Beispiel #1
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 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))
Beispiel #2
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 def dump(self, fh):
     prRowv(fh, "srcQCds: ", self.srcAln.qSeq)
     prRowv(fh, "srcTCds: ", self.srcAln.tSeq)
     self.destAln.dump(fh)
Beispiel #3
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 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
Beispiel #5
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 def dump(self, fh):
     prRowv(fh, "srcQCds: ", self.srcAln.qSeq)
     prRowv(fh, "srcTCds: ", self.srcAln.tSeq)
     self.destAln.dump(fh)
Beispiel #6
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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
Beispiel #7
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 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))
Beispiel #8
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 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))