Metadata-Version: 2.4
Name: untangler
Version: 0.1.0
Summary: RNA-seq transcript-level analysis and clustering tool
Author: Joshua Levendis
License-Expression: GPL-3.0-only
Project-URL: Homepage, https://github.com/levend1s/untangler
Project-URL: Repository, https://github.com/levend1s/untangler
Project-URL: Issues, https://github.com/levend1s/untangler/issues
Keywords: RNA-seq,transcript analysis,BAM,bioinformatics
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.9
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: pandas
Requires-Dist: numpy
Requires-Dist: pysam
Requires-Dist: scikit-learn
Requires-Dist: scipy
Requires-Dist: matplotlib
Requires-Dist: statsmodels
Requires-Dist: gffpandas
Requires-Dist: igv-reports
Dynamic: license-file

# untangler
Assembler for DNA, aligner for RNA against DNA, untangler for RNA subclusters

## Install from PyPI

```bash
python -m pip install untangler
```

## Install from source

```bash
python -m pip install .
```

## Run from a source checkout

```bash
python3 -m venv .venv
source .venv/bin/activate
python -m pip install --upgrade pip
python -m pip install -e .
python untangler.py --help
```

The editable install uses the dependencies declared in `pyproject.toml` while
running the code directly from the checkout. For example:

```bash
python untangler.py cluster_transcripts \
	--ids PF3D7_1007900 \
	-i config.txt \
	-o ./cluster_transcripts_PF3D7_1007900_28 \
	--cluster_cols introns,m6A \
	--predict introns \
	-t 0.6 -f --generate_igv_reports
```

For local development, install the editable package:

```bash
python -m pip install -e .
```

## Build and upload

```bash
python -m pip install build twine
python -m build
python -m twine upload dist/*
```

## Usage

```bash
untangler cluster_transcripts --ids PF3D7_1007900 \
	-i config.txt \
	-o ./cluster_transcripts_PF3D7_1007900_28 \
	--cluster_cols introns,m6A \
	--predict introns \
	-t 0.6 -f --generate_igv_reports
```
