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nextgenusfs / gene2product

Curated list of gene names and product descriptions that pass NCBI genome submission rules.
BSD 2-Clause "Simplified" License
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update-gene2product.py not working #13

Closed DrPintoThe2nd closed 3 years ago

DrPintoThe2nd commented 3 years ago

Hi Jon,

Per usual, thank you for all your work on this software. Truly amazing! I recently annotated an invertebrate using v1.5.0 and thought I'd submit a few new gene product names. Sorry in advance, as I am not really a python person:

I forked the repository and tried to update, "python update-gene2product.py Gene2Products.new-names-passed.txt" and hit this error: ''' Traceback (most recent call last): File "update-gene2product.py", line 22, in for line in db: io.UnsupportedOperation: not readable '''

I worked around this (and the next error) by adding "a+" to lines 22 and 43, then I ran into this error and I don't know what it wants...

''' "Traceback (most recent call last): File "update-gene2product.py", line 65, in os.rename(os.path.join(currentdir, 'ncbi_cleaned_gene_products.txt'), os.path.join(currentdir, 'ncbi_cleaned_gene_products.v'+version+'.txt')) TypeError: can only concatenate str (not "NoneType") to str " '''

I've attached my list of gene names in hopes that, if nothing else, someone can update the list for me.

Gene2Products.new-names-passed.txt

Cheers! -bjp

nextgenusfs commented 3 years ago

Ok thanks for reporting -- I'll add these terms and look into the issues with the script. Appreciate you contributing!

nextgenusfs commented 3 years ago

I think should be fixed now for next time, you can run a git pull on your fork and should get the updated script. The last PR someone added append to the file opens which wasn't correct -- which I think is why it wasn't working in python 3.