beta2blocks

[gibberwocky]

Hi

It's been a wee while since I played with this. I'm just looking at it again now, and I'm getting an error when attempting to run the beta_to_table tool:

./wgbs_tools/src/python/beta_to_blocks.py:39: FutureWarning: is_monotonic is deprecated and will be removed in a future version. Use is_monotonic_increasing instead. if not pd.Index(df['startCpG']).is_monotonic: ./wgbs_tools/src/python/beta_to_blocks.py:42: FutureWarning: is_monotonic is deprecated and will be removed in a future version. Use is_monotonic_increasing instead. if not pd.Index(df['endCpG']).is_monotonic: Traceback (most recent call last): File "./wgbs_tools/wgbstools", line 96, in <module> main() File "./wgbs_tools/wgbstools", line 63, in main importlib.import_module(args.command).main() File "./wgbs_tools/src/python/beta_to_table.py", line 154, in main for chunk in chunks: File "./wgbs_tools/src/python/beta_to_table.py", line 137, in beta2table_generator yield get_table(subset_blocks, gf, min_cov, threads, verbose) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "./wgbs_tools/src/python/beta_to_table.py", line 99, in get_table with np.warnings.catch_warnings(): ^^^^^^^^^^^ File "./myconda/envs/meth/lib/python3.11/site-packages/numpy/__init__.py", line 284, in __getattr__ raise AttributeError("module {!r} has no attribute " AttributeError: module 'numpy' has no attribute 'warnings'. Did you mean: 'hanning'?

Here's my pip list:

numpy 1.24.1 pandas 1.5.3 pip 22.3 python-dateutil 2.8.2 pytz 2022.7.1 scipy 1.10.0 setuptools 65.5.0 six 1.16.0 wheel 0.37.1

Any thoughts?

Cheers

D

[gibberwocky]

Updated htslib, cloned the latest wgbs_tools, rebuilt genome, runs without error now.