def _getBlockColumns(self):
relStarts = []
sizes = []
for blk in self.blocks:
relStarts.append(str(blk.start - self.chromStart))
sizes.append(str(len(blk)))
return [intArrayJoin(sizes), intArrayJoin(relStarts)]
def toRow(self):
"convert PSL to array of strings"
row = [
str(self.match),
str(self.misMatch),
str(self.repMatch),
str(self.nCount),
str(self.qNumInsert),
str(self.qBaseInsert),
str(self.tNumInsert),
str(self.tBaseInsert), self.strand, self.qName,
str(self.qSize),
str(self.qStart),
str(self.qEnd), self.tName,
str(self.tSize),
str(self.tStart),
str(self.tEnd),
str(self.blockCount),
intArrayJoin([b.size for b in self.blocks]),
intArrayJoin([b.qStart for b in self.blocks]),
intArrayJoin([b.tStart for b in self.blocks])
]
if self.blocks[0].qSeq is not None:
row.append(strArrayJoin([b.qSeq for b in self.blocks]))
row.append(strArrayJoin([b.tSeq for b in self.blocks]))
return row
def __str__(self):
"return psl as a tab-separated string"
row = [str(self.match),
str(self.misMatch),
str(self.repMatch),
str(self.nCount),
str(self.qNumInsert),
str(self.qBaseInsert),
str(self.tNumInsert),
str(self.tBaseInsert),
self.strand,
self.qName,
str(self.qSize),
str(self.qStart),
str(self.qEnd),
self.tName,
str(self.tSize),
str(self.tStart),
str(self.tEnd),
str(self.blockCount),
intArrayJoin([b.size for b in self.blocks]),
intArrayJoin([b.qStart for b in self.blocks]),
intArrayJoin([b.tStart for b in self.blocks])]
if self.blocks[0].qSeq is not None:
row.append(strArrayJoin([b.qSeq for b in self.blocks]))
row.append(strArrayJoin([b.tSeq for b in self.blocks]))
return str.join("\t", row)
def getRow(self):
row = [
self.name, self.chrom, self.strand,
str(self.txStart),
str(self.txEnd),
str(self.cdsStart),
str(self.cdsEnd)
]
row.append(str(len(self.exons)))
starts = []
ends = []
for e in self.exons:
starts.append(e.start)
ends.append(e.end)
row.append(intArrayJoin(starts))
row.append(intArrayJoin(ends))
hasExt = (self.score is not None) or (self.name2 is not None) or (
self.cdsStartStat is not None) or self.hasExonFrames
if self.score is not None:
row.append(str(self.score))
elif hasExt:
row.append("0")
if self.name2 is not None:
row.append(self.name2)
elif hasExt:
row.append("")
if self.cdsStartStat is not None:
row.append(str(self.cdsStartStat))
row.append(str(self.cdsEndStat))
elif hasExt:
row.append(str(CdsStat.unknown))
row.append(str(CdsStat.unknown))
if self.hasExonFrames or hasExt:
frames = []
if self.hasExonFrames:
for e in self.exons:
frames.append(e.frame)
else:
for e in self.exons:
frames.append(-1)
row.append(intArrayJoin(frames))
return row
def getRow(self):
row = [self.chrom, str(self.chromStart), str(self.chromEnd), self.name]
if self.numCols > 4:
row.append(str(self.score));
if self.numCols > 5:
row.append(self.strand)
if self.numCols > 7:
row.append(str(self.thickStart))
row.append(str(self.thickEnd))
if self.numCols > 8:
row.append(str(self.itemRgb))
if self.numCols > 11:
row.append(str(len(self.blocks)))
relStarts = []
sizes = []
for blk in self.blocks:
relStarts.append(str(blk.relStart))
sizes.append(str(blk.size))
row.append(intArrayJoin(relStarts))
row.append(intArrayJoin(sizes))
return row
def getRow(self):
row = [self.name, self.chrom, self.strand, str(self.txStart), str(self.txEnd), str(self.cdsStart), str(self.cdsEnd)]
row.append(str(len(self.exons)))
starts = []
ends = []
for e in self.exons:
starts.append(e.start)
ends.append(e.end)
row.append(intArrayJoin(starts))
row.append(intArrayJoin(ends))
hasExt = (self.score is not None) or (self.name2 is not None) or (self.cdsStartStat is not None) or self.hasExonFrames
if self.score is not None:
row.append(str(self.score))
elif hasExt:
row.append("0");
if self.name2 is not None:
row.append(self.name2)
elif hasExt:
row.append("");
if self.cdsStartStat is not None:
row.append(str(self.cdsStartStat))
row.append(str(self.cdsEndStat))
elif hasExt:
row.append(str(CdsStat.unknown))
row.append(str(CdsStat.unknown))
if self.hasExonFrames or hasExt:
frames = []
if self.hasExonFrames:
for e in self.exons:
frames.append(e.frame)
else:
for e in self.exons:
frames.append(-1)
row.append(intArrayJoin(frames))
return row