Automatically re-annotate PFAM domains if they are incompatible
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Description
Hi,
I'm running version 0.1.26 and I'm getting the same error as #47
part of error message is below:
ERROR 06/07 22:04:58 pfam_id
Traceback (most recent call last):
File "/mnt/data/sbusi/antismash/.snakemake/conda/bf12a359/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 2656, in get_loc
return self._engine.getloc(key)
File "pandas/_libs/index.pyx", line 108, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 132, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 1601, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 1608, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'pfam_id'
Thank you for your help!
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Research direction
Start by reproducing the reported failure on version 0.1.26 and trace the pandas KeyError for pfam_id. Then inspect the PFAM-domain annotation flow to determine how incompatible domains should be re-annotated; no repository file or test is named, so the expected behavior still needs to be defined.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- pandas, python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100