key error

[anke-king]

Setup

I am reporting a problem with GSEApy version, Python version, and operating
system as follows:

3.9.18 | packaged by conda-forge | (main, Dec 23 2023, 16:36:46) 
[Clang 16.0.6 ]
CPython
macOS-12.4-x86_64-i386-64bit
1.1.1

(Please copy and run the above in your Python, and copy-and-paste the output)

Expected behaviour

prerank

Actual behaviour

key error: "gene_name"

Steps to reproduce

pre_res = gp.prerank(rnk = ranking, gene_sets = 'GO_Biological_Process_2021', seed = 6, permutation_num = 100, min_size = 5 )
ranking is df with 2 columns.

[zqfang]

can you print first 5 row of your ranking ?

make sure the first column is gene_symbol, the second column is ranking values

[anke-king]

This is how I calculate the rank:
df['Rank']=np.log10(df.padj)*df.log2FoldChange
df = df.sort_values('Rank', ascending = False).reset_index(drop = True)
ranking = df[['gene_name', 'Rank']]

and ranking.head(5) yields:
gene_name Rank
0 mCherry_F 715.775855
1 ORF_032 297.716912
2 ORF_061 286.317331
3 IFI44L 244.128925
4 ORF_029 223.571278

[zqfang]

can you print out the full error message ?

I don't know where the errors come from

[anke-king]

here is the entire error message:

KeyError Traceback (most recent call last)
Cell In[21], line 1
----> 1 pre_res = gp.prerank(rnk = ranking, gene_sets = 'GO_Biological_Process_2021', seed = 6, permutation_num = 100, min_size = 5 )

File ~/miniconda3/lib/python3.9/site-packages/gseapy/init.py:396, in prerank(rnk, gene_sets, outdir, pheno_pos, pheno_neg, min_size, max_size, permutation_num, weight, ascending, threads, figsize, format, graph_num, no_plot, seed, verbose, *arg, **kwargs)
375 weight = kwargs["weighted_score_type"]
377 pre = Prerank(
378 rnk,
379 gene_sets,
(...)
394 verbose,
395 )
--> 396 pre.run()
397 return pre

File ~/miniconda3/lib/python3.9/site-packages/gseapy/gsea.py:444, in Prerank.run(self)
441 assert self.min_size <= self.max_size
443 # parsing rankings
--> 444 dat2 = self.load_ranking()
445 assert len(dat2) > 1
446 self.ranking = dat2

File ~/miniconda3/lib/python3.9/site-packages/gseapy/gsea.py:418, in Prerank.load_ranking(self)
415 rank_metric = self._load_data(self.rnk) # gene id is the first column
416 if rank_metric.select_dtypes(np.number).shape[1] == 1:
417 # return series
--> 418 return self._load_ranking(rank_metric)
419 ## In case the input type multi-column ranking dataframe
420 # drop na gene id values
421 rank_metric = rank_metric.dropna(subset=rank_metric.columns[0])

File ~/miniconda3/lib/python3.9/site-packages/gseapy/gsea.py:385, in Prerank._load_ranking(self, rank_metric)
383 rank_metric.dropna(how="any", inplace=True)
384 # rename duplicate id, make them unique
--> 385 rank_metric = self.make_unique(rank_metric, col_idx=0)
386 # reset ranking index, because you have sort values and drop duplicates.
387 rank_metric.reset_index(drop=True, inplace=True)

File ~/miniconda3/lib/python3.9/site-packages/gseapy/base.py:246, in GSEAbase.make_unique(self, rank_metric, col_idx)
243 self.logger.info("Input gene rankings contains duplicated IDs")
244 mask = rank_metric.duplicated(subset=id_col, keep=False)
245 dups = (
--> 246 rank_metric.loc[mask, id_col]
247 .groupby(id_col)
248 .cumcount()
249 .map(lambda c: "" + str(c) if c else "")
250 )
251 rank_metric.loc[mask, id_col] = rank_metric.loc[mask, id_col] + dups
252 return rank_metric

File ~/miniconda3/lib/python3.9/site-packages/pandas/core/series.py:2238, in Series.groupby(self, by, axis, level, as_index, sort, group_keys, observed, dropna)
2235 raise TypeError("as_index=False only valid with DataFrame")
2236 axis = self._get_axis_number(axis)
-> 2238 return SeriesGroupBy(
2239 obj=self,
2240 keys=by,
2241 axis=axis,
2242 level=level,
2243 as_index=as_index,
2244 sort=sort,
2245 group_keys=group_keys,
2246 observed=observed,
2247 dropna=dropna,
2248 )

File ~/miniconda3/lib/python3.9/site-packages/pandas/core/groupby/groupby.py:1329, in GroupBy.init(self, obj, keys, axis, level, grouper, exclusions, selection, as_index, sort, group_keys, observed, dropna)
1326 self.dropna = dropna
1328 if grouper is None:
-> 1329 grouper, exclusions, obj = get_grouper(
1330 obj,
1331 keys,
1332 axis=axis,
1333 level=level,
1334 sort=sort,
1335 observed=False if observed is lib.no_default else observed,
1336 dropna=self.dropna,
1337 )
1339 if observed is lib.no_default:
1340 if any(ping._passed_categorical for ping in grouper.groupings):

File ~/miniconda3/lib/python3.9/site-packages/pandas/core/groupby/grouper.py:1043, in get_grouper(obj, key, axis, level, sort, observed, validate, dropna)
1041 in_axis, level, gpr = False, gpr, None
1042 else:
-> 1043 raise KeyError(gpr)
1044 elif isinstance(gpr, Grouper) and gpr.key is not None:
1045 # Add key to exclusions
1046 exclusions.add(gpr.key)

KeyError: 'gene_name'

[zqfang]

I think the issue is same to #251, can you install v1.1.2 and try again ? the error should be gone in the fixed version( v1.1.2)