bioinfo4321
commented
5 years ago issue seems to resolve by appropriately editing provided dbepams.tsv, issue closed.
Closed bioinfo4321 closed 5 years ago
bioinfo4321
commented
5 years ago issue seems to resolve by appropriately editing provided dbepams.tsv, issue closed.
Hi, I am not able to make beditor run with any PAM other than NG and NGG, for example, i tried NGA and got following error. Same configuration runs perfectly fine for NGG. Thanks for your response.
_ multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/user/miniconda/envs/beditor/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 3078, in get_loc return self._engine.get_loc(key) File "pandas/_libs/index.pyx", line 140, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 162, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1492, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1500, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'nucleotide mutation'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/home/user/miniconda/envs/beditor/lib/python3.6/multiprocessing/pool.py", line 119, in worker result = (True, func(*args, *kwds)) File "/home/user/miniconda/envs/beditor/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar return list(map(args)) File "/home/user/miniconda/envs/beditor/lib/python3.6/site-packages/beditor/pipeline.py", line 106, in pipeline_chunks dseq2dmutagenesis(cfg) File "/home/user/miniconda/envs/beditor/lib/python3.6/site-packages/beditor/lib/get_mutations.py", line 341, in dseq2dmutagenesis host=cfg['host']) File "/home/user/miniconda/envs/beditor/lib/python3.6/site-packages/beditor/lib/get_mutations.py", line 171, in get_possible_mutagenesis dmutagenesis['nucleotide mutation: count']=[len(s) for s in dmutagenesis['nucleotide mutation']] File "/home/user/miniconda/envs/beditor/lib/python3.6/site-packages/pandas/core/frame.py", line 2688, in getitem return self._getitem_column(key) File "/home/user/miniconda/envs/beditor/lib/python3.6/site-packages/pandas/core/frame.py", line 2695, in _getitem_column return self._get_item_cache(key) File "/home/user/miniconda/envs/beditor/lib/python3.6/site-packages/pandas/core/generic.py", line 2489, in _get_item_cache values = self._data.get(item) File "/home/user/miniconda/envs/beditor/lib/python3.6/site-packages/pandas/core/internals.py", line 4115, in get loc = self.items.get_loc(item) File "/home/user/miniconda/envs/beditor/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 3080, in get_loc return self._engine.get_loc(self._maybe_cast_indexer(key)) File "pandas/_libs/index.pyx", line 140, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 162, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1492, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1500, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'nucleotide mutation' """
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/home/user/miniconda/envs/beditor/bin/beditor", line 10, in
sys.exit(main())
File "/home/user/miniconda/envs/beditor/lib/python3.6/site-packages/beditor/pipeline.py", line 461, in main
test=args.test,force=args.force)
File "/home/user/miniconda/envs/beditor/lib/python3.6/site-packages/beditor/pipeline.py", line 405, in pipeline
pool.map(pipeline_chunks, chunkcfgps)
File "/home/user/miniconda/envs/beditor/lib/python3.6/multiprocessing/pool.py", line 266, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home/user/miniconda/envs/beditor/lib/python3.6/multiprocessing/pool.py", line 644, in get
raise self.value
KeyError: 'nucleotide mutation'