def getLiftUpBedFile(halPath, genomeName, genomeBedPath, outBedPath):
parentName = getParentGenomeName(halPath, genomeName)
runShellCommand(
"halLiftover %s %s %s %s %s_lotmp" %
(halPath, genomeName, genomeBedPath, parentName, outBedPath))
runShellCommand("cat %s_lotmp |sortBed |mergeBed > %s && rm -f %s_lotmp" %
(outBedPath, outBedPath, outBedPath))
def getLiftUpBedFile(halPath, genomeName, genomeBedPath, outBedPath):
parentName = getParentGenomeName(halPath, genomeName)
runShellCommand("halLiftover %s %s %s %s %s_lotmp" % (halPath,
genomeName,
genomeBedPath,
parentName,
outBedPath))
runShellCommand("cat %s_lotmp |sortBed |mergeBed > %s && rm -f %s_lotmp" %
(outBedPath, outBedPath, outBedPath))
def getHalTreeBackground(halPath, args, rootName=None):
root = rootName
if root is None:
root = getHalRootName(halPath)
for child in getHalChildrenNames(halPath, root):
bgFile = os.path.join(args.workDir, args.backgroundBedName % child)
if args.ar is True:
command = "halMaskExtract %s %s --maskFile %s --extend %d --extendPct %f" % (halPath, child, bgFile, args.arExtend, args.arExtendPct)
else:
command = "halStats %s --bedSequences %s > %s" % (halPath, child,
bgFile)
print command
runShellCommand(command)
getHalTreeBackground(halPath, args, child)
def getHalTreeBackground(halPath, args, rootName=None):
root = rootName
if root is None:
root = getHalRootName(halPath)
for child in getHalChildrenNames(halPath, root):
bgFile = os.path.join(args.workDir, args.backgroundBedName % child)
if args.ar is True:
command = "halMaskExtract %s %s --maskFile %s --extend %d --extendPct %f" % (halPath, child, bgFile, args.arExtend, args.arExtendPct)
else:
command = "halStats %s --bedSequences %s > %s" % (halPath, child,
bgFile)
print(command)
runShellCommand(command)
getHalTreeBackground(halPath, args, child)
def genomeLength(halPath, genome):
command = "halStats %s --bedSequences %s" % (halPath, genome)
genomeBed = runShellCommand(command)
length = 0
for line in genomeBed.split("\n"):
tokens = line.split()
if len(tokens) > 2:
length += int(tokens[2])
return length
def genomeLength(halPath, genome):
command = "halStats %s --bedSequences %s" % (halPath, genome)
genomeBed = runShellCommand(command)
length = 0
for line in genomeBed.split("\n"):
tokens = line.split()
if len(tokens) > 2:
length += int(tokens[2])
return length
def getSortBed(inBed, outBed=None):
if outBed is None:
runShellCommand("sortBed -i %s > %s_temp && mv %s_temp %s" %
(inBed, inBed, inBed, inBed))
else:
runShellCommand("sortBed -i %s > %s" % (inBed, outBed))
def getUnionBed(inBed1, inBed2, outBed):
runShellCommand("cat %s %s | sortBed | mergeBed > %s" % (inBed1, inBed2,
outBed))
def getSortBed(inBed, outBed = None):
if outBed is None:
runShellCommand("sortBed -i %s > %s_temp && mv %s_temp %s" % (
inBed, inBed, inBed, inBed))
else:
runShellCommand("sortBed -i %s > %s" % (inBed, outBed))
def getIntersectBed(inBed1, inBed2, outBed):
runShellCommand("intersectBed -a %s -b %s > %s" % (inBed1, inBed2, outBed))
def getSubtractBed(inBed1, inBed2, outBed):
runShellCommand("subtractBed -a %s -b %s > %s" % (inBed1, inBed2, outBed))
def getBranchLength(halPath, genomeName):
return float(
runShellCommand("halStats %s --branchLength %s" %
(halPath, genomeName)).strip("\n"))
def getAlignedBed(halPath, genomeName, outBedPath):
runShellCommand("halAlignedExtract %s %s | sortBed | mergeBed> %s" %
(halPath, genomeName, outBedPath))
def getBranchLength(halPath, genomeName):
return float(runShellCommand("halStats %s --branchLength %s" % (
halPath, genomeName)).strip("\n"))
def getParentGenomeName(halPath, genomeName):
return runShellCommand("halStats %s --parent %s" % (
halPath, genomeName)).strip("\n")
def getParentGenomeName(halPath, genomeName):
return runShellCommand("halStats %s --parent %s" %
(halPath, genomeName)).strip("\n")
def getUnionBed(inBed1, inBed2, outBed):
runShellCommand("cat %s %s | sortBed | mergeBed > %s" %
(inBed1, inBed2, outBed))
def getSubtractBed(inBed1, inBed2, outBed):
runShellCommand("subtractBed -a %s -b %s > %s" % (inBed1, inBed2, outBed))
def getIntersectBed(inBed1, inBed2, outBed):
runShellCommand("intersectBed -a %s -b %s > %s" % (inBed1, inBed2, outBed))
def getAlignedBed(halPath, genomeName, outBedPath):
runShellCommand("halAlignedExtract %s %s | sortBed | mergeBed> %s" %
(halPath, genomeName, outBedPath))
