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IndexError: Positional Indexers are Out-of-Bounds in Insulation Calculation #529

Closed g1g122 closed 3 months ago

g1g122 commented 3 months ago

Description: I encountered an IndexError while running the TAD analysis script on chromosome regions chr1 and chr2. The error seems to occur during the insulation score calculation step in the cooltools package. Below are the details of the error and the relevant code snippets.

Error Traceback: INFO:root:fallback to serial implementation. INFO:root:Processing region chr1 INFO:root:Processing region chr2 Traceback (most recent call last): File "/home/yhzheng/Software/anaconda3/envs/omics/lib/python3.9/site-packages/pandas/core/indexing.py", line 1714, in _get_list_axis return self.obj._take_with_is_copy(key, axis=axis) File "/home/yhzheng/Software/anaconda3/envs/omics/lib/python3.9/site-packages/pandas/core/generic.py", line 4150, in _take_with_is_copy result = self.take(indices=indices, axis=axis) File "/home/yhzheng/Software/anaconda3/envs/omics/lib/python3.9/site-packages/pandas/core/generic.py", line 4130, in take new_data = self._mgr.take( File "/home/yhzheng/Software/anaconda3/envs/omics/lib/python3.9/site-packages/pandas/core/internals/managers.py", line 891, in take indexer = maybe_convert_indices(indexer, n, verify=verify) File "/home/yhzheng/Software/anaconda3/envs/omics/lib/python3.9/site-packages/pandas/core/indexers/utils.py", line 282, in maybe_convert_indices raise IndexError("indices are out-of-bounds") IndexError: indices are out-of-bounds

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/home/yhzheng/Projects/Omics/CodeTest/TEST_TAD_analysis/TAD_analysis.py", line 206, in analyze_and_visualize(hg38_dir, hg38_output_dir, resolution, region, test) File "/home/yhzheng/Projects/Omics/CodeTest/TEST_TAD_analysis/TAD_analysis.py", line 63, in analyze_and_visualize insulation_table = insulation(clr, windows, verbose=True) File "/home/yhzheng/Software/anaconda3/envs/omics/lib/python3.9/site-packages/cooltools/api/insulation.py", line 713, in insulation ins_table = calculate_insulation_score( File "/home/yhzheng/Software/anaconda3/envs/omics/lib/python3.9/site-packages/cooltools/lib/common.py", line 541, in wrapper result = func(*args, **kwargs, map_functor=mymap) File "/home/yhzheng/Software/anaconda3/envs/omics/lib/python3.9/site-packages/cooltools/api/insulation.py", line 275, in calculate_insulation_score ins_table = pd.concat(ins_region_tables) File "/home/yhzheng/Software/anaconda3/envs/omics/lib/python3.9/site-packages/pandas/core/reshape/concat.py", line 382, in concat op = _Concatenator( File "/home/yhzheng/Software/anaconda3/envs/omics/lib/python3.9/site-packages/pandas/core/reshape/concat.py", line 445, in init objs, keys = self._clean_keys_and_objs(objs, keys) File "/home/yhzheng/Software/anaconda3/envs/omics/lib/python3.9/site-packages/pandas/core/reshape/concat.py", line 504, in _clean_keys_and_objs objs_list = list(objs) File "/home/yhzheng/Software/anaconda3/envs/omics/lib/python3.9/site-packages/cooltools/api/insulation.py", line 331, in _get_region_insulation ins_track, n_pixels, sum_balanced, sum_counts = insul_diamond( File "/home/yhzheng/Software/anaconda3/envs/omics/lib/python3.9/site-packages/cooltools/api/insulation.py", line 111, in insul_diamond diag_pixels = cooler.annotate(diag_pixels, bins[[clr_weight_name]]) File "/home/yhzheng/Software/anaconda3/envs/omics/lib/python3.9/site-packages/cooler/api.py", line 634, in annotate ann1.iloc[bin1 - bmin] File "/home/yhzheng/Software/anaconda3/envs/omics/lib/python3.9/site-packages/pandas/core/indexing.py", line 1191, in getitem return self._getitem_axis(maybe_callable, axis=axis) File "/home/yhzheng/Software/anaconda3/envs/omics/lib/python3.9/site-packages/pandas/core/indexing.py", line 1743, in _getitem_axis return self._get_list_axis(key, axis=axis) File "/home/yhzheng/Software/anaconda3/envs/omics/lib/python3.9/site-packages/pandas/core/indexing.py", line 1717, in _get_list_axis raise IndexError("positional indexers are out-of-bounds") from err IndexError: positional indexers are out-of-bounds

Relevant Code: clr = cooler.Cooler(f'{mcool_file}::resolutions/{resolution}') windows = [3resolution, 5resolution, 10resolution, 25resolution] insulation_table = insulation(clr, windows, verbose=True)

Environment: Python version: 3.9 cooltools version: 0.7.0

Any help or guidance on resolving this issue would be greatly appreciated. Thank you!

Phlya commented 3 months ago

You need to either update cooler to the latest version, or downgrade it to v0.9.3

g1g122 commented 3 months ago

You need to either update cooler to the latest version, or downgrade it to v0.9.3

Thank you so much for your help! Following your suggestions, my issue has been resolved. I really appreciate your guidance and prompt response!!

Phlya commented 3 months ago

Happy to help!