Allow qblast to accept lists of organisms to include/exclude #4516
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…onvert the argument to a Seq.
… a SeqRecord with a string.
| - organisms A dictionary that defines the organisms that will be | ||
| included/excluded in the search. The key is the name | ||
| of the organism, following the taxonomy convention | ||
| ie. "Bacteria (taxid:2)" and the value is a boolean |
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ie -> eg
I assume (please confirm) this works with any taxonomy node like "Bacteria" and not just leaf nodes (like a specific species)?
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On my use cases, it is indeed the case. And it does set difference between domains, eg.
{ "Bacteria (taxid:2)": False, "E. coli (taxid:562)": True }
Will give you results that are bacteria but not "E. coli". This particular behavior is what I am relying on for my use case.
If you decide to go forward with these changes, I will write a few tests to validate these properties.
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| if ORGANISM_REGEX.match(organism) is None: | ||
| raise ValueError( | ||
| "Organisms must be specified following the taxonomy convention. ie. 'Bacteria (taxid:2)'" |
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Is this explained in the latest qblast documentation from the NCBI? |
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Unfortunately, I could not find any official documentation for this functionality. I worked it out by inspecting the web requests performed by the "NCBI Blast" web page and reverse engineered the functionality. For this reason, I can understand you might not want to include the changes. |
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Allow qblast to accept an explicit list of organisms to include/exclude. That this is already possible to a limited degree by using the entrez query. However, I have a use case which requires me to build a complex list of organisms to exclude/include, which also queries qblast multiple times (with similar but not identical lists of organisms). This feature makes my use case easier to implement and prevents blast from having to do the entrez query as I already provide the correct names and taxids of the organisms.
Let me know if you are open to include this in biopython, I am happy to write a test if so.