def getSteps(halPath, maxBlock, scaleFactor, minLod0, cutOffFrac, minSeqFrac,
minCovFrac):
statsTable = getHalStats(halPath)
sequenceStatsTable = dict()
for row in statsTable:
sequenceStatsTable[row[0]] = getHalSequenceStats(halPath, row[0])
maxLen = getMaxGenomeLength(statsTable)
assert maxLen > 0
maxStep = math.ceil(float(maxLen) / float(maxBlock))
lodBaseStep = math.ceil(float(minLod0) / float(maxBlock))
baseStep = max(lodBaseStep, getMinAvgBlockSize(statsTable))
outList = []
step = baseStep
# last LOD is just "max" token which tells browser it and anything
# beyond is disabled.
lastIsMax = False
while True:
outList.append(step)
if step > maxStep * cutOffFrac:
break
minCoverage = 1.0
if minSeqFrac > 0. and minCovFrac > 0.:
minCoverageFrac = getMinCoverageFrac(sequenceStatsTable,
math.floor(step * minSeqFrac))
if minCoverageFrac < minCovFrac:
lastIsMax = True
break
step *= scaleFactor
return [int(x) for x in outList], lastIsMax
def partitionByGenomeCoords(options, refGenome):
"we are slicing the gnome coordinates directly"
sliceCmds = []
sliceOpts = []
seqOpts = copy.deepcopy(options)
assert seqOpts.splitBySequence is False
refSequenceStats = getHalSequenceStats(options.halFile, refGenome)
# auto compute slice size from numprocs
if seqOpts.sliceSize is None and seqOpts.numProc > 1:
if seqOpts.length is not None and seqOpts.length > 0:
refLen = seqOpts.length
else:
# use median of sequence lengths
refLen = int(statistics.median([r[1] for r in refSequenceStats]))
seqOpts.sliceSize = math.ceil(math.ceil(refLen / seqOpts.numProc))
for refSeqStat in refSequenceStats:
seqOpts.refSequence = refSeqStat[0]
for sStart, sLen, sIdx in computeSlices(seqOpts, refSeqStat[1]):
seqOpts.start = sStart
seqOpts.length = sLen
seqOpts.sliceNumber = sIdx
sliceCmds.append(getHal2MafCmd(seqOpts))
sliceOpts.append(copy.deepcopy(seqOpts))
return sliceCmds, sliceOpts
def writeChromSizes(options):
if options.chromSizes is not None:
csFile = open(options.chromSizes, "w")
refSequenceStats = getHalSequenceStats(options.halFile,
options.refGenome)
assert refSequenceStats is not None
for seqStat in refSequenceStats:
csFile.write("%s\t%s\n" % (seqStat[0], seqStat[1]))
csFile.close()
def writeChromSizes(options):
if options.chromSizes is not None:
csFile = open(options.chromSizes, "w")
refSequenceStats = getHalSequenceStats(options.halFile,
options.refGenome)
assert refSequenceStats is not None
for seqStat in refSequenceStats:
csFile.write("%s\t%s\n" % (seqStat[0], seqStat[1]))
csFile.close()
def runParallelSlices(options):
refGenome = options.refGenome
if refGenome is None:
refGenome = getHalRootName(options.halFile)
refSequenceStats = getHalSequenceStats(options.halFile, refGenome)
options.smallFile = False
options.firstSmallFile = True
sliceCmds = []
sliceOpts = []
# we are going to deal with sequence coordinates
if options.splitBySequence is True or options.refSequence is not None:
for sequence, seqLen, nt, nb in refSequenceStats:
if options.refSequence is None or sequence == options.refSequence:
seqOpts = copy.deepcopy(options)
if seqLen < options.smallSize:
seqOpts.smallFile = True
seqOpts.refGenome = refGenome
seqOpts.refSequence = sequence
index = 0
for sStart, sLen, sIdx in computeSlices(seqOpts, seqLen):
seqOpts.start = sStart
seqOpts.length = sLen
seqOpts.sliceNumber = sIdx
sliceCmds.append(getHal2MafCmd(seqOpts))
sliceOpts.append(copy.deepcopy(seqOpts))
if seqOpts.smallFile is True and seqLen > 0:
options.firstSmallFile = False
# we are slicing the gnome coordinates directly
else:
seqOpts = copy.deepcopy(options)
assert seqOpts.splitBySequence is False
genomeLen = getHalGenomeLength(seqOpts.halFile, refGenome)
# auto compute slice size from numprocs
if seqOpts.sliceSize == None and seqOpts.numProc > 1:
refLen = genomeLen
if seqOpts.length is not None and seqOpts.length > 0:
refLen = seqOpts.length
seqOpts.sliceSize = int(math.ceil(refLen / seqOpts.numProc))
index = 0
for sStart, sLen, sIdx in computeSlices(seqOpts, genomeLen):
seqOpts.start = sStart
seqOpts.length = sLen
seqOpts.sliceNumber = sIdx
sliceCmds.append(getHal2MafCmd(seqOpts))
sliceOpts.append(copy.deepcopy(seqOpts))
# run in parallel
runParallelShellCommands(sliceCmds, options.numProc)
# concatenate into output if desired
concatenateSlices(sliceOpts, sliceCmds)
def runParallelSlices(options):
refGenome = options.refGenome
if refGenome is None:
refGenome = getHalRootName(options.halFile)
refSequenceStats = getHalSequenceStats(options.halFile, refGenome)
options.smallFile = False
options.firstSmallFile = True
sliceCmds = []
sliceOpts = []
# we are going to deal with sequence coordinates
if options.splitBySequence is True or options.refSequence is not None:
for sequence, seqLen, nt, nb in refSequenceStats:
if options.refSequence is None or sequence == options.refSequence:
seqOpts = copy.deepcopy(options)
if seqLen < options.smallSize:
seqOpts.smallFile = True
seqOpts.refGenome = refGenome
seqOpts.refSequence = sequence
index = 0
for sStart, sLen, sIdx in computeSlices(seqOpts, seqLen):
seqOpts.start = sStart
seqOpts.length = sLen
seqOpts.sliceNumber = sIdx
sliceCmds.append(getHal2MafCmd(seqOpts))
sliceOpts.append(copy.deepcopy(seqOpts))
if seqOpts.smallFile is True and seqLen > 0:
options.firstSmallFile = False
# we are slicing the gnome coordinates directly
else:
seqOpts = copy.deepcopy(options)
assert seqOpts.splitBySequence is False
genomeLen = getHalGenomeLength(seqOpts.halFile, refGenome)
# auto compute slice size from numprocs
if seqOpts.sliceSize == None and seqOpts.numProc > 1:
refLen = genomeLen
if seqOpts.length is not None and seqOpts.length > 0:
refLen = seqOpts.length
seqOpts.sliceSize = int(math.ceil(refLen / seqOpts.numProc))
index = 0
for sStart, sLen, sIdx in computeSlices(seqOpts, genomeLen):
seqOpts.start = sStart
seqOpts.length = sLen
seqOpts.sliceNumber = sIdx
sliceCmds.append(getHal2MafCmd(seqOpts))
sliceOpts.append(copy.deepcopy(seqOpts))
# run in parallel
runParallelShellCommands(sliceCmds, options.numProc)
# concatenate into output if desired
concatenateSlices(sliceOpts, sliceCmds)
def runParallelSlices(options):
refGenome = options.refGenome
if refGenome is None:
refGenome = getHalRootName(options.halFile)
refSequenceStats = getHalSequenceStats(options.halFile, refGenome)
options.smallFile = False
options.firstSmallFile = True
sliceCmds = []
sliceOpts = []
if options.refSequence is not None:
refStat = [x for x in refSequenceStats if x[1] ==
options.refSequence]
if len(refStat != 1):
raise RuntimeError("Sequence %s not found in genome %s" % (
options.refSequence, options.refGenome))
totalLength = int(refStat[1])
else:
totalLength = getHalGenomeLength(options.halFile, refGenome)
seqOpts = copy.deepcopy(options)
# auto compute slice size from numprocs
if seqOpts.sliceSize == None and seqOpts.numProc > 1:
refLen = totalLength
if seqOpts.length is not None and seqOpts.length > 0:
refLen = seqOpts.length
seqOpts.sliceSize = int(math.ceil(refLen / seqOpts.numProc))
index = 0
for sStart, sLen, sIdx in computeSlices(seqOpts, totalLength):
seqOpts.start = sStart
seqOpts.length = sLen
seqOpts.sliceNumber = sIdx
sliceCmds.append(getHalPhyloPCmd(seqOpts))
sliceOpts.append(copy.deepcopy(seqOpts))
# run in parallel
runParallelShellCommands(sliceCmds, options.numProc)
# concatenate into output if desired
concatenateSlices(sliceOpts, sliceCmds)
writeChromSizes(options)
def runParallelSlices(options):
refGenome = options.refGenome
if refGenome is None:
refGenome = getHalRootName(options.halFile)
refSequenceStats = getHalSequenceStats(options.halFile, refGenome)
options.smallFile = False
options.firstSmallFile = True
sliceCmds = []
sliceOpts = []
if options.refSequence is not None:
refStat = [x for x in refSequenceStats if x[1] == options.refSequence]
if len(refStat != 1):
raise RuntimeError("Sequence %s not found in genome %s" %
(options.refSequence, options.refGenome))
totalLength = int(refStat[1])
else:
totalLength = getHalGenomeLength(options.halFile, refGenome)
seqOpts = copy.deepcopy(options)
# auto compute slice size from numprocs
if seqOpts.sliceSize == None and seqOpts.numProc > 1:
refLen = totalLength
if seqOpts.length is not None and seqOpts.length > 0:
refLen = seqOpts.length
seqOpts.sliceSize = int(math.ceil(refLen / seqOpts.numProc))
index = 0
for sStart, sLen, sIdx in computeSlices(seqOpts, totalLength):
seqOpts.start = sStart
seqOpts.length = sLen
seqOpts.sliceNumber = sIdx
sliceCmds.append(getHalPhyloPCmd(seqOpts))
sliceOpts.append(copy.deepcopy(seqOpts))
# run in parallel
runParallelShellCommands(sliceCmds, options.numProc)
# concatenate into output if desired
concatenateSlices(sliceOpts, sliceCmds)
writeChromSizes(options)
def partitionBySeqCoords(options, refGenome):
"we are going to deal with sequence coordinates"
refSequenceStats = getHalSequenceStats(options.halFile, refGenome)
sliceCmds = []
sliceOpts = []
for sequence, seqLen, nt, nb in refSequenceStats:
if options.refSequence is None or sequence == options.refSequence:
seqOpts = copy.deepcopy(options)
if seqLen < options.smallSize:
seqOpts.smallFile = True
seqOpts.refGenome = refGenome
seqOpts.refSequence = sequence
for sStart, sLen, sIdx in computeSlices(seqOpts, seqLen):
seqOpts.start = sStart
seqOpts.length = sLen
seqOpts.sliceNumber = sIdx
sliceCmds.append(getHal2MafCmd(seqOpts))
sliceOpts.append(copy.deepcopy(seqOpts))
if seqOpts.smallFile is True and seqLen > 0:
options.firstSmallFile = False
return sliceCmds, sliceOpts
