https://github.com/ctb/get-some-ncbi-genomes
Download one or more NCBI genomes; includes sourmash plugin.
https://github.com/ctb/get-some-ncbi-genomes
sourmash
Last synced: 9 months ago
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Download one or more NCBI genomes; includes sourmash plugin.
- Host: GitHub
- URL: https://github.com/ctb/get-some-ncbi-genomes
- Owner: ctb
- License: bsd-3-clause
- Created: 2023-07-29T20:20:14.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2025-08-28T15:45:30.000Z (10 months ago)
- Last Synced: 2025-09-28T02:02:13.066Z (9 months ago)
- Topics: sourmash
- Language: Python
- Homepage:
- Size: 20.5 KB
- Stars: 2
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# get-some-ncbi-genomes
## Installation
```
pip install get-some-ncbi-genomes
```
## Usage
Download one or more NCBI genomes, given accession.
Build a CSV file containing download info:
```
get-some-ncbi-genomes GCA_002440745.1 --csv xyz.csv
```
Download the genome files directly:
```
get-some-ncbi-genomes --output-dir genomes/ --download-genomes GCA_002440745.1
```
Use the sourmash plugin to download genome files and make an info.csv:
```
sourmash scripts get-genomes GCA_002440745.1
```
## Support
We suggest filing issues in [the main sourmash issue tracker](https://github.com/dib-lab/sourmash/issues) as that receives more attention!
## Dev docs
`get-some-ncbi-genomes` is developed at https://github.com/ctb/get-some-ncbi-genomes/
### 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/...`.