def test_GenCoorSet_load():
genset = GenCoorSet(name="Test_set")
bedfile = os.path.join(os.getenv("HOME"),
"gencoor_data/hg38/genes_hg38.bed")
bedfile2 = os.path.join(os.getenv("HOME"),
"gencoor_data/hg38/genes_hg38_test.bed")
genset.load(filename=bedfile, filetype="BED")
genset.save(filename=bedfile2, filetype="BED")
os.remove(bedfile2)
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")