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sourmash plugin to sketch many sequence files

Project description

sourmash_plugin_sketchall

Sketch many files at once with sourmash, using threads.

The sketchall plugin is a convenient way to:

  • automatically discover & sketch many sequence files in a directory hierarchy.
  • speed up sketching using multiple threads.

Installation

pip install sourmash_plugin_sketchall

This will use 8 processes to (attempt to) sketch all of the files underneath directory. Filenames ending in .sig or .sig.gz will be ignored.

Usage

The following command:

sourmash scripts sketchall examples -j 8

will use 8 threads to (attempt to) sketch all of the files underneath examples. Filenames ending in .sig, .sig.gz, .zip, and .sqldb will be ignored, and failed files will be reported (but failures will be ignored).

By default, sketchall will save signatures in place: sketches for examples/10.fa.gz are saved to examples/10.fa.gz.zip, and sketches for examples/subdir/2.fa.gz are saved to examples/subdir/2.fa.gz.zip.

With -o/--output-directory, sketchall will sketch into a new hierarchy of files; so, for example,

sourmash scripts sketchall examples -o sigs/

will save the sketch for examples/subdir/2.fa.gz to sigs/subdir/2.fa.gz.

The default signature format for sketchall is .zip. This can be changed by using --extension:

sourmash scripts sketchall examples -o sigs/ --extension .sig.gz

will create sigs/10.fa.gz.sig.gz and sigs/subdir/2.fa.gz.sig.gz.

The pattern for files to sketch can be set by using --pattern:

sourmash scripts sketchall examples --pattern "2.*.gz"

The parameter string used to sketch files can be changed with -p/--param-string:

sourmash scripts sketchall examples -p k=21 examples/ -o output.k21

After sketchall, sourmash sig cat can be used to collect all of the sketches into a single zip file, e.g.

sourmash sig cat sigs -o all-sigs.zip

Benchmarks and speedups

On a small collection of 64 genomes, using 4-8 threads more than doubles the speed of sketching - for larger files, speedups should approach linear scaling.

Wall time (s) Threads Efficiency
6.00 1 106%
2.84 4 306%
2.41 8 321%

Support

We suggest filing issues in the main sourmash issue tracker as that receives more attention!

Dev docs

sketchall is developed at https://github.com/sourmash-bio/sourmash_plugin_sketchall.

Testing

Run:

pytest tests

Generating a release

Bump version number in pyproject.toml and push.

Make a new release on github.

Then pull, and:

python -m build

followed by twine upload dist/....

Project details


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sourmash_plugin_sketchall-0.2.2.tar.gz (6.2 kB view hashes)

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