Metadata-Version: 2.4
Name: captnseq-toolkit
Version: 0.1.1
Summary: Analysis tools for CAPTn-seq transposon-insertion sequencing data (used by nf-core/captnseq)
Author: Simon Jeanneau
License: MIT
Project-URL: Homepage, https://github.com/simonjeanneau/captnseq-toolkit
Project-URL: Pipeline, https://github.com/nf-core/proposals/issues/173
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: scipy
Requires-Dist: matplotlib
Provides-Extra: test
Requires-Dist: pytest; extra == "test"
Dynamic: license-file

# captnseq-toolkit

Analysis tools for CAPTn-seq (transposon-insertion sequencing) data. This package holds the
scientific logic used by the [nf-core/captnseq](https://github.com/nf-core/proposals/issues/173)
pipeline, so the pipeline itself only contains Nextflow code.

## Install

```bash
pip install captnseq-toolkit        # once released on PyPI
conda install -c bioconda captnseq-toolkit   # once the Bioconda recipe is merged
```

## Usage

```bash
captnseq-toolkit --help
captnseq-toolkit sam2sites    --help   # SAM -> insertion sites (BED + bedGraph)
captnseq-toolkit sites2genes  --help   # insertion sites -> per-gene counts
captnseq-toolkit essentiality --help   # per-gene counts -> essential / ambiguous / non-essential
```

## Development

```bash
pip install -e ".[test]"
pytest
```

Releases are tagged `vX.Y.Z` (version comes from git tags via setuptools-scm).
