def getHalTreeMutations(halPath, args, rootName=None):
root = rootName
if root is None:
root = getHalRootName(halPath)
for child in getHalChildrenNames(halPath, root):
getHalBranchMutations(halPath, child, args)
getHalTreeMutations(halPath, args, child)
def getHalTreeMutations(halPath, args, rootName=None):
root = rootName
if root is None:
root = getHalRootName(halPath)
for child in getHalChildrenNames(halPath, root):
getHalBranchMutations(halPath, child, args)
getHalTreeMutations(halPath, args, child)
def computeTreePhyloP(args):
visitQueue = [args.root]
bigwigCmds = []
while len(visitQueue) > 0:
genome = visitQueue.pop()
bedFlags = ""
# Generate a bed file of all regions of
# genome that dont align to parent
bedInsertsFile = outFileName(args, genome, "bed", "inserts", True)
if genome != args.root:
runShellCommand(
"halAlignedExtract %s %s --alignedFile %s --complement" % (
args.hal, genome, bedInsertsFile))
bedFlags = "--refBed %s" % bedInsertsFile
# Run halPhyloP on the inserts
wigFile = outFileName(args, genome, "wig", "phyloP", False)
cmd = "halPhyloPMP.py %s %s %s %s --numProc %d %s" % (
args.hal, genome, args.mod, bedFlags, args.numProc, wigFile)
if args.subtree is not None:
cmd += " --subtree %s" % args.subtree
if args.prec is not None:
cmd += " --prec %d" % args.prec
runShellCommand(cmd)
runShellCommand("rm -f %s" % bedInsertsFile)
# Lift down from the parent, appending to the wig file computed above
if genome != args.root:
parent = getHalParentName(args.hal, genome)
parentWig = outFileName(args, parent, "wig", "phyloP", False)
if os.path.isfile(parentWig):
runShellCommand("halWiggleLiftover %s %s %s %s %s --append" % (
args.hal, parent, parentWig, genome, wigFile))
# Convert to bigwig if desired and delete wig file
if args.bigWig is True and os.path.isfile(wigFile):
sizesFile = outFileName(args, genome, "sizes", "chr", True)
bwFile = outFileName(args, genome, "bw", "phyloP", False)
bwCmd = "halStats %s --chromSizes %s > %s && " % (args.hal, genome,
sizesFile)
bwCmd += "wigToBigWig %s %s %s && " % (wigFile, sizesFile, bwFile)
bwCmd += "rm -f %s &&" % wigFile
bwCmd += "rm -f %s" % sizesFile
bigwigCmds.append(bwCmd)
# Recurse on children.
children = getHalChildrenNames(args.hal, genome)
for child in children:
visitQueue.append(child)
#parallel bigwig conversion
runParallelShellCommands(bigwigCmds, args.numProc)
