Limit of 25 proteins for UniProt mapping. about bioservices HOT 3 CLOSED

I have also had this issue using u.search(). Was trying to query 200 proteins, but the results were always 25 proteins.

prot_search = u.search(query="+OR+".join(proteins), columns='id,annotation_score,lineage', frmt='tsv')

Using python 3.8.11 and bioservices 1.10.4

Also, I used u.search() because u.get_df() doesn't allow specific columns.

Thanks.

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@joaosegurilho sorry for the later answer. I believe that in your case, using the parameter limit should help. For instance for 200 proteins, call the method with limit=200; if unsure, you can set a limit that is large enough e.g. 1000. :

prot_search = u.search(query="+OR+".join(proteins), columns='id,annotation_score,lineage', frmt='tsv', limit=200)

by default all uniprot calls have a limit of 25 results according to their API. I'll try to update the code to make it automatic in the future.

@ArnaudBelcour looks like there is also a limit of 25 on the mapping functionality but here I did not manage to implement the limit parameter. Not sure whether it is a bug in the uniprot API or not. So, the only solution for now is to split the input list in chunk of 25. similarly to the previous comment made here, I will try to update the code to make this process automatic in the future release.
best

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Should be fixed in v1.11.0 now available on pypi.

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