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View Code? Open in Web Editor NEWHARE: Genetic Feature Enrichment Analysis Pipeline
License: GNU General Public License v3.0
HARE: Genetic Feature Enrichment Analysis Pipeline
License: GNU General Public License v3.0
Dear author,
Firstly, thank you for developing this wonderful tool. I encountered an issue while testing it using the provided code, which is the same as in your tutorial. Here is the code:
hare intersect -g example_files/exampleGWAS.tsv -e reference_assets/harsRichard2020.GRCh37.bed -r reference_assets/UCSC.GRCh37.autosomes.annotation.bed -n 100 --cache_dir /gpfs/home/zhangyue/.vep --cache_version 105 -o hare.test
However, I encountered the following error:
----------------------------------------------------------------------
| |
| Welcome to the HARE genetic feature enrichment pipeline. |
| Please contact Olivia Smith at [email protected] to report issues. |
| |
----------------------------------------------------------------------
-----Workflow started at 2023-12-22 12:39:25.885827.
[args] GWAS summary statistics file: 'example_files/exampleGWAS.tsv'
[args] P-value significance threshold: 1e-06
[args] Minor allele frequency (MAF) threshold: 0.01
[args] VEP cache directory: '/gpfs/home/zhangyue/.vep', version 105
[args] Annotation max distance: 5000
[args] Biotypes included in analysis: protein_all
[args] Reference genome annotation file: 'reference_assets/UCSC.GRCh37.autosomes.annotation.bed'
[args] Reference genome build: GRCh37
[args] Element of interest BED file: 'reference_assets/harsRichard2020.GRCh37.bed'
[args] Simulation draws to be performed: 100
[args] Results will be written to hare.test.*
Loading GWAS summary statistics...OK
OK
Filtering SNPs for analysis...Traceback (most recent call last):
File "/gpfs/home/zhangyue/anaconda3/envs/hare-env/lib/python3.11/site-packages/pandas/core/indexes/base.py", line 3791, in get_loc
return self._engine.get_loc(casted_key)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "index.pyx", line 152, in pandas._libs.index.IndexEngine.get_loc
File "index.pyx", line 181, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 7080, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 7088, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'P'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/gpfs/home/zhangyue/anaconda3/envs/hare-env/bin/hare", line 8, in <module>
sys.exit(main())
^^^^^^
File "/gpfs/home/zhangyue/anaconda3/envs/hare-env/lib/python3.11/site-packages/hare.py", line 83, in main
run_intersect(intargs)
File "/gpfs/home/zhangyue/anaconda3/envs/hare-env/lib/python3.11/site-packages/hare.py", line 30, in run_intersect
intersect.main(**intersect_args)
File "/gpfs/home/zhangyue/anaconda3/envs/hare-env/lib/python3.11/site-packages/intersect.py", line 591, in main
snps_filepath = gwas_import(hareParameters, hareSettings)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/gpfs/home/zhangyue/anaconda3/envs/hare-env/lib/python3.11/site-packages/intersect.py", line 231, in gwas_import
gwas_df[argumentClass.p_col] = gwas_df[argumentClass.p_col].replace(to_replace=list([NaN,"-"]),value=1)
~~~~~~~^^^^^^^^^^^^^^^^^^^^^
File "/gpfs/home/zhangyue/anaconda3/envs/hare-env/lib/python3.11/site-packages/pandas/core/frame.py", line 3893, in __getitem__
indexer = self.columns.get_loc(key)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/gpfs/home/zhangyue/anaconda3/envs/hare-env/lib/python3.11/site-packages/pandas/core/indexes/base.py", line 3798, in get_loc
raise KeyError(key) from err
KeyError: 'P'
It seems like there is an issue with the 'P' key. Could you please help me understand what is happening?
Thanks in advance, and I hope to receive your early reply.
Gemma
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