def runM3D(infile, outfile, root, design):
job_options = "-l mem_free=4G -pe dedicated 1"
groups = [x for x in itertools.combinations(EXPERIMENTS, 2)]
# **code repeated - refactor**
for pair in groups:
pair = [re.sub("-agg", "", str(x)) for x in pair]
pair1, pair2 = pair
pair1_split = pair1.split("-")
pair2_split = pair2.split("-")
# only want pairs with one difference
# e.g treatment or tissue but not both
if not (pair1_split[0] != pair2_split[0]
and pair1_split[1] != pair2_split[1]):
outfile = ("%(root)s%(pair1)s_vs_%(pair2)s.tsv" % locals())
if pair1_split[0] != pair2_split[0]:
groups = [pair1_split[0], pair2_split[0]]
elif pair1_split[1] != pair2_split[1]:
groups = [pair1_split[1], pair2_split[1]]
else:
E.error(
"This pair does not contain any comparisons: %(pair)s" %
locals())
RRBS.calculateM3DStat(infile,
outfile,
design,
pair=pair,
groups=groups,
submit=True,
job_options=job_options)
def runM3DSpikeClusters(infiles, outfile):
job_options = "-l mem_free=4G -pe dedicated 1"
infile, design = infiles
RRBS.calculateM3DStat(infile,
outfile,
design,
submit=True,
job_options=job_options)