def __call__(self, parser, namespace, filename, option_string=None):
bt = myBedTools(myBedTools.binarybedfilegenome,
initialize=False,
ref_version=local_ref_version)
bt.read_as_regions(filename)
setattr(namespace, self.dest, bt)
pass
def __call__(self, parser, namespace, filenames, option_string=None):
sys.stderr.write("Merging %d bbg files\n" % len(filenames))
bt = myBedTools(myBedTools.binarybedfilegenome,
initialize=False,
ref_version=local_ref_version)
for f in filenames:
bt.read_as_regions(f)
pass
setattr(namespace, self.dest, bt)
pass
def __call__(self, parser, namespace, filenames, option_string=None):
sys.stderr.write("intersecting %d bbg files\n" % len(filenames))
bt = myBedTools(myBedTools.binarybedfilegenome,
initialize=False,
ref_version=local_ref_version)
bt.read_to_bases(myBedTools.binarybedfilegenome, filenames[0],
myBedTools.set_to_one)
for f in filenames[1:]:
bt.read_to_bases(myBedTools.binarybedfilegenome, f,
myBedTools.bitfn_and)
gc.collect()
pass
setattr(namespace, self.dest, bt)
pass
def fn_outer(i):
bt = myBedTools(myBedTools.binarybedfilegenome,
initialize=False,
ref_version=local_ref_version)
bt.read_as_regions(i)
return bt