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edgraham / GhostKoalaParser

Parser for Ghost Koala
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Importing KEGG annotation to anvi'o #5

Closed anaya1 closed 6 years ago

anaya1 commented 6 years ago

I have been trying to import functional KEGG annotations to anvi'o using GhostKoalaParse KEGG-to-anvio script. I am not sure what is going wrong but when running the command: python KEGG-to-anvio --KeggDB samples/KO_Orthology_ko00001.txt -i ~/Documents/BMS_extraction/user_ko.txt -o ~/Documents/BMS_extraction/ko_anvio.txt I am getting sth like this: Traceback (most recent call last): File "KEGG-to-anvio", line 38, in extracted= extracted.rename({'description':'function'},axis='columns') File "/Users/annaalessi/anaconda3/lib/python3.6/site-packages/pandas/core/frame.py", line 2746, in rename **kwargs) File "/Users/annaalessi/anaconda3/lib/python3.6/site-packages/pandas/core/generic.py", line 694, in rename 'argument "{0}"'.format(list(kwargs.keys())[0])) TypeError: rename() got an unexpected keyword argument "axis"

The file I used to run it, is here: user_ko.txt. Many thanks for your help and any suggestions.

edgraham commented 6 years ago

This looks like it may be a python 3 error. Try running the script in python 2 and let me know if it works. I can make the necessary adjustments to make it python 3 compatable if thats the case.

On Tue, Jan 30, 2018 at 3:09 AM, Anna Alessi notifications@github.com wrote:

I have been trying to import functional KEGG annotations to anvi'o using GhostKoalaParse KEGG-to-anvio script. I am not sure what is going wrong but when running the command: python KEGG-to-anvio --KeggDB samples/KO_Orthology_ko00001.txt -i ~/Documents/BMS_extraction/user_ko.txt -o ~/Documents/BMSextraction/ko anvio.txt I am getting sth like this: Traceback (most recent call last): File "KEGG-to-anvio", line 38, in extracted= extracted.rename({'description':'function'},axis='columns') File "/Users/annaalessi/anaconda3/lib/python3.6/site-packages/pandas/core/frame.py", line 2746, in rename **kwargs) File "/Users/annaalessi/anaconda3/lib/python3.6/site-packages/pandas/core/generic.py", line 694, in rename 'argument "{0}"'.format(list(kwargs.keys())[0])) TypeError: rename() got an unexpected keyword argument "axis"

The file I used to run it, is here: user_ko.txt https://github.com/edgraham/GhostKoalaParser/files/1677392/user_ko.txt. Many thanks for your help and any suggestions.

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