def get_binfiles(bedfiles, fastafile, shift, subtract=None):
if subtract:
binfiles = [bins([x, fastafile, "--binsize={0}".format(shift), \
"--subtract={0}".format(subtract)]) for x in bedfiles]
else:
binfiles = [bins([x, fastafile, "--binsize={0}".format(shift)]) \
for x in bedfiles]
binfiles = [BinFile(x) for x in binfiles]
return binfiles
def get_binfiles(bedfiles, fastafile, shift, mode="span", subtract=None):
binopts = ["--binsize={0}".format(shift)]
binopts.append("--mode={0}".format(mode))
if subtract:
binopts.append("--subtract={0}".format(subtract))
binfiles = [bins([x, fastafile] + binopts) for x in bedfiles if op.exists(x)]
binfiles = [BinFile(x) for x in binfiles]
return binfiles
def get_binfiles(bedfiles, fastafile, shift, mode="span", subtract=None):
binopts = ["--binsize={0}".format(shift)]
binopts.append("--mode={0}".format(mode))
if subtract:
binopts.append("--subtract={0}".format(subtract))
binfiles = [
bins([x, fastafile] + binopts) for x in bedfiles if op.exists(x)
]
binfiles = [BinFile(x) for x in binfiles]
return binfiles
def get_binfiles(inputfiles, fastafile, shift, mode="span", subtract=None, binned=False):
if not binned:
binopts = ["--binsize={0}".format(shift)]
binopts.append("--mode={0}".format(mode))
if subtract:
binopts.append("--subtract={0}".format(subtract))
binfiles = [bins([x, fastafile] + binopts) for x in inputfiles if op.exists(x)]
else:
binfiles = inputfiles
binfiles = [BinFile(x) for x in binfiles]
return binfiles
def get_binfiles(bedfiles, fastafile, shift):
binfiles = [bins([x, "--binsize={0}".format(shift), fastafile]) for x in bedfiles]
binfiles = [BinFile(x) for x in binfiles]
return binfiles