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With my genelist I am getting this error: TypeError: sequence item 109: expected str instance, float found
gseapy prerank -r ls D*rnk -g /Users/kopardevn/Downloads/h.all.v6.0.symbols.gmt -o prerank_test_report_2 Traceback (most recent call last): File "/Users/kopardevn/anaconda/bin/gseapy", line 11, in sys.exit(main()) File "/Users/kopardevn/anaconda/lib/python3.6/site-packages/gseapy/main.py", line 43, in main args.ascending, args.figsize, args.format, args.graph, args.seed) File "/Users/kopardevn/anaconda/lib/python3.6/site-packages/gseapy/gsea.py", line 300, in prerank rdict['genes'] = ",".join(dat2.ix[ind,'gene_name'].tolist()) TypeError: sequence item 109: expected str instance, float found
ls D*rnk
h.all.v6.0.symbols.gmt has been downloaded from http://software.broadinstitute.org/gsea/downloads.jsp and the genelist is
D.rnk.txt
The text was updated successfully, but these errors were encountered:
I made some format changes in the version 0.7.7. That's why your gene list is failed(My test gene list runs ok).
You could install gseapy-v0.7.8 using pip, which fixes your problem. Thanks. @kopardev
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With my genelist I am getting this error:
TypeError: sequence item 109: expected str instance, float found
gseapy prerank -r
ls D*rnk
-g /Users/kopardevn/Downloads/h.all.v6.0.symbols.gmt -o prerank_test_report_2Traceback (most recent call last):
File "/Users/kopardevn/anaconda/bin/gseapy", line 11, in
sys.exit(main())
File "/Users/kopardevn/anaconda/lib/python3.6/site-packages/gseapy/main.py", line 43, in main
args.ascending, args.figsize, args.format, args.graph, args.seed)
File "/Users/kopardevn/anaconda/lib/python3.6/site-packages/gseapy/gsea.py", line 300, in prerank
rdict['genes'] = ",".join(dat2.ix[ind,'gene_name'].tolist())
TypeError: sequence item 109: expected str instance, float found
h.all.v6.0.symbols.gmt has been downloaded from http://software.broadinstitute.org/gsea/downloads.jsp
and the genelist is
D.rnk.txt
The text was updated successfully, but these errors were encountered: