error after install with bioconda #7
Description
Hi oxygen311,
I've installed parebricks with conda install -c conda-forge -c bioconda PaReBrick. When I try to run the provided example code, I get the following error; any thoughts (e.g. is there a required version of bg)?
$ parebrick -t tree.nwk -b maf2synteny-output -l labels.csv
[2024-07-29 14:35:36,071] INFO - <Running module: Preprocess Data>
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[2024-07-29 14:35:36,135] INFO - Converting block coords to infercars format
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[2024-07-29 14:35:36,885] INFO - <Module finished: Preprocess Data>, elapsed 0.8142709732055664 seconds
[2024-07-29 14:35:36,885] INFO - <Running module: Parsers and check strains>
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[2024-07-29 14:35:37,644] INFO - Blocks count: 217
[2024-07-29 14:35:37,645] INFO - Unique one-copy blocks count: 125
[2024-07-29 14:35:37,660] INFO - Mean block coverage: 77.40723362525112 %
[2024-07-29 14:35:37,674] INFO - Mean common one-copy blocks coverage: 68.25079478567572 %
[2024-07-29 14:35:37,688] INFO - Mean 80 % rate one-copy blocks coverage: 71.16868232101604 %
[2024-07-29 14:35:37,742] INFO - Strains in blocks file count: 219
[2024-07-29 14:35:37,742] INFO - Strains in tree leafs count: 219
[2024-07-29 14:35:37,742] INFO - Intersected strains count: 219
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[2024-07-29 14:35:37,742] INFO - <Module finished: Parsers and check strains>, elapsed 0.8569958209991455 seconds
[2024-07-29 14:35:37,742] INFO - <Running module: Balanced rearrangements characters>
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Traceback (most recent call last):
File "/opt/miniconda3/envs/intel_env/bin/parebrick", line 10, in <module>
sys.exit(main())
^^^^^^
File "/opt/miniconda3/envs/intel_env/lib/python3.12/site-packages/parebrick/main.py", line 428, in main
balanced_rearrangements_characters()
File "/opt/miniconda3/envs/intel_env/lib/python3.12/site-packages/parebrick/utils/decorators.py", line 13, in wrapper
return_value = func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda3/envs/intel_env/lib/python3.12/site-packages/parebrick/main.py", line 209, in balanced_rearrangements_characters
b_characters = get_characters_balanced(preprocessed_data_folder + UNIQUE_GRIMM_FILENAME, genomes, logger)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda3/envs/intel_env/lib/python3.12/site-packages/parebrick/characters/balanced.py", line 73, in get_characters_balanced
bg = GRIMMReader.get_breakpoint_graph(open(grimm_file))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda3/envs/intel_env/lib/python3.12/site-packages/bg/grimm.py", line 310, in get_breakpoint_graph
edge.update_data(source=edge_specific_data)
File "/opt/miniconda3/envs/intel_env/lib/python3.12/site-packages/bg/edge.py", line 190, in update_data
recursive_dict_update(self.data, source)
File "/opt/miniconda3/envs/intel_env/lib/python3.12/site-packages/bg/utils.py", line 20, in recursive_dict_update
if isinstance(value, collections.Mapping) and isinstance(dict1_entry, collections.Mapping):
^^^^^^^^^^^^^^^^^^^
AttributeError: module 'collections' has no attribute 'Mapping'