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check if my gene name exists in Kegg pathway

Hi guys, please help me,

I use bioservices package , when I import a gene name that kegg cannot recognize it... the error is :

if 'PATHWAY' in dic.keys(): AttributeError: 'int' object has no attribute 'keys'

I wrote an if statement, but the same error has occurred. where I'm doing wrong?

This question is related to my previous post : C: retrieving pathways belong to my gene names

Thanks.

kegg python bioservices
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updated by lakhujanivijay lakhujanivijay • written by EFN • EFN

Can you show the full code? dic seems to be an int not a dict so it doesn't have keys.

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written by Gungor Budak Gungor Budak

Hello EFN,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

Thank you!

• 1 views • link
written by lakhujanivijay lakhujanivijay

that is a generic error by bioservices if it doesn't find a matching ID. Following code in bioservices/kegg.py is the problem:

 920         res = self.get(":".join([organism, gene]))
 921         dic = self.parse(res)
 922         if 'PATHWAY' in dic.keys():
 923             return dic['PATHWAY']
 924         else:
 925             self.logging.info("No pathway found ?")
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written by cpad0112 cpad0112

thank you, so greateful, your advice were always instructive for me

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written by EFN • EFN

Thank you! I usually work by bioservices, how can i connect to them myself?

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written by EFN • EFN

via github dev channel @EFN

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written by cpad0112 cpad0112

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