sourmash-plugin-directsketch 0.1.0

Download and Sketch GenBank Assembly Datasets

sourmash_plugin_directsketch

Installation

For now, git clone the repository and cd in.

mamba env create -f environment.yml
pip install -e .

When it's released, you'll be able to:

pip install sourmash_plugin_directsketch

Usage

First, create a file, e.g. acc.csv with GenBank identifiers and sketch names.

ident,name
GCA_000961135.2,GCA_000961135.2 Candidatus Aramenus sulfurataquae isolate AZ1-45
GCA_000175555.1,GCA_000175555.1 ACUK01000506.1 Saccharolobus solfataricus 98/2

Extra columns are ok, as long as the first two columns contain the identifier and sketch name

Run:

To run the test accession file at tests/test-data/acc.csv, run:

sourmash scripts gbsketch tests/test-data/acc.csv -o test.zip -f out_fastas -k --failed test.failed.csv -p dna,k=21,k=31,scaled=1000,abund -p protein,k=10,scaled=100,abund -r 1

Full Usage:

usage:  gbsketch [-h] [-q] [-d] -o OUTPUT [-f FASTAS] [-k] [--failed FAILED] [-p PARAM_STRING] [-c CORES] [-r RETRY_TIMES]
                 input_csv

download and sketch GenBank assembly datasets

positional arguments:
  input_csv             a txt file or csv file containing accessions in the first column

options:
  -h, --help            show this help message and exit
  -q, --quiet           suppress non-error output
  -d, --debug           provide debugging output
  -o OUTPUT, --output OUTPUT
                        output zip file for the signatures
  -f FASTAS, --fastas FASTAS
                        Write fastas here
  -k, --keep-fastas     write FASTA files in addition to sketching. Default: do not write FASTA files
  --failed FAILED       csv of failed accessions and download links (should be mostly protein).
  -p PARAM_STRING, --param-string PARAM_STRING
                        parameter string for sketching (default: k=31,scaled=1000)
  -c CORES, --cores CORES
                        number of cores to use (default is all available)
  -r RETRY_TIMES, --retry-times RETRY_TIMES
                        number of times to retry failed downloads

Support

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

Dev docs

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

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/....