sourmash-plugin-directsketch 0.3.0

Download and Sketch GenBank Assembly Datasets

sourmash_plugin_directsketch

tl;dr - download and sketch NCBI Assembly Datasets by accession

About

This plugin is an attempt to improve database generation by downloading assemblies, checking md5sum, and sketching to a sourmash zipfile. FASTA files can also be saved if desired. It's quite fast, but still very much at alpha level. Here be dragons.

Installation

pip install sourmash_plugin_directsketch

Usage

Create an input file

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

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

Three columns must be present: accession, name, and ftp_path. The ftp_path column can be empty, but no additional columns may be present.

What is ftp_path?

If you do not provide an ftp_path, gbsketch will use the accession to find the ftp_path for you.

If you choose to provide it, ftp_path must be the ftp_path column from NCBI's assembly summary files.

For reference:

• example ftp_path: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/036/600/915/GCA_036600915.1_ASM3660091v1
• bacteria assembly summary file: https://ftp.ncbi.nih.gov/genomes/genbank/bacteria/assembly_summary.txt

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] [--download-only] [--failed FAILED] [-p PARAM_STRING] [-c CORES]
                 [-r RETRY_TIMES] [-g | -m]
                 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
  --download-only       just download genomes; do not sketch
  --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
  -g, --genomes-only    just download and sketch genome (DNA) files
  -m, --proteomes-only  just download and sketch proteome (protein) files

Code of Conduct

This project is under the sourmash Code of Conduct.

Support

We suggest filing issues in the directsketch issue tracker or the main sourmash issue tracker.

Authors

• N. Tessa Pierce-Ward

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/....