sourmash plugin to calculate abundance profiles.
Project description
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 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/...
.
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