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arpcard / rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
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Error running rgi heatmap #284

Closed mradz19 closed 1 month ago

mradz19 commented 1 month ago

I am trying to run rgi heatmap on a metagenomic samples that were analyzed using rgi bwt. However I am getting this error:

rgi heatmap -i rgi_json/ -cat gene_family
Traceback (most recent call last):
  File "/kusers/ancillary/anaconda3/envs/rgi/bin/rgi", line 4, in <module>
    MainBase()
  File "/kusers/ancillary/anaconda3/envs/rgi/lib/python3.8/site-packages/app/MainBase.py", line 83, in __init__
    getattr(self, args.command)()
  File "/kusers/ancillary/anaconda3/envs/rgi/lib/python3.8/site-packages/app/MainBase.py", line 346, in heatmap
    self.heatmap_run(args)
  File "/kusers/ancillary/anaconda3/envs/rgi/lib/python3.8/site-packages/app/MainBase.py", line 365, in heatmap_run
    obj.run()
  File "/kusers/ancillary/anaconda3/envs/rgi/lib/python3.8/site-packages/app/Heatmap.py", line 469, in run
    complete_class_df= complete_class_df.set_index(["drug_class", "resistance_mechanism"], append=True)["gene_family"].apply(pd.Series).stack()
  File "/kusers/ancillary/anaconda3/envs/rgi/lib/python3.8/site-packages/pandas/core/generic.py", line 5989, in __getattr__
    return object.__getattribute__(self, name)
AttributeError: 'Series' object has no attribute 'stack'