def splitPooledBamfiles(infile, sentinel):
infile = P.snip(infile, ".sentinel") + ".bam"
outfile = P.snip(sentinel, ".sentinel")
params = '2'
try:
module = P.snip(IDR.__file__, ".py")
except ValueError:
module = P.snip(IDR.__file__, ".pyc")
P.submit(module, "splitBam", params, infile, outfile)
P.touch(sentinel)
def findNPeaksForPooledPseudoreplicates(infiles, outfile):
idr_thresh = PARAMS["idr_options_pooled_consistency_threshold"]
try:
module = P.snip(IDR.__file__, ".py")
except ValueError:
module = P.snip(IDR.__file__, ".pyc")
P.submit(module,
"findNPeaks",
params=[
str(idr_thresh),
],
infiles=infiles,
outfiles=outfile)
def findNPeaksForIndividualReplicates(infiles, outfile):
idr_thresh = PARAMS["idr_options_inter_replicate_threshold"]
try:
module = P.snip(IDR.__file__, ".py")
except ValueError:
module = P.snip(IDR.__file__, ".pyc")
P.submit(module,
"findNPeaks",
params=[
str(idr_thresh),
],
infiles=infiles,
outfiles=outfile)
def splitBamfiles(infile, sentinel):
"""
For all tracks, split the filtered bamfile in two using pysam
"""
infile = P.snip(infile, ".sentinel") + ".bam"
outfile = P.snip(sentinel, ".sentinel")
params = '2'
try:
module = P.snip(IDR.__file__, ".py")
except ValueError:
module = P.snip(IDR.__file__, ".pyc")
P.submit(module, "splitBam", params, infile, outfile)
P.touch(sentinel)
