def __init__(self, id_, dataFile):
super(HtslibReference, self).__init__(id_)
self._fastaFilePath = dataFile
fastaFile = self.openFile(dataFile)
numReferences = len(fastaFile.references)
if numReferences != 1:
raise exceptions.NotExactlyOneReferenceException(
self._id, numReferences)
self._refName = fastaFile.references[0]
# refData = fastaFile.fetch(self._refName)
self._md5checksum = "TODO" # hashlib.md5(refData).hexdigest()
def __init__(self, parentContainer, name, dataFile):
super(HtslibReference, self).__init__(parentContainer, name)
self._fastaFilePath = dataFile
fastaFile = self.openFile(dataFile)
numReferences = len(fastaFile.references)
if numReferences != 1:
raise exceptions.NotExactlyOneReferenceException(
self.getId(), numReferences)
self._refName = fastaFile.references[0]
self._length = fastaFile.lengths[0]
# refData = fastaFile.fetch(self._refName)
self._md5checksum = "TODO" # hashlib.md5(refData).hexdigest()
fastaFile.close()
def __init__(self, parentContainer, localId, dataFile, metadata):
super(HtslibReference, self).__init__(parentContainer, localId)
self._fastaFilePath = dataFile
fastaFile = self.getFileHandle(dataFile)
numReferences = len(fastaFile.references)
if numReferences != 1:
raise exceptions.NotExactlyOneReferenceException(
self._fastaFilePath, numReferences)
if fastaFile.references[0] != localId:
raise exceptions.InconsistentReferenceNameException(
self._fastaFilePath)
self._length = fastaFile.lengths[0]
try:
self._md5checksum = metadata["md5checksum"]
self._sourceUri = metadata["sourceUri"]
self._ncbiTaxonId = metadata["ncbiTaxonId"]
self._isDerived = metadata["isDerived"]
self._sourceDivergence = metadata["sourceDivergence"]
self._sourceAccessions = metadata["sourceAccessions"]
except KeyError as err:
raise exceptions.MissingReferenceMetadata(dataFile, str(err))