def getTransBin(self):
"""
Get bins for transcript coordination conversion
"""
if not hasattr(self, 'TransBin'):
self.TransBin = CoorFunc.binize_Trans(self, bw=100000)
return self.TransBin
def getGeneBin(self):
"""
Get bins for gene coordination conversion
"""
if not hasattr(self, 'GeneBin'):
self.GeneBin = CoorFunc.binize_Gene(self, bw=100000)
return self.GeneBin
def geneCoor2genomeCoor(self, geneID, pos):
"""
geneID -- Gene id
pos -- Gene-based position
Convert gene-based coordinates to genome-based coordinates
Return: [chrID, chrPos, Strand]
"""
return CoorFunc.geneCoor2genomeCoor(self, geneID, pos)
def transCoor2genomeCoor(self, transID, pos):
"""
transID -- Transcript id
pos -- Transcript-based position
Convert transcript-based coordinates to genome-based coordinates
Return [chrID, chrPos, Strand]
"""
return CoorFunc.transCoor2genomeCoor(self, transID, pos)
def transCoor2geneCoor(self, transID, start, end):
"""
transID -- Transcript id
start -- Transcript-based start position
end -- Transcript-based end position
Convert transcript-based coordinates to gene-based coordinates
return [ [chrID, chrStart, chrEnd, geneID, geneStart, geneEnd], ... ]
"""
GeneBin = self.getGeneBin()
return CoorFunc.transCoor2geneCoor(GeneBin, self, transID, Start, End)
def geneCoor2transCoor(self, geneID, start, end):
"""
geneID -- Gene id
start -- Gene-based start position
end -- Gene-based end position
Convert gene-based coordinates to transcript-based coordinates
Return [chrID, chrStart, chrEnd, transID, transStart, transEnd], ... ]
"""
TransBin = self.getTransBin()
return CoorFunc.geneCoor2transCoor(TransBin, self, geneID, start, end)
def genomeCoor2geneCoor(self, chrID, start, end, strand):
"""
chrID -- Chromosome id
start -- Chromosome-based start position
end -- Chromosome-based end position
strand -- Chromosome strand
Convert genome-based coordinates to gene-based coordinates
Return [ [chrID, chrStart, chrEnd, geneID, geneStart, geneEnd], ... ]
"""
GeneBin = self.getGeneBin()
return CoorFunc.genomeCoor2geneCoor(GeneBin, self, chrID, start, end, strand)
def genomeCoor2transCoor(self, chrID, start, end, strand):
"""
chrID -- Chromosome id
start -- Chromosome-based start position
end -- Chromosome-based end position
strand -- Chromosome strand
Convert genome-based coordinates to transcript-based coordinates
Return [ [chrID, chrStart, chrEnd, transID, transStart, transEnd], ... ]
"""
TransBin = self.getTransBin()
return CoorFunc.genomeCoor2transCoor(TransBin, self, chrID, start, end, strand)
def geneCoor2genomeCoor(self, GeneID, Pos):
return CoorFunc.geneCoor2genomeCoor(self, GeneID, Pos)
def genomeCoor2geneCoor(self, Chr, Start, End, Strand):
GeneBin = self.getGeneBin()
return CoorFunc.genomeCoor2geneCoor(GeneBin, self, Chr, Start, End, Strand)
def genomeCoor2transCoor(self, Chr, Start, End, Strand):
TransBin = self.getTransBin()
return CoorFunc.genomeCoor2transCoor(TransBin, self, Chr, Start, End, Strand)
def transCoor2geneCoor(self, TransID, Start, End):
GeneBin = self.getGeneBin()
return CoorFunc.transCoor2geneCoor(GeneBin, self, TransID, Start, End)
def geneCoor2transCoor(self, GeneID, Start, End):
TransBin = self.getTransBin()
return CoorFunc.geneCoor2transCoor(TransBin, self, GeneID, Start, End)
def geneCoor2transCoor(self, GeneID, Start, End):
TransBin = self.getTransBin()
return CoorFunc.geneCoor2transCoor(TransBin, self, GeneID, Start, End)
def getTransBin(self):
if hasattr(self, 'TransBin'):
pass
else:
self.TransBin = CoorFunc.binize_Trans(self, bw=100000)
return self.TransBin
def geneCoor2genomeCoor(self, GeneID, Pos):
return CoorFunc.geneCoor2genomeCoor(self, GeneID, Pos)
def getTransBin(self):
if hasattr(self, 'TransBin'):
pass
else:
self.TransBin = CoorFunc.binize_Trans(self, bw=100000)
return self.TransBin
def getGeneBin(self):
if hasattr(self, 'GeneBin'):
pass
else:
self.GeneBin = CoorFunc.binize_Gene(self, bw=100000)
return self.GeneBin
def transCoor2geneCoor(self, TransID, Start, End):
GeneBin = self.getGeneBin()
return CoorFunc.transCoor2geneCoor(GeneBin, self, TransID, Start, End)
def transCoor2genomeCoor(self, TransID, Pos):
return CoorFunc.transCoor2genomeCoor(self, TransID, Pos)
def genomeCoor2geneCoor(self, Chr, Start, End, Strand):
GeneBin = self.getGeneBin()
return CoorFunc.genomeCoor2geneCoor(GeneBin, self, Chr, Start, End,
Strand)
def transCoor2genomeCoor(self, TransID, Pos):
return CoorFunc.transCoor2genomeCoor(self, TransID, Pos)
def genomeCoor2transCoor(self, Chr, Start, End, Strand):
TransBin = self.getTransBin()
return CoorFunc.genomeCoor2transCoor(TransBin, self, Chr, Start, End,
Strand)
def getGeneBin(self):
if hasattr(self, 'GeneBin'):
pass
else:
self.GeneBin = CoorFunc.binize_Gene(self, bw=100000)
return self.GeneBin
