def runIDROnIndividualReplicates(infiles, outfile):
"""
Run IDR consecutively for each pairwise combination of a particular
EXPERIMENT
"""
# set IDR parameters (HACK!) WrapperIDR is in /ifs/devel/CGAT
chr_table = os.path.join(PARAMS["annotations_dir"],
PARAMS_ANNOTATIONS["interface_contigs"])
idr_script = os.path.join(os.path.dirname(P.__file__), "WrapperIDR.py")
# iterate through pairwise combinations of infiles
for infile1, infile2 in itertools.combinations(infiles, 2):
# get statement
statement = IDR.getIDRStatement(infile1,
infile2,
outfile,
PARAMS["idr_options_overlap_ratio"],
PARAMS["idr_options_ranking_measure"],
chr_table,
idr_script)
# run
E.info("applyIDR: processing %s and %s" % (infile1, infile2))
job_options = "-l mem_free=5G"
P.run()
def runIDROnIndividualReplicates(infiles, outfile):
"""
Run IDR consecutively for each pairwise combination of a particular
EXPERIMENT
"""
# set IDR parameters (HACK!) WrapperIDR is in /ifs/devel/CGAT
chr_table = os.path.join(PARAMS["annotations_dir"],
PARAMS_ANNOTATIONS["interface_contigs"])
idr_script = os.path.join(os.path.dirname(P.__file__), "WrapperIDR.py")
# iterate through pairwise combinations of infiles
for infile1, infile2 in itertools.combinations(infiles, 2):
# get statement
statement = IDR.getIDRStatement(infile1,
infile2,
outfile,
PARAMS["idr_options_overlap_ratio"],
PARAMS["idr_options_ranking_measure"],
chr_table,
idr_script)
# run
E.info("applyIDR: processing %s and %s" % (infile1, infile2))
job_options = "-l mem_free=5G"
P.run()
def runIDROnPooledPseudoreplicates(infiles, outfile):
"""
Run IDR analysis on pooled pseudoreplicates for each EXPERIMENT
"""
# set IDR parameters
chr_table = os.path.join(PARAMS["annotations_dir"],
PARAMS_ANNOTATIONS["interface_contigs"])
# get statement
statement = IDR.getIDRStatement(infiles[0], infiles[1], outfile,
PARAMS["idr_options_overlap_ratio"],
PARAMS["idr_options_ranking_measure"],
chr_table)
# run
E.info("applyIDR: processing %s and %s" % (infiles[0], infiles[1]))
job_memory = "5G"
P.run()
def runIDROnPseudoreplicates(infiles, outfile):
"""
Run IDR analysis on pseudoreplicates for each TRACK
"""
# set IDR parameters
chr_table = os.path.join(PARAMS["annotations_dir"],
PARAMS_ANNOTATIONS["interface_contigs"])
idr_script = os.path.join(os.path.dirname(P.__file__), "WrapperIDR.py")
# get statement
statement = IDR.getIDRStatement(infiles[0], infiles[1], outfile,
PARAMS["idr_options_overlap_ratio"],
PARAMS["idr_options_ranking_measure"],
chr_table, idr_script)
# run
E.info("applyIDR: processing %s and %s" % (infiles[0], infiles[1]))
job_options = "-l mem_free=5G"
P.run()
def runIDROnPooledPseudoreplicates(infiles, outfile):
"""
Run IDR analysis on pooled pseudoreplicates for each EXPERIMENT
"""
# set IDR parameters
chr_table = os.path.join(PARAMS["annotations_dir"],
PARAMS["annotations_interface_contigs"])
# get statement
statement = IDR.getIDRStatement(infiles[0],
infiles[1],
outfile,
PARAMS["idr_options_overlap_ratio"],
PARAMS["idr_options_ranking_measure"],
chr_table)
# run
E.info("applyIDR: processing %s and %s" % (infiles[0], infiles[1]))
job_memory = "5G"
P.run()
def runIDROnPooledPseudoreplicates(infiles, outfile):
"""
Run IDR analysis on pooled pseudoreplicates for each EXPERIMENT
"""
# set IDR parameters
chr_table = os.path.join(PARAMS["annotations_dir"],
PARAMS_ANNOTATIONS["interface_contigs"])
idr_script = os.path.join(os.path.dirname(P.__file__), "WrapperIDR.py")
# get statement
statement = IDR.getIDRStatement(infiles[0],
infiles[1],
outfile,
PARAMS["idr_options_overlap_ratio"],
PARAMS["idr_options_ranking_measure"],
chr_table,
idr_script)
# run
E.info("applyIDR: processing %s and %s" % (infiles[0], infiles[1]))
job_options = "-l mem_free=5G"
P.run()
