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immcantation / presto

pRESTO is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq). pRESTO is a bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
https://presto.readthedocs.io
GNU Affero General Public License v3.0
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runUClust supports vsearch 2.4.2 but not usearch v9.2 #52

Closed ssnn-airr closed 7 years ago

ssnn-airr commented 7 years ago

Original report by Anonymous.

For runUClust in presto.Applications to take usearch v9.2 as an argument, the following change must be made to cmd...

cmd = [cluster_exec,
       '-cluster_fast', in_handle.name,
       '-uc', out_handle.name,
       '-id', str(ident),
       '-qmask', 'none',
       '-minseqlength', '1',
       '-threads', '1']

cmd = [cluster_exec, '--usersort',
       '--input', in_handle.name,
       '--uc', out_handle.name,
       '--id', str(ident),
       '-minlen', '1']
ssnn-airr commented 7 years ago

Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).

I can't reproduce. usearch v9.2.64 seems to generate the same output as 9.0.2132.

Also, I don't see anything in the release notes about argument changes?

I only did a simple test by running ClusterSets on the same data using different versions. Are you getting this error a different way?

ssnn-airr commented 7 years ago

Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).

Seeing as I can't reproduce, I'm closing this. Please reopen if it pops up.