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svalkiers / clusTCR

CDR3 clustering module providing a new method for fast and accurate clustering of large data sets of CDR3 amino acid sequences, and offering functionalities for downstream analysis of clustering results.
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Error in the clustcr.input.datasets #33

Closed DimChatz closed 2 years ago

DimChatz commented 2 years ago

Runtime error

When running the code for the first time, using the example from the Evaluating part of the documantation I reached this error:

/home/dimchatz/anaconda3/envs/clustering/lib/python3.9/site-packages/clustcr/clustering/mcl.py:136: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. nodelist = nodelist.append(nodes) Total time to run '_twostep': 0.713s Traceback (most recent call last): File "/home/dimchatz/Desktop/clusTCR_trial.py", line 5, in <module> epitopes = datasets.test_epitope() AttributeError: module 'clustcr.input.datasets' has no attribute 'test_epitope'

I have updated the package and looked through google but nothing came up

svalkiers commented 2 years ago

Thank you for reporting this error. I see this issue is caused due to a typo in the documentation. Indeed .test_epitope() is not a valid method. Rather it should be .test_epitopes() with an "s" at the end. Our apologies for this inconvenience.