def __init__(self, seed=0, numCalls=1, variantDensity=0.5):
self._randomSeed = seed
self._numCalls = numCalls
self._variantDensity = variantDensity
now = protocol.convertDatetime(datetime.datetime.now())
self._created = now
self._updated = now
def __init__(self, parentContainer, localId):
super(AbstractReadGroup, self).__init__(parentContainer, localId)
datetimeNow = datetime.datetime.now()
now = protocol.convertDatetime(datetimeNow)
self._iso8601 = datetimeNow.strftime("%Y-%m-%dT%H:%M:%SZ")
self._creationTime = now
self._updateTime = now
def __init__(self, parentContainer, localId):
super(AbstractReadGroup, self).__init__(parentContainer, localId)
datetimeNow = datetime.datetime.now()
now = protocol.convertDatetime(datetimeNow)
self._iso8601 = datetimeNow.strftime("%Y-%m-%dT%H:%M:%SZ")
self._creationTime = now
self._updateTime = now
def __init__(self, randomSeed, numCalls, variantDensity, variantSetId):
super(SimulatedVariantSet, self).__init__(variantSetId)
self._randomSeed = randomSeed
self._numCalls = numCalls
for j in range(numCalls):
self.addCallSet("simCallSet_{}".format(j))
self._variantDensity = variantDensity
now = protocol.convertDatetime(datetime.datetime.now())
self._creationTime = now
self._updatedTime = now
def __init__(self, randomSeed, numCalls, variantDensity, variantSetId):
super(SimulatedVariantSet, self).__init__(variantSetId)
self._randomSeed = randomSeed
self._numCalls = numCalls
for j in range(numCalls):
self.addCallSet("simCallSet_{}".format(j))
self._variantDensity = variantDensity
now = protocol.convertDatetime(datetime.datetime.now())
self._creationTime = now
self._updatedTime = now
def __init__(self, variantSetId, vcfPath):
self._variantSetId = variantSetId
self._created = protocol.convertDatetime(datetime.datetime.now())
self._chromTabixFileMap = {}
for vcfFile in glob.glob(os.path.join(vcfPath, "*.vcf.gz")):
tabixFile = pysam.Tabixfile(vcfFile)
for chrom in tabixFile.contigs:
if chrom in self._chromTabixFileMap:
raise Exception("cannot have overlapping VCF files.")
self._chromTabixFileMap[chrom] = tabixFile
def __init__(self, variantSetId, vcfPath):
self._variantSetId = variantSetId
self._created = protocol.convertDatetime(datetime.datetime.now())
self._chromTabixFileMap = {}
for vcfFile in glob.glob(os.path.join(vcfPath, "*.vcf.gz")):
tabixFile = pysam.Tabixfile(vcfFile)
for chrom in tabixFile.contigs:
if chrom in self._chromTabixFileMap:
raise Exception("cannot have overlapping VCF files.")
self._chromTabixFileMap[chrom] = tabixFile
def __init__(
self, parentContainer, referenceSet, localId, randomSeed=1,
numCalls=1, variantDensity=1):
super(SimulatedVariantSet, self).__init__(parentContainer, localId)
self._referenceSet = referenceSet
self._randomSeed = randomSeed
self._numCalls = numCalls
for j in range(numCalls):
self.addCallSetFromName("simCallSet_{}".format(j))
self._variantDensity = variantDensity
now = protocol.convertDatetime(datetime.datetime.now())
self._creationTime = now
self._updatedTime = now
def __init__(self, variantSetId, vcfPath):
self._variantSetId = variantSetId
self._created = protocol.convertDatetime(datetime.datetime.now())
# Read in Tabix-index VCF files from vcfPath is a path.
# self.tb chrom -> vcf dict
self._tabixMap = {}
for fn in glob.glob(os.path.join(vcfPath, "*.vcf.gz")):
tabixfile = pysam.Tabixfile(fn)
for chrom in tabixfile.contigs:
if chrom in self._tabixMap:
raise Exception("cannot have overlapping VCF files.")
self._tabixMap[chrom] = tabixfile
def __init__(self, id_):
self._id = id_
now = protocol.convertDatetime(datetime.datetime.now())
self._creationTime = now
self._updateTime = now
def __init__(self, parentContainer, localId):
super(AbstractReadGroup, self).__init__(parentContainer, localId)
now = protocol.convertDatetime(datetime.datetime.now())
self._creationTime = now
self._updateTime = now
