INSTRUCTION stringlengths 1 8.43k | RESPONSE stringlengths 75 104k |
|---|---|
Returns a generator over the ( referenceSet nextPageToken ) pairs defined by the specified request. | def referenceSetsGenerator(self, request):
"""
Returns a generator over the (referenceSet, nextPageToken) pairs
defined by the specified request.
"""
results = []
for obj in self.getDataRepository().getReferenceSets():
include = True
if request.md5... |
Returns a generator over the ( reference nextPageToken ) pairs defined by the specified request. | def referencesGenerator(self, request):
"""
Returns a generator over the (reference, nextPageToken) pairs
defined by the specified request.
"""
referenceSet = self.getDataRepository().getReferenceSet(
request.reference_set_id)
results = []
for obj in r... |
Returns a generator over the ( variantSet nextPageToken ) pairs defined by the specified request. | def variantSetsGenerator(self, request):
"""
Returns a generator over the (variantSet, nextPageToken) pairs defined
by the specified request.
"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._topLevelObjectGenerator(
request, d... |
Returns a generator over the ( variantAnnotationSet nextPageToken ) pairs defined by the specified request. | def variantAnnotationSetsGenerator(self, request):
"""
Returns a generator over the (variantAnnotationSet, nextPageToken)
pairs defined by the specified request.
"""
compoundId = datamodel.VariantSetCompoundId.parse(
request.variant_set_id)
dataset = self.getD... |
Returns a generator over the ( read nextPageToken ) pairs defined by the specified request | def readsGenerator(self, request):
"""
Returns a generator over the (read, nextPageToken) pairs defined
by the specified request
"""
if not request.reference_id:
raise exceptions.UnmappedReadsNotSupported()
if len(request.read_group_ids) < 1:
raise... |
Returns a generator over the ( variant nextPageToken ) pairs defined by the specified request. | def variantsGenerator(self, request):
"""
Returns a generator over the (variant, nextPageToken) pairs defined
by the specified request.
"""
compoundId = datamodel.VariantSetCompoundId \
.parse(request.variant_set_id)
dataset = self.getDataRepository().getDatas... |
Returns a generator over the ( variantAnnotaitons nextPageToken ) pairs defined by the specified request. | def variantAnnotationsGenerator(self, request):
"""
Returns a generator over the (variantAnnotaitons, nextPageToken) pairs
defined by the specified request.
"""
compoundId = datamodel.VariantAnnotationSetCompoundId.parse(
request.variant_annotation_set_id)
dat... |
Returns a generator over the ( features nextPageToken ) pairs defined by the ( JSON string ) request. | def featuresGenerator(self, request):
"""
Returns a generator over the (features, nextPageToken) pairs
defined by the (JSON string) request.
"""
compoundId = None
parentId = None
if request.feature_set_id != "":
compoundId = datamodel.FeatureSetCompoun... |
Returns a generator over the ( continuous nextPageToken ) pairs defined by the ( JSON string ) request. | def continuousGenerator(self, request):
"""
Returns a generator over the (continuous, nextPageToken) pairs
defined by the (JSON string) request.
"""
compoundId = None
if request.continuous_set_id != "":
compoundId = datamodel.ContinuousSetCompoundId.parse(
... |
Returns a generator over the ( phenotypes nextPageToken ) pairs defined by the ( JSON string ) request | def phenotypesGenerator(self, request):
"""
Returns a generator over the (phenotypes, nextPageToken) pairs
defined by the (JSON string) request
"""
# TODO make paging work using SPARQL?
compoundId = datamodel.PhenotypeAssociationSetCompoundId.parse(
request.ph... |
Returns a generator over the ( phenotypes nextPageToken ) pairs defined by the ( JSON string ) request | def genotypesPhenotypesGenerator(self, request):
"""
Returns a generator over the (phenotypes, nextPageToken) pairs
defined by the (JSON string) request
"""
# TODO make paging work using SPARQL?
compoundId = datamodel.PhenotypeAssociationSetCompoundId.parse(
r... |
Returns a generator over the ( callSet nextPageToken ) pairs defined by the specified request. | def callSetsGenerator(self, request):
"""
Returns a generator over the (callSet, nextPageToken) pairs defined
by the specified request.
"""
compoundId = datamodel.VariantSetCompoundId.parse(
request.variant_set_id)
dataset = self.getDataRepository().getDataset... |
Returns a generator over the ( featureSet nextPageToken ) pairs defined by the specified request. | def featureSetsGenerator(self, request):
"""
Returns a generator over the (featureSet, nextPageToken) pairs
defined by the specified request.
"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._topLevelObjectGenerator(
request, d... |
Returns a generator over the ( continuousSet nextPageToken ) pairs defined by the specified request. | def continuousSetsGenerator(self, request):
"""
Returns a generator over the (continuousSet, nextPageToken) pairs
defined by the specified request.
"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._topLevelObjectGenerator(
requ... |
Returns a generator over the ( rnaQuantificationSet nextPageToken ) pairs defined by the specified request. | def rnaQuantificationSetsGenerator(self, request):
"""
Returns a generator over the (rnaQuantificationSet, nextPageToken)
pairs defined by the specified request.
"""
dataset = self.getDataRepository().getDataset(request.dataset_id)
return self._topLevelObjectGenerator(
... |
Returns a generator over the ( rnaQuantification nextPageToken ) pairs defined by the specified request. | def rnaQuantificationsGenerator(self, request):
"""
Returns a generator over the (rnaQuantification, nextPageToken) pairs
defined by the specified request.
"""
if len(request.rna_quantification_set_id) < 1:
raise exceptions.BadRequestException(
"Rna Qu... |
Returns a generator over the ( expressionLevel nextPageToken ) pairs defined by the specified request. | def expressionLevelsGenerator(self, request):
"""
Returns a generator over the (expressionLevel, nextPageToken) pairs
defined by the specified request.
Currently only supports searching over a specified rnaQuantification
"""
rnaQuantificationId = request.rna_quantificati... |
Runs a get request by converting the specified datamodel object into its protocol representation. | def runGetRequest(self, obj):
"""
Runs a get request by converting the specified datamodel
object into its protocol representation.
"""
protocolElement = obj.toProtocolElement()
jsonString = protocol.toJson(protocolElement)
return jsonString |
Runs the specified request. The request is a string containing a JSON representation of an instance of the specified requestClass. We return a string representation of an instance of the specified responseClass in JSON format. Objects are filled into the page list using the specified object generator which must return ... | def runSearchRequest(
self, requestStr, requestClass, responseClass, objectGenerator):
"""
Runs the specified request. The request is a string containing
a JSON representation of an instance of the specified requestClass.
We return a string representation of an instance of th... |
Runs a listReferenceBases request for the specified ID and request arguments. | def runListReferenceBases(self, requestJson):
"""
Runs a listReferenceBases request for the specified ID and
request arguments.
"""
# In the case when an empty post request is made to the endpoint
# we instantiate an empty ListReferenceBasesRequest.
if not request... |
Returns a callset with the given id | def runGetCallSet(self, id_):
"""
Returns a callset with the given id
"""
compoundId = datamodel.CallSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(compoundId.variant_set_id)
callSet... |
Returns information about the service including protocol version. | def runGetInfo(self, request):
"""
Returns information about the service including protocol version.
"""
return protocol.toJson(protocol.GetInfoResponse(
protocol_version=protocol.version)) |
Takes a flask request from the frontend and attempts to parse into an AnnouncePeerRequest. If successful it will log the announcement to the announcement table with some other metadata gathered from the request. | def runAddAnnouncement(self, flaskrequest):
"""
Takes a flask request from the frontend and attempts to parse
into an AnnouncePeerRequest. If successful, it will log the
announcement to the `announcement` table with some other metadata
gathered from the request.
"""
... |
Takes a ListPeersRequest and returns a ListPeersResponse using a page_token and page_size if provided. | def runListPeers(self, request):
"""
Takes a ListPeersRequest and returns a ListPeersResponse using
a page_token and page_size if provided.
"""
return self.runSearchRequest(
request,
protocol.ListPeersRequest,
protocol.ListPeersResponse,
... |
Returns a variant with the given id | def runGetVariant(self, id_):
"""
Returns a variant with the given id
"""
compoundId = datamodel.VariantCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(compoundId.variant_set_id)
gaVaria... |
Runs a getBiosample request for the specified ID. | def runGetBiosample(self, id_):
"""
Runs a getBiosample request for the specified ID.
"""
compoundId = datamodel.BiosampleCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
biosample = dataset.getBiosample(id_)
return self.r... |
Runs a getIndividual request for the specified ID. | def runGetIndividual(self, id_):
"""
Runs a getIndividual request for the specified ID.
"""
compoundId = datamodel.BiosampleCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
individual = dataset.getIndividual(id_)
return se... |
Returns JSON string of the feature object corresponding to the feature compoundID passed in. | def runGetFeature(self, id_):
"""
Returns JSON string of the feature object corresponding to
the feature compoundID passed in.
"""
compoundId = datamodel.FeatureCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
featureSet =... |
Returns a readGroupSet with the given id_ | def runGetReadGroupSet(self, id_):
"""
Returns a readGroupSet with the given id_
"""
compoundId = datamodel.ReadGroupSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
readGroupSet = dataset.getReadGroupSet(id_)
return se... |
Returns a read group with the given id_ | def runGetReadGroup(self, id_):
"""
Returns a read group with the given id_
"""
compoundId = datamodel.ReadGroupCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
readGroupSet = dataset.getReadGroupSet(compoundId.read_group_set_id)
... |
Runs a getReference request for the specified ID. | def runGetReference(self, id_):
"""
Runs a getReference request for the specified ID.
"""
compoundId = datamodel.ReferenceCompoundId.parse(id_)
referenceSet = self.getDataRepository().getReferenceSet(
compoundId.reference_set_id)
reference = referenceSet.getRe... |
Runs a getReferenceSet request for the specified ID. | def runGetReferenceSet(self, id_):
"""
Runs a getReferenceSet request for the specified ID.
"""
referenceSet = self.getDataRepository().getReferenceSet(id_)
return self.runGetRequest(referenceSet) |
Runs a getVariantSet request for the specified ID. | def runGetVariantSet(self, id_):
"""
Runs a getVariantSet request for the specified ID.
"""
compoundId = datamodel.VariantSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(id_)
return s... |
Runs a getFeatureSet request for the specified ID. | def runGetFeatureSet(self, id_):
"""
Runs a getFeatureSet request for the specified ID.
"""
compoundId = datamodel.FeatureSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
featureSet = dataset.getFeatureSet(id_)
return s... |
Runs a getContinuousSet request for the specified ID. | def runGetContinuousSet(self, id_):
"""
Runs a getContinuousSet request for the specified ID.
"""
compoundId = datamodel.ContinuousSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
continuousSet = dataset.getContinuousSet(id_)
... |
Runs a getDataset request for the specified ID. | def runGetDataset(self, id_):
"""
Runs a getDataset request for the specified ID.
"""
dataset = self.getDataRepository().getDataset(id_)
return self.runGetRequest(dataset) |
Runs a getVariantSet request for the specified ID. | def runGetVariantAnnotationSet(self, id_):
"""
Runs a getVariantSet request for the specified ID.
"""
compoundId = datamodel.VariantAnnotationSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
variantSet = dataset.getVariantSet(c... |
Runs a getRnaQuantification request for the specified ID. | def runGetRnaQuantification(self, id_):
"""
Runs a getRnaQuantification request for the specified ID.
"""
compoundId = datamodel.RnaQuantificationCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
rnaQuantificationSet = dataset.getR... |
Runs a getRnaQuantificationSet request for the specified ID. | def runGetRnaQuantificationSet(self, id_):
"""
Runs a getRnaQuantificationSet request for the specified ID.
"""
compoundId = datamodel.RnaQuantificationSetCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
rnaQuantificationSet = dat... |
Runs a getExpressionLevel request for the specified ID. | def runGetExpressionLevel(self, id_):
"""
Runs a getExpressionLevel request for the specified ID.
"""
compoundId = datamodel.ExpressionLevelCompoundId.parse(id_)
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
rnaQuantificationSet = dataset.getRnaQuan... |
Runs the specified SearchReadGroupSetsRequest. | def runSearchReadGroupSets(self, request):
"""
Runs the specified SearchReadGroupSetsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchReadGroupSetsRequest,
protocol.SearchReadGroupSetsResponse,
self.readGroupSetsGenerator) |
Runs the specified search SearchIndividualsRequest. | def runSearchIndividuals(self, request):
"""
Runs the specified search SearchIndividualsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchIndividualsRequest,
protocol.SearchIndividualsResponse,
self.individualsGenerator) |
Runs the specified SearchBiosamplesRequest. | def runSearchBiosamples(self, request):
"""
Runs the specified SearchBiosamplesRequest.
"""
return self.runSearchRequest(
request, protocol.SearchBiosamplesRequest,
protocol.SearchBiosamplesResponse,
self.biosamplesGenerator) |
Runs the specified SearchReadsRequest. | def runSearchReads(self, request):
"""
Runs the specified SearchReadsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchReadsRequest,
protocol.SearchReadsResponse,
self.readsGenerator) |
Runs the specified SearchReferenceSetsRequest. | def runSearchReferenceSets(self, request):
"""
Runs the specified SearchReferenceSetsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchReferenceSetsRequest,
protocol.SearchReferenceSetsResponse,
self.referenceSetsGenerator) |
Runs the specified SearchReferenceRequest. | def runSearchReferences(self, request):
"""
Runs the specified SearchReferenceRequest.
"""
return self.runSearchRequest(
request, protocol.SearchReferencesRequest,
protocol.SearchReferencesResponse,
self.referencesGenerator) |
Runs the specified SearchVariantSetsRequest. | def runSearchVariantSets(self, request):
"""
Runs the specified SearchVariantSetsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchVariantSetsRequest,
protocol.SearchVariantSetsResponse,
self.variantSetsGenerator) |
Runs the specified SearchVariantAnnotationSetsRequest. | def runSearchVariantAnnotationSets(self, request):
"""
Runs the specified SearchVariantAnnotationSetsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchVariantAnnotationSetsRequest,
protocol.SearchVariantAnnotationSetsResponse,
self.var... |
Runs the specified SearchVariantRequest. | def runSearchVariants(self, request):
"""
Runs the specified SearchVariantRequest.
"""
return self.runSearchRequest(
request, protocol.SearchVariantsRequest,
protocol.SearchVariantsResponse,
self.variantsGenerator) |
Runs the specified SearchVariantAnnotationsRequest. | def runSearchVariantAnnotations(self, request):
"""
Runs the specified SearchVariantAnnotationsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchVariantAnnotationsRequest,
protocol.SearchVariantAnnotationsResponse,
self.variantAnnotati... |
Runs the specified SearchCallSetsRequest. | def runSearchCallSets(self, request):
"""
Runs the specified SearchCallSetsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchCallSetsRequest,
protocol.SearchCallSetsResponse,
self.callSetsGenerator) |
Runs the specified SearchDatasetsRequest. | def runSearchDatasets(self, request):
"""
Runs the specified SearchDatasetsRequest.
"""
return self.runSearchRequest(
request, protocol.SearchDatasetsRequest,
protocol.SearchDatasetsResponse,
self.datasetsGenerator) |
Returns a SearchFeatureSetsResponse for the specified SearchFeatureSetsRequest object. | def runSearchFeatureSets(self, request):
"""
Returns a SearchFeatureSetsResponse for the specified
SearchFeatureSetsRequest object.
"""
return self.runSearchRequest(
request, protocol.SearchFeatureSetsRequest,
protocol.SearchFeatureSetsResponse,
... |
Returns a SearchFeaturesResponse for the specified SearchFeaturesRequest object. | def runSearchFeatures(self, request):
"""
Returns a SearchFeaturesResponse for the specified
SearchFeaturesRequest object.
:param request: JSON string representing searchFeaturesRequest
:return: JSON string representing searchFeatureResponse
"""
return self.runSe... |
Returns a SearchContinuousSetsResponse for the specified SearchContinuousSetsRequest object. | def runSearchContinuousSets(self, request):
"""
Returns a SearchContinuousSetsResponse for the specified
SearchContinuousSetsRequest object.
"""
return self.runSearchRequest(
request, protocol.SearchContinuousSetsRequest,
protocol.SearchContinuousSetsRespo... |
Returns a SearchContinuousResponse for the specified SearchContinuousRequest object. | def runSearchContinuous(self, request):
"""
Returns a SearchContinuousResponse for the specified
SearchContinuousRequest object.
:param request: JSON string representing searchContinuousRequest
:return: JSON string representing searchContinuousResponse
"""
return... |
Returns a SearchRnaQuantificationSetsResponse for the specified SearchRnaQuantificationSetsRequest object. | def runSearchRnaQuantificationSets(self, request):
"""
Returns a SearchRnaQuantificationSetsResponse for the specified
SearchRnaQuantificationSetsRequest object.
"""
return self.runSearchRequest(
request, protocol.SearchRnaQuantificationSetsRequest,
protoc... |
Returns a SearchRnaQuantificationResponse for the specified SearchRnaQuantificationRequest object. | def runSearchRnaQuantifications(self, request):
"""
Returns a SearchRnaQuantificationResponse for the specified
SearchRnaQuantificationRequest object.
"""
return self.runSearchRequest(
request, protocol.SearchRnaQuantificationsRequest,
protocol.SearchRnaQu... |
Returns a SearchExpressionLevelResponse for the specified SearchExpressionLevelRequest object. | def runSearchExpressionLevels(self, request):
"""
Returns a SearchExpressionLevelResponse for the specified
SearchExpressionLevelRequest object.
"""
return self.runSearchRequest(
request, protocol.SearchExpressionLevelsRequest,
protocol.SearchExpressionLev... |
Populates the instance variables of this Dataset from the specified database row. | def populateFromRow(self, dataset):
"""
Populates the instance variables of this Dataset from the
specified database row.
"""
self._description = dataset.description
self.setAttributesJson(dataset.attributes) |
Adds the specified variantSet to this dataset. | def addVariantSet(self, variantSet):
"""
Adds the specified variantSet to this dataset.
"""
id_ = variantSet.getId()
self._variantSetIdMap[id_] = variantSet
self._variantSetNameMap[variantSet.getLocalId()] = variantSet
self._variantSetIds.append(id_) |
Adds the specified biosample to this dataset. | def addBiosample(self, biosample):
"""
Adds the specified biosample to this dataset.
"""
id_ = biosample.getId()
self._biosampleIdMap[id_] = biosample
self._biosampleIds.append(id_)
self._biosampleNameMap[biosample.getName()] = biosample |
Adds the specified individual to this dataset. | def addIndividual(self, individual):
"""
Adds the specified individual to this dataset.
"""
id_ = individual.getId()
self._individualIdMap[id_] = individual
self._individualIds.append(id_)
self._individualNameMap[individual.getName()] = individual |
Adds the specified featureSet to this dataset. | def addFeatureSet(self, featureSet):
"""
Adds the specified featureSet to this dataset.
"""
id_ = featureSet.getId()
self._featureSetIdMap[id_] = featureSet
self._featureSetIds.append(id_)
name = featureSet.getLocalId()
self._featureSetNameMap[name] = feat... |
Adds the specified continuousSet to this dataset. | def addContinuousSet(self, continuousSet):
"""
Adds the specified continuousSet to this dataset.
"""
id_ = continuousSet.getId()
self._continuousSetIdMap[id_] = continuousSet
self._continuousSetIds.append(id_)
name = continuousSet.getLocalId()
self._contin... |
Adds the specified readGroupSet to this dataset. | def addReadGroupSet(self, readGroupSet):
"""
Adds the specified readGroupSet to this dataset.
"""
id_ = readGroupSet.getId()
self._readGroupSetIdMap[id_] = readGroupSet
self._readGroupSetNameMap[readGroupSet.getLocalId()] = readGroupSet
self._readGroupSetIds.appen... |
Adds the specified rnaQuantification set to this dataset. | def addRnaQuantificationSet(self, rnaQuantSet):
"""
Adds the specified rnaQuantification set to this dataset.
"""
id_ = rnaQuantSet.getId()
self._rnaQuantificationSetIdMap[id_] = rnaQuantSet
self._rnaQuantificationSetIds.append(id_)
name = rnaQuantSet.getLocalId()... |
Returns the VariantSet with the specified name or raises a VariantSetNotFoundException otherwise. | def getVariantSet(self, id_):
"""
Returns the VariantSet with the specified name, or raises a
VariantSetNotFoundException otherwise.
"""
if id_ not in self._variantSetIdMap:
raise exceptions.VariantSetNotFoundException(id_)
return self._variantSetIdMap[id_] |
Returns a VariantSet with the specified name or raises a VariantSetNameNotFoundException if it does not exist. | def getVariantSetByName(self, name):
"""
Returns a VariantSet with the specified name, or raises a
VariantSetNameNotFoundException if it does not exist.
"""
if name not in self._variantSetNameMap:
raise exceptions.VariantSetNameNotFoundException(name)
return s... |
Adds the specified g2p association set to this backend. | def addPhenotypeAssociationSet(self, phenotypeAssociationSet):
"""
Adds the specified g2p association set to this backend.
"""
id_ = phenotypeAssociationSet.getId()
self._phenotypeAssociationSetIdMap[id_] = phenotypeAssociationSet
self._phenotypeAssociationSetNameMap[
... |
Returns the FeatureSet with the specified id or raises a FeatureSetNotFoundException otherwise. | def getFeatureSet(self, id_):
"""
Returns the FeatureSet with the specified id, or raises a
FeatureSetNotFoundException otherwise.
"""
if id_ not in self._featureSetIdMap:
raise exceptions.FeatureSetNotFoundException(id_)
return self._featureSetIdMap[id_] |
Returns the FeatureSet with the specified name or raises an exception otherwise. | def getFeatureSetByName(self, name):
"""
Returns the FeatureSet with the specified name, or raises
an exception otherwise.
"""
if name not in self._featureSetNameMap:
raise exceptions.FeatureSetNameNotFoundException(name)
return self._featureSetNameMap[name] |
Returns the ContinuousSet with the specified id or raises a ContinuousSetNotFoundException otherwise. | def getContinuousSet(self, id_):
"""
Returns the ContinuousSet with the specified id, or raises a
ContinuousSetNotFoundException otherwise.
"""
if id_ not in self._continuousSetIdMap:
raise exceptions.ContinuousSetNotFoundException(id_)
return self._continuous... |
Returns the ContinuousSet with the specified name or raises an exception otherwise. | def getContinuousSetByName(self, name):
"""
Returns the ContinuousSet with the specified name, or raises
an exception otherwise.
"""
if name not in self._continuousSetNameMap:
raise exceptions.ContinuousSetNameNotFoundException(name)
return self._continuousSet... |
Returns a Biosample with the specified name or raises a BiosampleNameNotFoundException if it does not exist. | def getBiosampleByName(self, name):
"""
Returns a Biosample with the specified name, or raises a
BiosampleNameNotFoundException if it does not exist.
"""
if name not in self._biosampleNameMap:
raise exceptions.BiosampleNameNotFoundException(name)
return self._... |
Returns the Biosample with the specified id or raises a BiosampleNotFoundException otherwise. | def getBiosample(self, id_):
"""
Returns the Biosample with the specified id, or raises
a BiosampleNotFoundException otherwise.
"""
if id_ not in self._biosampleIdMap:
raise exceptions.BiosampleNotFoundException(id_)
return self._biosampleIdMap[id_] |
Returns an individual with the specified name or raises a IndividualNameNotFoundException if it does not exist. | def getIndividualByName(self, name):
"""
Returns an individual with the specified name, or raises a
IndividualNameNotFoundException if it does not exist.
"""
if name not in self._individualNameMap:
raise exceptions.IndividualNameNotFoundException(name)
return ... |
Returns the Individual with the specified id or raises a IndividualNotFoundException otherwise. | def getIndividual(self, id_):
"""
Returns the Individual with the specified id, or raises
a IndividualNotFoundException otherwise.
"""
if id_ not in self._individualIdMap:
raise exceptions.IndividualNotFoundException(id_)
return self._individualIdMap[id_] |
Returns a ReadGroupSet with the specified name or raises a ReadGroupSetNameNotFoundException if it does not exist. | def getReadGroupSetByName(self, name):
"""
Returns a ReadGroupSet with the specified name, or raises a
ReadGroupSetNameNotFoundException if it does not exist.
"""
if name not in self._readGroupSetNameMap:
raise exceptions.ReadGroupSetNameNotFoundException(name)
... |
Returns the ReadGroupSet with the specified name or raises a ReadGroupSetNotFoundException otherwise. | def getReadGroupSet(self, id_):
"""
Returns the ReadGroupSet with the specified name, or raises
a ReadGroupSetNotFoundException otherwise.
"""
if id_ not in self._readGroupSetIdMap:
raise exceptions.ReadGroupNotFoundException(id_)
return self._readGroupSetIdMa... |
Returns the RnaQuantification set with the specified name or raises an exception otherwise. | def getRnaQuantificationSetByName(self, name):
"""
Returns the RnaQuantification set with the specified name, or raises
an exception otherwise.
"""
if name not in self._rnaQuantificationSetNameMap:
raise exceptions.RnaQuantificationSetNameNotFoundException(name)
... |
Returns the RnaQuantification set with the specified name or raises a RnaQuantificationSetNotFoundException otherwise. | def getRnaQuantificationSet(self, id_):
"""
Returns the RnaQuantification set with the specified name, or raises
a RnaQuantificationSetNotFoundException otherwise.
"""
if id_ not in self._rnaQuantificationSetIdMap:
raise exceptions.RnaQuantificationSetNotFoundExceptio... |
Parses the ( probably ) intended values out of the specified BAM header dictionary which is incompletely parsed by pysam. This is caused by some tools incorrectly using spaces instead of tabs as a seperator. | def parseMalformedBamHeader(headerDict):
"""
Parses the (probably) intended values out of the specified
BAM header dictionary, which is incompletely parsed by pysam.
This is caused by some tools incorrectly using spaces instead
of tabs as a seperator.
"""
headerString = " ".join(
"{}... |
Returns an iterator over the specified reads | def _getReadAlignments(
self, reference, start, end, readGroupSet, readGroup):
"""
Returns an iterator over the specified reads
"""
# TODO If reference is None, return against all references,
# including unmapped reads.
samFile = self.getFileHandle(self._dataU... |
Convert a pysam ReadAlignment to a GA4GH ReadAlignment | def convertReadAlignment(self, read, readGroupSet, readGroupId):
"""
Convert a pysam ReadAlignment to a GA4GH ReadAlignment
"""
samFile = self.getFileHandle(self._dataUrl)
# TODO fill out remaining fields
# TODO refine in tandem with code in converters module
ret ... |
Adds the specified ReadGroup to this ReadGroupSet. | def addReadGroup(self, readGroup):
"""
Adds the specified ReadGroup to this ReadGroupSet.
"""
id_ = readGroup.getId()
self._readGroupIdMap[id_] = readGroup
self._readGroupIds.append(id_) |
Returns the ReadGroup with the specified id if it exists in this ReadGroupSet or raises a ReadGroupNotFoundException otherwise. | def getReadGroup(self, id_):
"""
Returns the ReadGroup with the specified id if it exists in this
ReadGroupSet, or raises a ReadGroupNotFoundException otherwise.
"""
if id_ not in self._readGroupIdMap:
raise exceptions.ReadGroupNotFoundException(id_)
return se... |
Returns the GA4GH protocol representation of this ReadGroupSet. | def toProtocolElement(self):
"""
Returns the GA4GH protocol representation of this ReadGroupSet.
"""
readGroupSet = protocol.ReadGroupSet()
readGroupSet.id = self.getId()
readGroupSet.read_groups.extend(
[readGroup.toProtocolElement()
for readGrou... |
Returns a string ID suitable for use in the specified GA ReadAlignment object in this ReadGroupSet. | def getReadAlignmentId(self, gaAlignment):
"""
Returns a string ID suitable for use in the specified GA
ReadAlignment object in this ReadGroupSet.
"""
compoundId = datamodel.ReadAlignmentCompoundId(
self.getCompoundId(), gaAlignment.fragment_name)
return str(c... |
Returns the GA4GH protocol representation of this read group set s ReadStats. | def getStats(self):
"""
Returns the GA4GH protocol representation of this read group set's
ReadStats.
"""
stats = protocol.ReadStats()
stats.aligned_read_count = self._numAlignedReads
stats.unaligned_read_count = self._numUnalignedReads
return stats |
Returns an iterator over the specified reads | def getReadAlignments(self, reference, start=None, end=None):
"""
Returns an iterator over the specified reads
"""
return self._getReadAlignments(reference, start, end, self, None) |
Populates the instance variables of this ReadGroupSet from the specified database row. | def populateFromRow(self, readGroupSetRecord):
"""
Populates the instance variables of this ReadGroupSet from the
specified database row.
"""
self._dataUrl = readGroupSetRecord.dataurl
self._indexFile = readGroupSetRecord.indexfile
self._programs = []
for ... |
Populates the instance variables of this ReadGroupSet from the specified dataUrl and indexFile. If indexFile is not specified guess usual form. | def populateFromFile(self, dataUrl, indexFile=None):
"""
Populates the instance variables of this ReadGroupSet from the
specified dataUrl and indexFile. If indexFile is not specified
guess usual form.
"""
self._dataUrl = dataUrl
self._indexFile = indexFile
... |
Returns the GA4GH protocol representation of this ReadGroup. | def toProtocolElement(self):
"""
Returns the GA4GH protocol representation of this ReadGroup.
"""
# TODO this is very incomplete, but we don't have the
# implementation to fill out the rest of the fields currently
readGroup = protocol.ReadGroup()
readGroup.id = se... |
Returns the GA4GH protocol representation of this read group s ReadStats. | def getStats(self):
"""
Returns the GA4GH protocol representation of this read group's
ReadStats.
"""
stats = protocol.ReadStats()
stats.aligned_read_count = self.getNumAlignedReads()
stats.unaligned_read_count = self.getNumUnalignedReads()
# TODO base_cou... |
Returns the GA4GH protocol representation of this read group s Experiment. | def getExperiment(self):
"""
Returns the GA4GH protocol representation of this read group's
Experiment.
"""
experiment = protocol.Experiment()
experiment.id = self.getExperimentId()
experiment.instrument_model = pb.string(self.getInstrumentModel())
experim... |
Populate the instance variables using the specified SAM header. | def populateFromHeader(self, readGroupHeader):
"""
Populate the instance variables using the specified SAM header.
"""
self._sampleName = readGroupHeader.get('SM', None)
self._description = readGroupHeader.get('DS', None)
if 'PI' in readGroupHeader:
self._pred... |
Populate the instance variables using the specified DB row. | def populateFromRow(self, readGroupRecord):
"""
Populate the instance variables using the specified DB row.
"""
self._sampleName = readGroupRecord.samplename
self._biosampleId = readGroupRecord.biosampleid
self._description = readGroupRecord.description
self._pred... |
Returns the filename of the specified path without its extensions. This is usually how we derive the default name for a given object. | def getNameFromPath(filePath):
"""
Returns the filename of the specified path without its extensions.
This is usually how we derive the default name for a given object.
"""
if len(filePath) == 0:
raise ValueError("Cannot have empty path for name")
fileName = os.path.split(os.path.normpat... |
Exits the repo manager with error status. | def repoExitError(message):
"""
Exits the repo manager with error status.
"""
wrapper = textwrap.TextWrapper(
break_on_hyphens=False, break_long_words=False)
formatted = wrapper.fill("{}: error: {}".format(sys.argv[0], message))
sys.exit(formatted) |
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