Prerank empties out the dictionary

[jolespin]

It's not working for some reason. I also don't know why it's emptying out my dictionary.

[zqfang]

Your gene_sets input has to be dictionary.

 gene_set = { 'GO:008138': ['b1838','b1411','b2737','b0049'], ...}

[jolespin]

Not sure how I'm just seeing this now but it's still doing it. My example above was a dictionary which is why I did .items so I could show the structure of the key value pairs.

[jolespin]

Here's the code:

import pandas as pd
import gseapy as gp #version 

'0.10.1'
import numpy as np
import pickle

# Get gene rank weights
with open("data_files/gene_weights.dict.pkl", "rb") as f:
    genes = pd.Series(pickle.load(f))
rnk = genes.to_frame().reset_index()
rnk.columns = [0,1]    

# Make directories and containers
outdir = "prerank_output_testing"


# Get gene set
with open("data_files/ecocyc_pathways.dict.pkl", "rb") as f:
    gene_sets = pickle.load(f)

print("gene_sets is a {} type".format(type(gene_sets)))
print("First 10 items:", dict(list(gene_sets.items())[:10]))
print("There are a total of {} items".format(len(gene_sets)))

pre_res = gp.prerank(
    rnk=rnk, 
    gene_sets=gene_sets,
    processes=4,
    min_size=5,
    permutation_num=1000, 
    outdir=outdir,
    seed=0, 
    no_plot=False,

)

Here's the data_files directory:
data_files.zip

Can I request that we reopen this?

[dawe]

Following up on this issue, I am using prerank on "KEGG_2021_Human" and I realized a gene list ('Non-homologous end-joining') is constantly removed from the testable ones. It is true it only contains 13 genes, but the same odd behaviour happens when I set min_size=5.