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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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RGI Heatmap category #236

Closed kayobianco closed 1 year ago

kayobianco commented 1 year ago

I'm trying to use the command "rgi heatmap -clus both -cat drug_class -i "$output_dir" -o "$heatmap_output"" but the -cat command has problems and output is as below: File "/home/kayobianco/miniconda3/envs/rgi/bin/rgi", line 4, in MainBase() File "/home/kayobianco/miniconda3/envs/rgi/lib/python3.8/site-packages/app/MainBase.py", line 83, in init getattr(self, args.command)() File "/home/kayobianco/miniconda3/envs/rgi/lib/python3.8/site-packages/app/MainBase.py", line 346, in heatmap self.heatmap_run(args) File "/home/kayobianco/miniconda3/envs/rgi/lib/python3.8/site-packages/app/MainBase.py", line 365, in heatmap_run obj.run() File "/home/kayobianco/miniconda3/envs/rgi/lib/python3.8/site-packages/app/Heatmap.py", line 438, in run df = self.create_categories(drug_class, df) File "/home/kayobianco/miniconda3/envs/rgi/lib/python3.8/site-packages/app/Heatmap.py", line 97, in create_categories df = df.append([df.loc[model]](len(class_dict[model])-1)) File "/home/kayobianco/miniconda3/envs/rgi/lib/python3.8/site-packages/pandas/core/generic.py", line 5989, in getattr return object.getattribute(self, name) AttributeError: 'DataFrame' object has no attribute 'append' Traceback (most recent call last): File "/home/kayobianco/miniconda3/envs/rgi/bin/rgi", line 4, in MainBase() File "/home/kayobianco/miniconda3/envs/rgi/lib/python3.8/site-packages/app/MainBase.py", line 83, in init getattr(self, args.command)() File "/home/kayobianco/miniconda3/envs/rgi/lib/python3.8/site-packages/app/MainBase.py", line 346, in heatmap self.heatmap_run(args) File "/home/kayobianco/miniconda3/envs/rgi/lib/python3.8/site-packages/app/MainBase.py", line 365, in heatmap_run obj.run() File "/home/kayobianco/miniconda3/envs/rgi/lib/python3.8/site-packages/app/Heatmap.py", line 438, in run df = self.create_categories(drug_class, df) File "/home/kayobianco/miniconda3/envs/rgi/lib/python3.8/site-packages/app/Heatmap.py", line 97, in create_categories df = df.append([df.loc[model]](len(class_dict[model])-1)) File "/home/kayobianco/miniconda3/envs/rgi/lib/python3.8/site-packages/pandas/core/generic.py", line 5989, in getattr return object.getattribute(self, name) AttributeError: 'DataFrame' object has no attribute 'append' Traceback (most recent call last): File "/home/kayobianco/miniconda3/envs/rgi/bin/rgi", line 4, in MainBase() File "/home/kayobianco/miniconda3/envs/rgi/lib/python3.8/site-packages/app/MainBase.py", line 83, in init getattr(self, args.command)() File "/home/kayobianco/miniconda3/envs/rgi/lib/python3.8/site-packages/app/MainBase.py", line 346, in heatmap self.heatmap_run(args) File "/home/kayobianco/miniconda3/envs/rgi/lib/python3.8/site-packages/app/MainBase.py", line 365, in heatmap_run obj.run() File "/home/kayobianco/miniconda3/envs/rgi/lib/python3.8/site-packages/app/Heatmap.py", line 438, in run df = self.create_categories(drug_class, df) File "/home/kayobianco/miniconda3/envs/rgi/lib/python3.8/site-packages/app/Heatmap.py", line 97, in create_categories df = df.append([df.loc[model]]*(len(class_dict[model])-1)) File "/home/kayobianco/miniconda3/envs/rgi/lib/python3.8/site-packages/pandas/core/generic.py", line 5989, in getattr return object.getattribute(self, name) AttributeError: 'DataFrame' object has no attribute 'append'

dukz commented 1 year ago

I resolved this by downgrading the pandas package to 1.5.3.

conda install pandas=1.5.3