypeCountForwardStrand":0,"genotypeCountReverseStrand":0,"gobyGenotypeIndex":1,"qualityScoresForwardStrand":[],"qualityScoresReverseStrand":[],"readIndicesForwardStrand":[],"readIndicesReverseStrand":[],"readMappingQualityForwardStrand":[],"readMappingQualityReverseStrand":[],"numVariationsInReads":[],"insertSizes":[],"targetAlignedLengths":[],"queryAlignedLengths":[],"queryPositions":[],"pairFlags":[],"distancesToReadVariationsForwardStrand":[],"distancesToReadVariationsReverseStrand":[],"distanceToStartOfRead":[],"distanceToEndOfRead":[]},{"type":"CountInfo","matchesReference":false,"isCalled":false,"isIndel":false,"fromSequence":"A","toSequence":"G","genotypeCountForwardStrand":0,"genotypeCountReverseStrand":0,"gobyGenotypeIndex":3,"qualityScoresForwardStrand":[],"qualityScoresReverseStrand":[],"readIndicesForwardStrand":[],"readIndicesReverseStrand":[],"readMappingQualityForwardStrand":[],"readMappingQualityReverseStrand":[],"numVariationsInReads":[],"insertSizes":[],"targetAlignedLengths":[],"queryAlignedLengths":[],"queryPositions":[],"pairFlags":[],"distancesToReadVariationsForwardStrand":[],"distancesToReadVariationsReverseStrand":[],"distanceToStartOfRead":[],"distanceToEndOfRead":[]},{"type":"CountInfo","matchesReference":false,"isCalled":false,"isIndel":false,"fromSequence":"A","toSequence":"N","genotypeCountForwardStrand":0,"genotypeCountReverseStrand":0,"gobyGenotypeIndex":4,"qualityScoresForwardStrand":[],"qualityScoresReverseStrand":[],"readIndicesForwardStrand":[],"readIndicesReverseStrand":[],"readMappingQualityForwardStrand":[],"readMappingQualityReverseStrand":[],"numVariationsInReads":[],"insertSizes":[],"targetAlignedLengths":[],"queryAlignedLengths":[],"queryPositions":[],"pairFlags":[],"distancesToReadVariationsForwardStrand":[],"distancesToReadVariationsReverseStrand":[],"distanceToStartOfRead":[],"distanceToEndOfRead":[]}]}]}' \
''
import ujson
record = ujson.loads(json_string)
print(record)
mappers, all_modules = configure_mappers(ploidy=2,
extra_genotypes=3,
num_samples=1)
mapper = BatchOfInstances(mappers=mappers, all_modules=all_modules)
out = mapper([record], tensor_cache=NoCache())
print(out)