def depthFunc(self,taskPrefix,dependencies,bamFile,outFile) :
outputPath=outFile
outputFilename=os.path.basename(outputPath)
tmpDir=os.path.join(outputPath+".tmpdir")
makeTmpDirCmd = getMkdirCmd() + [tmpDir]
dirTask=self.addTask(preJoin(taskPrefix,"makeTmpDir"), makeTmpDirCmd, dependencies=dependencies, isForceLocal=True)
tmpFiles = []
scatterTasks = set()
def getChromosomeGroups(params) :
"""
Iterate through chromosomes/contigs and group small contigs together. This functions as a generator yielding
successive contig groups.
"""
minSize=200000
group = []
headSize = 0
chromCount = len(params.chromSizes)
assert(len(params.chromOrder) == chromCount)
for chromIndex in range(chromCount) :
chromLabel = params.chromOrder[chromIndex]
if chromLabel in params.chromIsSkipped : continue
chromSize = params.chromSizes[chromLabel]
if headSize+chromSize <= minSize :
group.append((chromIndex,chromLabel))
headSize += chromSize
else :
if len(group) != 0 : yield(group)
group = [(chromIndex,chromLabel)]
headSize = chromSize
if len(group) != 0 : yield(group)
for chromGroup in getChromosomeGroups(self.params) :
assert(len(chromGroup) > 0)
cid = getRobustChromId(chromGroup[0][0], chromGroup[0][1])
if len(chromGroup) > 1 :
cid += "_to_"+getRobustChromId(chromGroup[-1][0], chromGroup[-1][1])
tmpFiles.append(os.path.join(tmpDir,outputFilename+"_"+cid))
cmd = [self.params.getChromDepthBin,"--ref", self.params.referenceFasta, "--align-file", bamFile, "--output", tmpFiles[-1]]
for (chromIndex,chromLabel) in chromGroup :
cmd.extend(["--chrom",chromLabel])
scatterTasks.add(self.addTask(preJoin(taskPrefix,"estimateChromDepth_"+cid),cmd,dependencies=dirTask,memMb=self.params.estimateMemMb))
assert(len(tmpFiles) != 0)
catCmd = [self.params.catScript,"--output",outputPath]+tmpFiles
catTask = self.addTask(preJoin(taskPrefix,"catChromDepth"),catCmd,dependencies=scatterTasks, isForceLocal=True)
nextStepWait = set()
nextStepWait.add(catTask)
return nextStepWait
def depthFunc(self,taskPrefix,dependencies,bamFile,outFile) :
outputPath=outFile
outputFilename=os.path.basename(outputPath)
tmpDir=os.path.join(outputPath+".tmpdir")
makeTmpDirCmd = getMkdirCmd() + [tmpDir]
dirTask=self.addTask(preJoin(taskPrefix,"makeTmpDir"), makeTmpDirCmd, dependencies=dependencies, isForceLocal=True)
tmpFiles = []
scatterTasks = set()
def getChromosomeGroups(params) :
"""
Iterate chromosomes/contigs and 'clump' small contigs together
"""
minSize=200000
group = []
headSize = 0
chromCount = len(params.chromSizes)
assert(len(params.chromOrder) == chromCount)
for chromIndex in range(chromCount) :
chromLabel = params.chromOrder[chromIndex]
chromSize = params.chromSizes[chromLabel]
if headSize+chromSize <= minSize :
group.append((chromIndex,chromLabel))
headSize += chromSize
else :
if len(group) != 0 : yield(group)
group = [(chromIndex,chromLabel)]
headSize = chromSize
if len(group) != 0 : yield(group)
for chromGroup in getChromosomeGroups(self.params) :
assert(len(chromGroup) > 0)
cid = getRobustChromId(chromGroup[0][0], chromGroup[0][1])
if len(chromGroup) > 1 :
cid += "_to_"+getRobustChromId(chromGroup[-1][0], chromGroup[-1][1])
tmpFiles.append(os.path.join(tmpDir,outputFilename+"_"+cid))
cmd = [self.params.mantaGetChromDepthBin,"--align-file",bamFile,"--output",tmpFiles[-1]]
for (chromIndex,chromLabel) in chromGroup :
cmd.extend(["--chrom",chromLabel])
scatterTasks.add(self.addTask(preJoin(taskPrefix,"estimateChromDepth_"+cid),cmd,dependencies=dirTask))
catCmd = [self.params.mantaCat,"--output",outputPath]+tmpFiles
catTask = self.addTask(preJoin(taskPrefix,"catChromDepth"),catCmd,dependencies=scatterTasks, isForceLocal=True)
nextStepWait = set()
nextStepWait.add(catTask)
return nextStepWait
def depthFunc(self,taskPrefix,dependencies,bamFile,outFile) :
outputPath=outFile
outputFilename=os.path.basename(outputPath)
tmpDir=os.path.join(outputPath+".tmpdir")
dirTask=self.addTask(preJoin(taskPrefix,"makeTmpDir"), "mkdir -p "+tmpDir, dependencies=dependencies, isForceLocal=True)
tmpFiles = []
scatterTasks = set()
for (chromIndex, chromLabel) in enumerate(self.params.chromOrder) :
cid = getRobustChromId(chromIndex, chromLabel)
tmpFiles.append(os.path.join(tmpDir,outputFilename+"_"+cid))
cmd = [self.params.mantaGetChromDepthBin,"--align-file",bamFile,"--chrom",chromLabel,"--output",tmpFiles[-1]]
scatterTasks.add(self.addTask(preJoin(taskPrefix,"estimateChromDepth_"+cid),cmd,dependencies=dirTask))
catCmd = "cat " + " ".join(["'%s'" % (x) for x in tmpFiles]) + " > '%s'" % (outputPath)
catTask = self.addTask(preJoin(taskPrefix,"catChromDepth"),catCmd,dependencies=scatterTasks, isForceLocal=True)
nextStepWait = set()
nextStepWait.add(catTask)
return nextStepWait
