'DataFrame' object has no attribute 'append'

[rubickkkkk]

ERROR:AttributeError: 'DataFrame' object has no attribute 'append'

I am reporting a problem with GSEApy==1.1.2, Pandas==2.1.4 , and Python==3.11.6
system as follows:

I use the code as follow:

result = adata_mi.uns['dea_lei_mi'] groups = result['names'].dtype.names for group in groups : degs = pd.DataFrame({ key: result[key][group] for key in ['names','scores', 'pvals','pvals_adj','logfoldchanges']}) degs_sig = degs[degs.pvals_adj < 0.05] degs_up = degs_sig[degs_sig.logfoldchanges > 0] degs_dw = degs_sig[degs_sig.logfoldchanges < 0] enr_dw = gp.enrichr(degs_dw["names"].tolist(), gene_sets=['GO_Biological_Process_2023'], outdir=None)

and reporting the error:

`AttributeError Traceback (most recent call last)
/tmp/ipykernel_941722/3709642233.py in ?()
6 degs = pd.DataFrame({ key: result[key][group] for key in ['names','scores', 'pvals','pvals_adj','logfoldchanges']})
7 degs_sig = degs[degs.pvals_adj < 0.05]
8 degs_up = degs_sig[degs_sig.logfoldchanges > 0]
9 degs_dw = degs_sig[degs_sig.logfoldchanges < 0]
---> 10 enr_dw = gp.enrichr(degs_dw["names"].tolist(),
11 gene_sets=['GO_Biological_Process_2023'],
12 outdir=None)
13 enr_dw.res2d.Term = enr_dw.res2d.Term.str.split(" (GO").str[0]

/home/test/anaconda3/envs/scrna/lib/python3.11/site-packages/gseapy/enrichr.py in ?(gene_list, gene_sets, organism, description, outdir, background, cutoff, format, figsize, top_term, no_plot, verbose)

/home/test/anaconda3/envs/scrna/lib/python3.11/site-packages/gseapy/enrichr.py in ?(self)
423 "{}.background.genes.txt".format(self.background),
424 ),
425 )
426 self._logger.info(
--> 427 "Using all annotated genes with GO_ID as background: %s" % self.background
428 )
429 # input id type: entrez or gene_name
430 if self._isezid:

/home/test/anaconda3/envs/scrna/lib/python3.11/site-packages/pandas/core/generic.py in ?(self, name)

AttributeError: 'DataFrame' object has no attribute 'append'`

I have already tried to change the append method in enrichr.py , but it didn't work.

as follow:

line 617 :self.results = pd.concat([self.results, res], ignore_index=True)

moreover, as for the type of input gene_list, I have tried 1. degs_dw["names"].tolist() 2. degs_dw.names

[rubickkkkk]

the code

result = adata_mi.uns['dea_lei_mi']
groups = result['names'].dtype.names
for group in groups :
    degs = pd.DataFrame({ key: result[key][group]  for key in ['names','scores', 'pvals','pvals_adj','logfoldchanges']})
    degs_sig = degs[degs.pvals_adj < 0.05]
    degs_up = degs_sig[degs_sig.logfoldchanges > 0]
    degs_dw = degs_sig[degs_sig.logfoldchanges < 0]
    enr_dw = gp.enrichr(degs_dw["names"].tolist(),
                    gene_sets=['GO_Biological_Process_2023'],
                    outdir=None)

[zqfang]

Can you send me the full error message output?

The error message is in line 426, not line 617. (BTW, you should not change line 617)

[zqfang]

the lastest PR will not have this issue anymore