untangler

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

Install from PyPI

python -m pip install untangler

Install from source

python -m pip install .

Run from a source checkout

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:

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:

python -m pip install -e .

Build and upload

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

Usage

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