MRG: add utility functions for zip reading; use in index, multisearch #105
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3 tasks
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@ctb this is ready for review |
ctb
reviewed
Sep 9, 2023
src/utils.rs
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| sketchlist.push(sm); | ||
| } else { | ||
| // track number of paths that have no matching sigs | ||
| skipped_paths.fetch_add(1, atomic::Ordering::SeqCst); |
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do we need atomic types? This loop doesn't look like it's parallelized, right?
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Nope, not parallelized.
There is a parallel zip library we could use if we want, but probably not needed except when reading from genbank-scale zips.
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removed atomic in 1ea65be
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I like overall, but want to dig in to code a bit. |
ctb
reviewed
Sep 11, 2023
ctb
reviewed
Sep 11, 2023
ctb
approved these changes
Sep 12, 2023
This was referenced Sep 12, 2023
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Extracted from #99, because all the changes were getting unruly.
This should be easier to review - contains the functions & modifications to use them in
indexandmultisearch, with tests.New in
utils.py:Renamed:
read_signatures_from_zip-->load_sketches_from_zipload_sketch_fromfile-->load_fasta_fromfileNote: In the case of reading a pathlist from a zip file, this means we extract the sig files and store them in a temp directory which will be deleted when it goes out of scope. This adds a little overhead, but I think it could worth it for the simplicity of being able to specify a zip database. Open to removing, though.