def main(args=None):
args = parse_arguments().parse_args(args)
if args.scaleFactors:
scaleFactors = [float(x) for x in args.scaleFactors.split(":")]
else:
scaleFactors = [1, 1]
# the getRatio function is called and receives
# the function_args per each tile that is considered
FUNC = getRatio
function_args = {
'valueType': args.ratio,
'scaleFactors': scaleFactors,
'pseudocount': args.pseudocount
}
writeBedGraph_bam_and_bw.writeBedGraph(
[(args.bigwig1, 'bigwig'), (args.bigwig2, 'bigwig')],
args.outFileName,
0,
FUNC,
function_args,
tileSize=args.binSize,
region=args.region,
blackListFileName=args.blackListFileName,
numberOfProcessors=args.numberOfProcessors,
format=args.outFileFormat,
smoothLength=False,
missingDataAsZero=not args.skipNonCoveredRegions,
extendPairedEnds=False)
def main(args=None):
args = parse_arguments().parse_args(args)
if args.scaleFactors:
scaleFactors = [float(x) for x in args.scaleFactors.split(":")]
else:
scaleFactors = [1, 1]
# the getRatio function is called and receives
# the function_args per each tile that is considered
FUNC = getRatio
function_args = {'valueType': args.ratio,
'scaleFactors': scaleFactors,
'pseudocount': args.pseudocount}
writeBedGraph_bam_and_bw.writeBedGraph(
[(args.bigwig1, 'bigwig'),
(args.bigwig2, 'bigwig')],
args.outFileName, 0, FUNC,
function_args, tileSize=args.binSize, region=args.region,
numberOfProcessors=args.numberOfProcessors,
format=args.outFileFormat,
smoothLength=False,
missingDataAsZero=not args.skipNonCoveredRegions,
extendPairedEnds=False)
def main(args=None):
args = parse_arguments().parse_args(args)
if args.scaleFactors:
scaleFactors = [float(x) for x in args.scaleFactors.split(":")]
else:
scaleFactors = [1, 1]
# the getRatio function is called and receives
# the function_args per each tile that is considered
FUNC = getRatio
function_args = {'valueType': args.ratio,
'scaleFactors': scaleFactors,
'pseudocount': args.pseudocount}
# Preload deepBlue files, which need to then be deleted
deepBlueFiles = []
for idx, fname in enumerate([args.bigwig1, args.bigwig2]):
if db.isDeepBlue(fname):
deepBlueFiles.append([fname, idx])
if len(deepBlueFiles) > 0:
sys.stderr.write("Preloading the following deepBlue files: {}\n".format(",".join([x[0] for x in deepBlueFiles])))
foo = db.deepBlue(deepBlueFiles[0][0], url=args.deepBlueURL, userKey=args.userKey)
regs = db.makeChromTiles(foo)
for x in deepBlueFiles:
x.extend([args, regs])
if len(deepBlueFiles) > 1 and args.numberOfProcessors > 1:
pool = multiprocessing.Pool(args.numberOfProcessors)
res = pool.map_async(db.preloadWrapper, deepBlueFiles).get(9999999)
else:
res = list(map(db.preloadWrapper, deepBlueFiles))
# substitute the file names with the temp files
for (ftuple, r) in zip(deepBlueFiles, res):
if ftuple[1] == 0:
args.bigwig1 = r
else:
args.bigwig2 = r
deepBlueFiles = [[x[0], x[1]] for x in deepBlueFiles]
del regs
writeBedGraph_bam_and_bw.writeBedGraph(
[(args.bigwig1, getType(args.bigwig1)),
(args.bigwig2, getType(args.bigwig2))],
args.outFileName, 0, FUNC,
function_args, tileSize=args.binSize, region=args.region,
blackListFileName=args.blackListFileName,
verbose=args.verbose,
numberOfProcessors=args.numberOfProcessors,
format=args.outFileFormat,
smoothLength=False,
missingDataAsZero=not args.skipNonCoveredRegions,
extendPairedEnds=False)
# Clean up temporary bigWig files, if applicable
if not args.deepBlueKeepTemp:
for k, v in deepBlueFiles:
if v == 0:
os.remove(args.bigwig1)
else:
os.remove(args.bigwig2)
else:
for k, v in deepBlueFiles:
foo = args.bigwig1
if v == 1:
foo = args.bigwig2
print("{} is stored in {}".format(k, foo))
def main(args=None):
args = parse_arguments().parse_args(args)
if args.scaleFactors:
scaleFactors = [float(x) for x in args.scaleFactors.split(":")]
else:
scaleFactors = [1, 1]
# the getRatio function is called and receives
# the function_args per each tile that is considered
FUNC = getRatio
function_args = {'valueType': args.ratio,
'scaleFactors': scaleFactors,
'pseudocount': args.pseudocount}
# Preload deepBlue files, which need to then be deleted
deepBlueFiles = []
for idx, fname in enumerate([args.bigwig1, args.bigwig2]):
if db.isDeepBlue(fname):
deepBlueFiles.append([fname, idx])
if len(deepBlueFiles) > 0:
sys.stderr.write("Preloading the following deepBlue files: {}\n".format(",".join([x[0] for x in deepBlueFiles])))
foo = db.deepBlue(deepBlueFiles[0][0], url=args.deepBlueURL, userKey=args.userKey)
regs = db.makeChromTiles(foo)
for x in deepBlueFiles:
x.extend([args, regs])
if len(deepBlueFiles) > 1 and args.numberOfProcessors > 1:
pool = multiprocessing.Pool(args.numberOfProcessors)
res = pool.map_async(db.preloadWrapper, deepBlueFiles).get(9999999)
else:
res = list(map(db.preloadWrapper, deepBlueFiles))
# substitute the file names with the temp files
for (ftuple, r) in zip(deepBlueFiles, res):
if ftuple[1] == 0:
args.bigwig1 = r
else:
args.bigwig2 = r
deepBlueFiles = [[x[0], x[1]] for x in deepBlueFiles]
del regs
writeBedGraph_bam_and_bw.writeBedGraph(
[(args.bigwig1, getType(args.bigwig1)),
(args.bigwig2, getType(args.bigwig2))],
args.outFileName, 0, FUNC,
function_args, tileSize=args.binSize, region=args.region,
blackListFileName=args.blackListFileName,
verbose=args.verbose,
numberOfProcessors=args.numberOfProcessors,
format=args.outFileFormat,
smoothLength=False,
missingDataAsZero=not args.skipNonCoveredRegions,
extendPairedEnds=False)
# Clean up temporary bigWig files, if applicable
if not args.deepBlueKeepTemp:
for k, v in deepBlueFiles:
if v == 0:
os.remove(args.bigwig1)
else:
os.remove(args.bigwig2)
else:
for k, v in deepBlueFiles:
foo = args.bigwig1
if v == 1:
foo = args.bigwig2
print("{} is stored in {}".format(k, foo))