Make PROTEIN.udb file available in fasta format

[sulheim]

Currently it seems like you need the paid version of usearch to run probannopy because of the size of the PROTEIN.udb file. Would it be possible to provide the database in e.g. a fasta format so it could be used with blastp?

[kingb12]

It has been a while since I set any of this up, but my understanding was that usearch 32-bit was sufficient. This might be what you're looking for though: https://probanno-data.s3.amazonaws.com/
Apologies if thats not a great way to read it, but in that bucket is the OTU_FID_ROLE file (e.g. https://probanno-data.s3.amazonaws.com/OTU_FID_ROLE, as well as:

https://probanno-data.s3.amazonaws.com/PROTEIN_FASTA
https://probanno-data.s3.amazonaws.com/PROTEIN_FASTA.pin
https://probanno-data.s3.amazonaws.com/PROTEIN_FASTA.phr
https://probanno-data.s3.amazonaws.com/PROTEIN_FASTA.psq

It has been a while since I've set up/used blastp, so let me know if that wasn't what you were looking for. If it is I can add an additional zipped version to the bucket for later convenience.

[sulheim]

Thanks, this is exactly what I was looking for. However this revealed another issue (bug?):

The otu_fid_role_key is only added to the Datafiles dict if usearch is chosen as the searc program

        self.DataFiles = dict()
        if self.searchProgram == 'usearch':
            self.DataFiles['otu_fid_role_file'] = os.path.join(self.dataFolderPath, 'OTU_FID_ROLE')
        else:
            self.DataFiles['protein_fasta_file'] = os.path.join(self.dataFolderPath, 'PROTEIN_FASTA')

and this key is needed regardless search program in the function rolesetProbabilititesMarble in the ProbAnnotationWorker.py file.

This is easiliy solved by just adding the otu_fid_role_key to the dict regardless of search program. I've fixed this in my fork, so if you agree I can make a PR

[sulheim]

A comment regarding the memory limit with usearch 32-bit. This is only an issue on windows because most Linux-distributions use Physical Address Extension which extends the memory limit beyond 4GB