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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:

histogram

Create a nice histogram figure for a metagenome:

% sourmash scripts abundhist examples/SRR606249-abund-100k.sig.zip --figure hist.png

will create this figure:

histogram

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/....

Project details


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sourmash_plugin_abundhist-0.3.1.tar.gz (4.9 kB view hashes)

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