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ruggleslab / jukebox

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Table conversion #10

Closed tsoratto closed 4 years ago

tsoratto commented 4 years ago

Hi, I am trying to convert my humann2_genefamilies table to wham format using the script humann_2_wham.py, but I am getting this error: Traceback (most recent call last): File "humann_2_wham.py", line 54, in acc=R.group(2) AttributeError: 'NoneType' object has no attribute 'group'

Thank you for your help.

jcooperdevlin commented 4 years ago

Hi!

Could you show the first few lines of the file you are trying to convert?

tsoratto commented 4 years ago

image

jcooperdevlin commented 4 years ago

Thank you!

It appears from the first few lines the features do not have names, "Uniref50unknown". WHAM expects some kind of accession ID before the species name, for example... "UniRef90C5EH42: Sporulation_protein_AB|g__Clostridiales_noname.s__Clostridiales_1_7_47FAA"

Perhaps there was an issue with naming these features when running humann2_rename_table? Feel free to attach the file so I can help troubleshoot further.

tsoratto commented 4 years ago

Thank you for the help!

Some of then is like you said and others no. I am attaching the file.

humann2_pathabundance.txt

_

jcooperdevlin commented 4 years ago

Great, thank you!

The file you attached seems to be a pathway file which can be converted with a different script. humann_2_wham_pathways.py which should generate the appropriate WHAM file. However, you will need to add a "#" at the very beginning of the file to mark it as a humann2 output.

I hope that works!