FET in command line

[Div]

Hi,

I am trying to get the Fisher exact test to work on the command line version of the program.

This is the version of GO-Elite I am using: v.1.2.5-Py

The tutorial tells me that I should enter -- permutations "FisherExactTest" to specify that I want to use FET instead of permuted P values. However, I get an error saying that permutations needs to be an integer.

(It works on the GUI version but I would like to get it working on the command line)

Can you please help me and let me know what I am doing incorrectly?

Thanks.

[Nathan Salomonis]

Hi Divya,

It looks like there is a line that needs to be fixed. In the source code (GO_Elite.py) find:

        permutations = int(permutations);change_threshold = int(change_threshold)

and change to:

        try: permutations = int(permutations)
        except Exception: pass
        change_threshold = int(change_threshold)

This then runs fine for me, then.

Best,

Nathan

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