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CalcProfile numpy error on HPC cluster #58

@DollyCM

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@DollyCM

Hello,
I am using SHAPEmapper2.2 for my RNA structure probing analyses and I am getting the following error for calculating profile from mutations. It gives the following error irrespective of python version (tried with python v2.7, 3.9 and 3.11. It also fails with the example data provided with the tool.

Could you kindly help resolve this error?

Partial Log output:
/storage/workspaces/ips_reislab/reislab/Software/shapemapper2/internals/python/pyshapemap/../../bin/make_reactivity_profiles.py:208: DeprecationWarning: 'U' mode is deprecated
f = open(fastaname, "rU")
/storage/workspaces/ips_reislab/reislab/Software/shapemapper2/internals/python/pyshapemap/../../bin/make_reactivity_profiles.py:240: DeprecationWarning: 'U' mode is deprecated
f = open(filename, "rU")
Traceback (most recent call last):
File "/storage/workspaces/ips_reislab/reislab/Software/shapemapper2/internals/python/pyshapemap/../../bin/make_reactivity_profiles.py", line 425, in
addtl_column_names = load_counts(p.counts[i])
File "/storage/workspaces/ips_reislab/reislab/Software/shapemapper2/internals/python/pyshapemap/../../bin/make_reactivity_profiles.py", line 330, in load_counts
counts = np.zeros(length, dtype=np.int)
File "/storage/homefs/dm23z608/.local/lib/python3.9/site-packages/numpy/init.py", line 394, 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

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