ENH: adds --p-n-threads option to trim-alignment
#174
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nbokulich
requested changes
Feb 7, 2024
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thanks @mikerobeson ! Small comment inline. Have you tested the performance speed-up with multi-threading? I can take a look, but curious how much of a bump we see.
| """ | ||
| Trim alignment based on primer alignment or explicitly specified | ||
| positions. When at least one primer sequence is given, primer-based | ||
| trimming will be performed, otherwise position-based trimming is done. | ||
| trimming will be performed via the `addfragments` option of mafft, | ||
| otherwise position-based trimming is done. |
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the n_threads param would not be effective as far as I can tell when position-based trimming is done, so this should be mentioned in the param description
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RE param description: Oooh, good catch! Will fix!
RE multi threading: Yes this does scale well. The table below is based on ~5k sequences randomly subsampled from SILVA's 50k position FASTA alignment file, on my M1 Max laptop. Mirroring @colinbrislawn's results.
| threads | time |
|---|---|
| 8 | 6m 40.278s |
| 4 | 9m 20.686s |
| 2 | 14m 36.920s |
| 1 | 25m 13.873s |
Example command:
qiime rescript trim-alignment \
--i-aligned-sequences silva-138-1-nr99-aln-dna-ss01.qza \
--p-primer-fwd GTGYCAGCMGCCGCGGTAA \
--p-primer-rev CCGYCAATTYMTTTRAGTTT \
--p-n-threads 8 \
--o-trimmed-sequences silva-138-1-nr99-aln-dna-ss01-v4v5-trimmed.qza \
--verbose
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Fixes #127
Also, made some minor help text and documentation edits.