https://github.com/ctb/sourmash_plugin_abundhist
A plugin to display abundance histograms of k-mers based on sourmash sketches
https://github.com/ctb/sourmash_plugin_abundhist
sourmash
Last synced: 8 months ago
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A plugin to display abundance histograms of k-mers based on sourmash sketches
- Host: GitHub
- URL: https://github.com/ctb/sourmash_plugin_abundhist
- Owner: ctb
- License: bsd-3-clause
- Created: 2023-07-30T11:13:38.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2025-09-15T13:02:04.000Z (10 months ago)
- Last Synced: 2025-09-15T14:46:42.881Z (10 months ago)
- Topics: sourmash
- Language: Python
- Homepage:
- Size: 247 KB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# sourmash_plugin_abundhist
## Installation
```
pip install sourmash_plugin_abundhist
```
## Usage
### Example
#### Basic command-line usage:
```
% sourmash scripts abundhist examples/SRR606249-abund-100k.sig.zip
== This is sourmash version 4.8.3.dev0. ==
== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==
loaded 1 total that matched ksize & molecule type
36 [3487] ****************************************
72 [ 485] ******
107 [ 171] **
143 [ 38] *
178 [ 5]
214 [ 3]
249 [ 7] *
285 [ 0]
320 [ 2]
356 [ 2]
```
#### Create a nice histogram figure for an isolate reads data set
```
sourmash scripts abundhist --max 100 --min 1 --bins 100 examples/reads.sig.gz --figure examples/ecoli-reads.png --ymax=200
```
will create:
#### Create a nice histogram figure for a metagenome:
```
% sourmash scripts abundhist examples/SRR606249-abund-100k.sig.zip --figure hist.png
```
will create this figure:
## 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
`abundhist` is developed at https://github.com/ctb/sourmash_plugin_abundhist.
### 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/...`.