def test_split_by_strands():
genset = GenCoorSet(name="Test_set")
bedfile = os.path.join(os.getenv("HOME"),
"gencoor_data/hg38/genes_hg38.bed")
genset.load(filename=bedfile, filetype="BED")
res = genset.split_by_strands()
assert set([g.strand for g in res["+"]]) == set(["+"])
assert set([g.strand for g in res["-"]]) == set(["-"])
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)
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
if len(signals) > 1:
print("There are more than one BED files sharing the same tags, only the first one will be used.")
arrs = bed_sig2arr(beds[0], [signals[0]], exp, arg)
a = arrs[signals[0]]
hm = axes[i, j].imshow(a, cmap='hot', interpolation='None')
# Y ticks
axes[i, j].get_yaxis().set_ticks([])
# X ticks
x_label_list = ['-'+arg["--ext"], '0', arg["--ext"]]
xmin, xmax = axes[i, j].get_xlim()
axes[i, j].set_xticks([xmin, int(0.5 * (xmax - xmin)), xmax])
axes[i, j].set_xticklabels(x_label_list)
# labels
if j == 0:
axes[i, j].set_ylabel(row)
if i == 0:
regions = GenCoorSet(name=beds[0])
regions.load(filename=exp.get_file(beds[0]))
axes[i, j].set_title(col+" ("+str(len(regions))+")")
cbar_ax = fig.add_axes([0.9, 0.15, 0.02, 0.7])
fig.colorbar(hm, cax=cbar_ax)
set_yaxis(n_row, n_col, axes, arg)
fig.savefig(arg["<output_file>"], bbox_inches='tight')
# elif arg["boxplot"]:
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")