Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
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'
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'