issues with enrichr

[SaBay89]

Setup

I am reporting a problem with GSEApy version 0.10.5, Python version 3.8.8, and operating
system in windows (jupyter notebook) as follows:

import gseapy

# assign a list object to enrichr
gl = ['SCARA3', 'LOC100044683', 'CMBL', 'CLIC6', 'IL13RA1', 'TACSTD2', 'DKKL1', 'CSF1',
     'SYNPO2L', 'TINAGL1', 'PTX3', 'BGN', 'HERC1', 'EFNA1', 'CIB2', 'PMP22', 'TMEM173']

gseapy.enrichr(gene_list=gl, gene_sets='KEGG_2016', outdir='test')

# or a txt file path.
gseapy.enrichr(gene_list='gene_list.txt', gene_sets='KEGG_2016',
               outdir='test', cutoff=0.05, format='png' )

I get the following error:

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

Can you explain what is wrong ? Thank you

[rachebouche]

I have the same error
python = 3.11
pandas = 2.0.3
code :

gene_symbols = ['GNAI1', 'SPP1', 'IKZF1', 'TGFBR2', 'TLR4', 'MBOAT7', 'CCNB2', 'MYLK', 'CDKN1A', 'ZNF586', 'WASHC4', 'SRC', 'UGDH', 'CDK6', 'HMG20B']

gp.enrichr(gene_list=gene_symbols, gene_sets="GO_Biological_Process_2023", outdir=None)

It seems to be an error related to pandas. Maybe it could be corrected by using pandas.concat() instead of pandas.DataFrame.append() ?

---

AttributeError Traceback (most recent call last)
/tmp/ipykernel_98143/1600401673.py in ?()
----> 1 gp.enrichr(gene_list=gene_symbols, gene_sets="GO_Biological_Process_2023", outdir=None, )

~/miniconda3/envs/dataproc/lib/python3.11/site-packages/gseapy/enrichr.py in ?(gene_list, gene_sets, description, outdir, cutoff, format, figsize, top_term, no_plot, verbose)
299 :return: An Enrichr object, which obj.res2d contains your enrichr query.
300 """
301 enr = Enrichr(gene_list, gene_sets, description, outdir,
302 cutoff, format, figsize, top_term, no_plot, verbose)
--> 303 enr.run()
304
305 return enr

~/miniconda3/envs/dataproc/lib/python3.11/site-packages/gseapy/enrichr.py in ?(self)
169 shortID, res = self.get_results(genes_list)
170 # Remember gene set library used
171 res["Gene_set"] = self._gs
172 # Append to master dataframe
--> 173 self.results = self.results.append(res, ignore_index=True)
174 self.res2d = res
175 sleep(2)
176 if self._outdir is None: continue

~/miniconda3/envs/dataproc/lib/python3.11/site-packages/pandas/core/generic.py in ?(self, name)
...
5987 ):
5988 return self[name]
-> 5989 return object.getattribute(self, name)

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

[zqfang]

Hello, could you please update GSEApy to the latest version? This should fix the issue we are currently experiencing. Thank you.