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TypeERROR #21

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kopardev opened this issue Apr 20, 2017 · 1 comment
Closed

TypeERROR #21

kopardev opened this issue Apr 20, 2017 · 1 comment

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@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_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

h.all.v6.0.symbols.gmt has been downloaded from http://software.broadinstitute.org/gsea/downloads.jsp
and the genelist is

D.rnk.txt

@zqfang
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zqfang commented Apr 20, 2017

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

@zqfang zqfang added the bug label Apr 21, 2017
@zqfang zqfang added the fixed label Jun 26, 2017
@zqfang zqfang closed this as completed Sep 7, 2017
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