YalamanchiliLab / PolyAMiner-Bulk

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Empty fdf matrix in MakeAPAMatrix.MakeMatrix() #5

Open zmx21 opened 10 months ago

zmx21 commented 10 months ago

Hello,

I have received the following error while running the provided test script Traceback (most recent call last): File "/remote/idiap.svm/group.genomics/zmxu/PolyAMiner-Bulk/Demo/../PolyA-miner.py", line 486, in <module> main() File "/remote/idiap.svm/group.genomics/zmxu/PolyAMiner-Bulk/Demo/../PolyA-miner.py", line 283, in main if MakeAPAMatrix.MakeMatrix(args.o, args.p, args.outPrefix, args.pa_p, args.pa_a, args.pa_m, controls, treated, args.apa_min, args.gene_min, args.mode,controls+treated,logBook,args.pa_usage) == 1: File "/remote/idiap.svm/group.genomics/zmxu/PolyAMiner-Bulk/lib/MakeAPAMatrix.py", line 172, in MakeMatrix cdf = fdf[['feature_id', 'gene_id'] + controls] File "/idiap/home/zmxu/.local/lib/python3.9/site-packages/pandas/core/frame.py", line 3899, in __getitem__ indexer = self.columns._get_indexer_strict(key, "columns")[1] File "/idiap/home/zmxu/.local/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 6114, in _get_indexer_strict self._raise_if_missing(keyarr, indexer, axis_name) File "/idiap/home/zmxu/.local/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 6175, in _raise_if_missing raise KeyError(f"None of [{key}] are in the [{axis_name}]") KeyError: "None of [Index(['feature_id', 'gene_id', 'control1_.subset.sorted',\n 'control2_.subset.sorted', 'control3_.subset.sorted'],\n dtype='object')] are in the [columns]"

Upon further investigation, it looks like the fdf dataframe was never populated and remains empty - hence the error. Any idea what could be happening? Thanks!

Zejian-Wang commented 1 month ago

Hi zmx21,

I got the same error about it, have you solve this issues?

Thank you!

Best, ZJ