def writeSets(self, fh, subsetNameSeparator=" ", setNameFormatter=str):
"write TSV of subsets and ids to an open file"
fileOps.prRowv(fh, "subset", "ids")
for subset in self.subsets.getSubsets():
fileOps.prRowv(
fh,
self.formatSubsetName(subset, subsetNameSeparator,
setNameFormatter),
self.getSubsetCounts(subset))
def dump(self, fh):
prRowv(fh, "srcQCds: ", self.srcAln.qSeq)
prRowv(fh, "srcTCds: ", self.srcAln.tSeq)
self.destAln.dump(fh)
def writeSets(self, fh, subsetNameSeparator=" "):
"write TSV of subsets and ids to an open file"
fileOps.prRowv(fh, "subset", "ids")
for subset in self.subsets.getSubsets():
fileOps.prRowv(fh, subsetNameSeparator.join(subset),
self.getSubsetCounts(subset))
def makeChromBedTmp(target, hal, chrom, chromSize):
"create a BED file in local tmp covering one chromosome"
bedFile = getGlobalTempPath(target, chrom, "bed")
with open(bedFile, "w") as fh:
fileOps.prRowv(fh, chrom, 0, chromSize)
return bedFile
def dump(self, fh):
prRowv(fh, "srcQCds: ", self.srcAln.qSeq)
prRowv(fh, "srcTCds: ", self.srcAln.tSeq)
self.destAln.dump(fh)
def makeChromBedTmp(target, hal, chrom, chromSize):
"create a BED file in local tmp covering one chromosome"
bedFile = getLocalTempPath(target, chrom, "bed")
with open(bedFile, "w") as fh:
fileOps.prRowv(fh, chrom, 0, chromSize)
return bedFile
def writeSets(self, fh, subsetNameSeparator=" ", setNameFormatter=str):
"write TSV of subsets and ids to an open file"
fileOps.prRowv(fh, "subset", "ids")
for subset in self.subsets.getSubsets():
fileOps.prRowv(fh, self.formatSubsetName(subset, subsetNameSeparator, setNameFormatter), self.getSubsetCounts(subset))
def writeSets(self, fh, subsetNameSeparator=" "):
"write TSV of subsets and ids to an open file"
fileOps.prRowv(fh, "subset", "ids")
for subset in self.subsets.getSubsets():
fileOps.prRowv(fh, subsetNameSeparator.join(subset), self.getSubsetCounts(subset))