run peakachu pool after a score function, but receive a numpy error:
commands:
peakachu score_genome -r 10000 -m CTCF-ChIAPET-peakachu-pretrained.10million.10kb.pkl -p ChIA-PET_mm10_10000.hic.cool -O ChIA-PET_mm10 --minimum-prob 0
peakachu pool -r 10000 -i ChIA-PET_mm10 -t .98 -o ChIA-PET_mm10.loops
error:
Traceback (most recent call last):
File "/softwares/anaconda3/envs/peakachu/bin/peakachu", line 91, in
run()
File "/softwares/anaconda3/envs/peakachu/bin/peakachu", line 87, in run
args.func(args)
File "/softwares/anaconda3/envs/peakachu/lib/python3.10/site-packages/peakachu/call_loops.py", line 14, in main
clusters, score_pool = peakacluster.parse_peakachu(args.infile, args.threshold, res)
File "/softwares/anaconda3/envs/peakachu/lib/python3.10/site-packages/peakachu/peakacluster.py", line 21, in parse_peakachu
tmp = local_clustering(D[c], min_count=3, r=2)
File "/softwares/anaconda3/envs/peakachu/lib/python3.10/site-packages/peakachu/peakacluster.py", line 162, in local_clustering
_cluster_core(sort_list, r, visited, final_list)
File "/softwares/anaconda3/envs/peakachu/lib/python3.10/site-packages/peakachu/peakacluster.py", line 126, in _cluster_core
rad = np.int(np.round(max([euclidean(cen,q) for q in Local]))) + r
File "/softwares/anaconda3/envs/peakachu/lib/python3.10/site-packages/numpy/init.py", line 305, in getattr
raise AttributeError(former_attrs[attr])
AttributeError: module 'numpy' has no attribute 'int'.
np.int was a deprecated alias for the builtin int. To avoid this error in existing code, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations. Did you mean: 'inf'?
Any ideas? Thanks!
run peakachu pool after a score function, but receive a numpy error:
commands:
peakachu score_genome -r 10000 -m CTCF-ChIAPET-peakachu-pretrained.10million.10kb.pkl -p ChIA-PET_mm10_10000.hic.cool -O ChIA-PET_mm10 --minimum-prob 0
peakachu pool -r 10000 -i ChIA-PET_mm10 -t .98 -o ChIA-PET_mm10.loops
error:
Traceback (most recent call last):
File "/softwares/anaconda3/envs/peakachu/bin/peakachu", line 91, in
run()
File "/softwares/anaconda3/envs/peakachu/bin/peakachu", line 87, in run
args.func(args)
File "/softwares/anaconda3/envs/peakachu/lib/python3.10/site-packages/peakachu/call_loops.py", line 14, in main
clusters, score_pool = peakacluster.parse_peakachu(args.infile, args.threshold, res)
File "/softwares/anaconda3/envs/peakachu/lib/python3.10/site-packages/peakachu/peakacluster.py", line 21, in parse_peakachu
tmp = local_clustering(D[c], min_count=3, r=2)
File "/softwares/anaconda3/envs/peakachu/lib/python3.10/site-packages/peakachu/peakacluster.py", line 162, in local_clustering
_cluster_core(sort_list, r, visited, final_list)
File "/softwares/anaconda3/envs/peakachu/lib/python3.10/site-packages/peakachu/peakacluster.py", line 126, in _cluster_core
rad = np.int(np.round(max([euclidean(cen,q) for q in Local]))) + r
File "/softwares/anaconda3/envs/peakachu/lib/python3.10/site-packages/numpy/init.py", line 305, in getattr
raise AttributeError(former_attrs[attr])
AttributeError: module 'numpy' has no attribute 'int'.
np.intwas a deprecated alias for the builtinint. To avoid this error in existing code, useintby itself. Doing this will not modify any behavior and is safe. When replacingnp.int, you may wish to use e.g.np.int64ornp.int32to specify the precision. If you wish to review your current use, check the release note link for additional information.The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations. Did you mean: 'inf'?
Any ideas? Thanks!