class MapTester(object):
"test object that collects results"
def __init__(self):
self.mappings = []
self.mapper = PslMap(self)
def mapBlock(self, psl, blk, qRngStart, qRngEnd, tRngStart, tRngEnd):
self.mappings.append(("blk", psl.qName, blk.iBlk, qRngStart, qRngEnd,
tRngStart, tRngEnd))
@staticmethod
def __iBlkOrNone(blk):
return blk.iBlk if blk != None else None
def mapGap(self, psl, prevBlk, nextBlk, qRngStart, qRngEnd, tRngStart,
tRngEnd):
self.mappings.append(
("gap", psl.qName, MapTester.__iBlkOrNone(prevBlk),
MapTester.__iBlkOrNone(nextBlk), qRngStart, qRngEnd, tRngStart,
tRngEnd))
def __joinMappings(self):
"join mappings into a tuple for testing and clear for next test"
m = tuple(self.mappings)
self.mappings = []
return m
def targetToQueryMap(self, psl, tRngStart, tRngEnd):
self.mapper.targetToQueryMap(psl, tRngStart, tRngEnd)
return self.__joinMappings()
def queryToTargetMap(self, psl, qRngStart, qRngEnd):
self.mapper.queryToTargetMap(psl, qRngStart, qRngEnd)
return self.__joinMappings()
class MapTester(object):
"test object that collects results"
def __init__(self):
self.mappings = []
self.mapper = PslMap(self)
def mapBlock(self, psl, blk, qRngStart, qRngEnd, tRngStart, tRngEnd):
self.mappings.append(("blk", psl.qName, blk.iBlk, qRngStart, qRngEnd, tRngStart, tRngEnd))
@staticmethod
def __iBlkOrNone(blk):
return blk.iBlk if blk != None else None
def mapGap(self, psl, prevBlk, nextBlk, qRngStart, qRngEnd, tRngStart, tRngEnd):
self.mappings.append(("gap", psl.qName, MapTester.__iBlkOrNone(prevBlk), MapTester.__iBlkOrNone(nextBlk), qRngStart, qRngEnd, tRngStart, tRngEnd))
def __joinMappings(self):
"join mappings into a tuple for testing and clear for next test"
m = tuple(self.mappings)
self.mappings = []
return m
def targetToQueryMap(self, psl, tRngStart, tRngEnd):
self.mapper.targetToQueryMap(psl, tRngStart, tRngEnd)
return self.__joinMappings()
def queryToTargetMap(self, psl, qRngStart, qRngEnd):
self.mapper.queryToTargetMap(psl, qRngStart, qRngEnd)
return self.__joinMappings()
class PslMapBedMaker(object):
" object that collects blocks from pslMap and creates a bed in the end"
__slots__ = ("chrom", "chromStart", "chromEnd", "name", "score", "strand", "thickStart", "thickEnd", "itemRgb", "blockCount", "blockSizes", "blockStarts", "mapper")
def __init__(self):
self.mapper = PslMap(self)
self.clear()
def clear(self):
" reset for next mapping "
self.chrom = None
self.chromStart = None
self.chromEnd = None
self.name = None
self.score = 0
self.strand = None
self.thickStart = None
self.thickEnd = None
self.itemRgb = "0"
self.blockCount = 0
self.blockSizes = []
self.blockStarts = []
def mapBlock(self, psl, blk, qRngStart, qRngEnd, tRngStart, tRngEnd):
" callback for pslMap "
self.chromEnd = tRngEnd
self.blockCount += 1
self.blockSizes.append(tRngEnd-tRngStart)
self.blockStarts.append(tRngStart)
def mapGap(self, psl, prevBlk, nextBlk, qRngStart, qRngEnd, tRngStart, tRngEnd):
" call back pslMap "
pass
def mapQuery(self, psl, qRngStart, qRngEnd):
" call this method to get qRngStart-qRngEnd mapped through the psl as a bed "
self.mapper.queryToTargetMap(psl, qRngStart, qRngEnd)
self.chrom = psl.tName
self.name = psl.qName
self.strand = psl.strand
return self._toBed()
def _toBed(self):
" return bed feature as row "
if len(self.blockStarts)==0:
return None
self.chromStart = self.blockStarts[0]
self.thickStart = self.chromStart
self.thickEnd = self.chromEnd
self.score = sum(self.blockSizes)
blockSizeStr = ",".join([str(x) for x in self.blockSizes])
chromStart = self.chromStart
blockStartStr = ",".join([str(x-chromStart) for x in self.blockStarts])
bedRow = [self.chrom, self.chromStart, self.chromEnd, self.name, \
self.score, self.strand, self.thickStart, self.thickEnd, \
self.itemRgb, len(self.blockSizes), blockSizeStr, blockStartStr]
bedRow = [str(x) for x in bedRow]
return bedRow
def __init__(self):
self.mappings = []
self.mapper = PslMap(self)
def __init__(self):
self.mapper = PslMap(self)
self.clear()
def __init__(self):
self.mappings = []
self.mapper = PslMap(self)
def __init__(self):
self.mapper = PslMap(self)
self.clear()
class PslMapBedMaker(object):
" object that collects blocks from pslMap and creates a bed in the end"
__slots__ = ("chrom", "chromStart", "chromEnd", "name", "score", "strand",
"thickStart", "thickEnd", "itemRgb", "blockCount",
"blockSizes", "blockStarts", "mapper")
def __init__(self):
self.mapper = PslMap(self)
self.clear()
def clear(self):
" reset for next mapping "
self.chrom = None
self.chromStart = None
self.chromEnd = None
self.name = None
self.score = 0
self.strand = None
self.thickStart = None
self.thickEnd = None
self.itemRgb = "0"
self.blockCount = 0
self.blockSizes = []
self.blockStarts = []
def mapBlock(self, psl, blk, qRngStart, qRngEnd, tRngStart, tRngEnd):
" callback for pslMap "
self.chromEnd = tRngEnd
self.blockCount += 1
self.blockSizes.append(tRngEnd - tRngStart)
self.blockStarts.append(tRngStart)
def mapGap(self, psl, prevBlk, nextBlk, qRngStart, qRngEnd, tRngStart,
tRngEnd):
" call back pslMap "
pass
def mapQuery(self, psl, qRngStart, qRngEnd):
" call this method to get qRngStart-qRngEnd mapped through the psl as a bed "
self.mapper.queryToTargetMap(psl, qRngStart, qRngEnd)
self.chrom = psl.tName
self.name = psl.qName
self.strand = psl.strand
return self._toBed()
def _toBed(self):
" return bed feature as row "
if len(self.blockStarts) == 0:
return None
self.chromStart = self.blockStarts[0]
self.thickStart = self.chromStart
self.thickEnd = self.chromEnd
self.score = sum(self.blockSizes)
blockSizeStr = ",".join([str(x) for x in self.blockSizes])
chromStart = self.chromStart
blockStartStr = ",".join(
[str(x - chromStart) for x in self.blockStarts])
bedRow = [self.chrom, self.chromStart, self.chromEnd, self.name, \
self.score, self.strand, self.thickStart, self.thickEnd, \
self.itemRgb, len(self.blockSizes), blockSizeStr, blockStartStr]
bedRow = [str(x) for x in bedRow]
return bedRow
class PslMapBedMaker(object):
" object that collects blocks from pslMap and creates a bed in the end"
__slots__ = ("chrom", "chromStart", "chromEnd", "name", "score", "strand",
"thickStart", "thickEnd", "itemRgb", "blockCount", "blockSizes",
"blockStarts", "mapper", "chromSize")
def __init__(self):
self.mapper = PslMap(self)
self.clear()
def clear(self):
" reset for next mapping "
self.chrom = None
self.chromStart = None
self.chromEnd = None
self.name = None
self.score = 0
self.strand = None
self.thickStart = None
self.thickEnd = None
self.itemRgb = "0"
self.blockCount = 0
self.blockSizes = []
self.blockStarts = []
self.chromSize = 0
def mapBlock(self, psl, blk, qRngStart, qRngEnd, tRngStart, tRngEnd):
" callback for pslMap "
logging.debug("Got blk: %d-%d, len %d" % (tRngStart, tRngEnd, tRngEnd - tRngStart))
self.blockCount += 1
self.blockSizes.append(tRngEnd - tRngStart)
self.blockStarts.append(tRngStart)
def mapGap(self, psl, prevBlk, nextBlk, qRngStart, qRngEnd, tRngStart, tRngEnd):
" call back pslMap "
pass
def mapQuery(self, psl, qRngStart, qRngEnd):
" call this method to get qRngStart-qRngEnd mapped through the psl as a bed "
# must be reversed somewhere upstream
assert(psl.strand[0] == "+")
# if psl.strand=="-":
# the +1 here is weird but seems to be true
# end = mapPsl.qSize - rnaVar.start + 1
# start = mapPsl.qSize - rnaVar.end + 1
# logging.debug("Inversing map coordinates to %d/%d" % (start, end))
# logging.debug("Reversing map psl")
# psl = psl.reverseComplement()
self.chromSize = psl.tSize
self.mapper.queryToTargetMap(psl, qRngStart, qRngEnd)
self.chrom = psl.tName
self.name = psl.qName
self.strand = psl.strand
def getBed(self, name=None):
" return bed feature as a 12-tuple, default name is query name "
if len(self.blockStarts) == 0:
return None
if self.strand[-1] == "-":
logging.debug("Reversing coords")
self.blockStarts.reverse()
self.blockSizes.reverse()
# pslToBed.c:
# for (i=0; i<blockCount; ++i)
# chromStarts[i] = chromSize - chromStarts[i] - bed->blockSizes[i];
chromSize = self.chromSize
chromStarts = self.blockStarts
blockSizes = self.blockSizes
for i in range(0, len(self.blockStarts)):
self.blockStarts[i] = chromSize - chromStarts[i] - blockSizes[i]
self.chromStart = self.blockStarts[0]
self.chromEnd = self.blockStarts[-1] + self.blockSizes[-1]
self.thickStart = self.chromStart
self.thickEnd = self.chromEnd
self.score = sum(self.blockSizes)
blockSizeStr = ",".join([str(x) for x in self.blockSizes])
chromStart = self.chromStart
blockStartStr = ",".join([str(x - chromStart) for x in self.blockStarts])
# default bed name is query name
if not name:
name = self.name
bedRow = [self.chrom, self.chromStart, self.chromEnd, name, \
self.score, self.strand[-1], self.thickStart, self.thickEnd, \
self.itemRgb, len(self.blockSizes), blockSizeStr, blockStartStr]
bedRow = [str(x) for x in bedRow]
return bedRow
class PslMapBedMaker(object):
" object that collects blocks from pslMap and creates a bed in the end"
__slots__ = ("chrom", "chromStart", "chromEnd", "name", "score", "strand",
"thickStart", "thickEnd", "itemRgb", "blockCount",
"blockSizes", "blockStarts", "mapper", "chromSize")
def __init__(self):
self.mapper = PslMap(self)
self.clear()
def clear(self):
" reset for next mapping "
self.chrom = None
self.chromStart = None
self.chromEnd = None
self.name = None
self.score = 0
self.strand = None
self.thickStart = None
self.thickEnd = None
self.itemRgb = "0"
self.blockCount = 0
self.blockSizes = []
self.blockStarts = []
self.chromSize = 0
def mapBlock(self, psl, blk, qRngStart, qRngEnd, tRngStart, tRngEnd):
" callback for pslMap "
logging.debug("Got blk: %d-%d, len %d" %
(tRngStart, tRngEnd, tRngEnd - tRngStart))
self.blockCount += 1
self.blockSizes.append(tRngEnd - tRngStart)
self.blockStarts.append(tRngStart)
def mapGap(self, psl, prevBlk, nextBlk, qRngStart, qRngEnd, tRngStart,
tRngEnd):
" call back pslMap "
pass
def mapQuery(self, psl, qRngStart, qRngEnd):
" call this method to get qRngStart-qRngEnd mapped through the psl as a bed "
# must be reversed somewhere upstream
assert (psl.strand[0] == "+")
# if psl.strand=="-":
# the +1 here is weird but seems to be true
# end = mapPsl.qSize - rnaVar.start + 1
# start = mapPsl.qSize - rnaVar.end + 1
# logging.debug("Inversing map coordinates to %d/%d" % (start, end))
# logging.debug("Reversing map psl")
# psl = psl.reverseComplement()
self.chromSize = psl.tSize
self.mapper.queryToTargetMap(psl, qRngStart, qRngEnd)
self.chrom = psl.tName
self.name = psl.qName
self.strand = psl.strand
def getBed(self, name=None):
" return bed feature as a 12-tuple, default name is query name "
if len(self.blockStarts) == 0:
return None
if self.strand[-1] == "-":
logging.debug("Reversing coords")
self.blockStarts.reverse()
self.blockSizes.reverse()
# pslToBed.c:
# for (i=0; i<blockCount; ++i)
# chromStarts[i] = chromSize - chromStarts[i] - bed->blockSizes[i];
chromSize = self.chromSize
chromStarts = self.blockStarts
blockSizes = self.blockSizes
for i in range(0, len(self.blockStarts)):
self.blockStarts[
i] = chromSize - chromStarts[i] - blockSizes[i]
self.chromStart = self.blockStarts[0]
self.chromEnd = self.blockStarts[-1] + self.blockSizes[-1]
self.thickStart = self.chromStart
self.thickEnd = self.chromEnd
self.score = sum(self.blockSizes)
blockSizeStr = ",".join([str(x) for x in self.blockSizes])
chromStart = self.chromStart
blockStartStr = ",".join(
[str(x - chromStart) for x in self.blockStarts])
# default bed name is query name
if not name:
name = self.name
bedRow = [self.chrom, self.chromStart, self.chromEnd, name, \
self.score, self.strand[-1], self.thickStart, self.thickEnd, \
self.itemRgb, len(self.blockSizes), blockSizeStr, blockStartStr]
bedRow = [str(x) for x in bedRow]
return bedRow
