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gkichaev / PAINTOR_V3.0

Fast, integrative fine mapping with functional data
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CANVIS script won't run #39

Open bogdanknez opened 5 years ago

bogdanknez commented 5 years ago

I've managed to run through the entire PAINTOR pipeline up until the visualization point. For running CANVIS.py, I've set up a virtual environment with all the most updated packages required, as suggested on the PAINTOR wiki page for visualization. Once inside my environment, I've tried executing the code with

python CANVIS.py \ -l ctla4.results \ -z Zscore \ -r ctla4.LD1 \ -a ctla4.annotations

However, when I execute the above, the script runs for several seconds before outputting the below. Is there anything I can do in order to get this to run? Not sure what is causing these error messages? Again, the files that I am inputting to execute this are the exact output files of the previous PAINTOR pipeline (unmodified in any way). Thanks for your help.

Traceback (most recent call last): File "/gpfs2/well/jknight/bogdan/PAINTOR_V3.0/python-virtual-environments/env/lib/python3.5/site-packages/pandas/core/indexes/base.py", line 2657, in get_loc return self._engine.get_loc(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: 'BP'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "CANVIS.py", line 520, in main() File "CANVIS.py", line 493, in main ld_name, annotations, annotation_names, interval, bp_head) File "CANVIS.py", line 44, in Read_Input location = zscore_data[bp_head] File "/gpfs2/well/jknight/bogdan/PAINTOR_V3.0/python-virtual-environments/env/lib/python3.5/site-packages/pandas/core/frame.py", line 2927, in getitem indexer = self.columns.get_loc(key) File "/gpfs2/well/jknight/bogdan/PAINTOR_V3.0/python-virtual-environments/env/lib/python3.5/site-packages/pandas/core/indexes/base.py", line 2659, in get_loc return self._engine.get_loc(self._maybe_cast_indexer(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: 'BP'

JiaShun-Xiao commented 4 years ago

see this pull request https://github.com/gkichaev/PAINTOR_V3.0/pull/44