def bed_sig2arr(bedname, sig_names, exp, arg):
regions = GenCoorSet(name=bedname)
regions.load(filename=exp.get_file(bedname))
if arg["--test"]:
regions.list = regions.list[0:50]
regions.relocate(mode='center as center', width=2*int(arg["--ext"]))
sig = SignalProfile(regions, genome=arg["--genome"],
bin=int(arg["--bin"]), step=int(arg["--step"]),
cores=int(arg["--cores"]))
for signal in sig_names:
if exp.get_file(signal).endswith(".bw") or exp.get_file(signal).endswith(".bigwig"):
sig.load_bigwig(filename=exp.get_file(signal), label=signal,
disable_progressbar=False, verbal=False)
elif exp.get_file(signal).endswith(".bam"):
sig.load_bam(filename=exp.get_file(signal), label=signal,
disable_progressbar=False, verbal=False)
res = sig.cov2array()
return res
Blablabla
Options:
"""
from docopt import docopt
from gencoor.coordinates import GenCoorSet
import os
if __name__ == '__main__':
arg = docopt(__doc__)
if arg["resize"]:
gc = GenCoorSet(name="input")
gc.load(arg["<input_BED_file_path>"], filetype="BED")
gc.relocate(mode='center as center', width=int(arg["<length>"]))
gc.save(arg["<output_BED_file_path>"], filetype="BED")
elif arg["split_strand"]:
name = os.path.basename(arg["<input_BED_file_path>"]).split(".")[0]
print(
os.path.join(arg["<output_BED_directory_path>"],
name + "_" + "+" + ".bed"))
gc = GenCoorSet(name="input")
gc.load(arg["<input_BED_file_path>"], filetype="BED")
res = gc.split_by_strands()
for k, g in res.items():
g.save(os.path.join(arg["<output_BED_directory_path>"],
name + "_" + k + ".bed"),
filetype="BED")
