pyJellyfish : Python wrapper around Jellyfish
Introduction
This tool essentially serves as an installer for the k-mer counter Jellyfish for use with Python. A small bundle of utilities is also included. A typical use-case for this package would be km: https://github.com/iric-soft/km.
Citing
- Guillaume Marcais and Carl Kingsford, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics (2011) 27(6): 764-770; doi: https://doi.org/10.1093/bioinformatics/btr011
Install
With pip
python -m venv $HOME/.virtualenvs/km
source $HOME/.virtualenvs/km/bin/activate
pip install --upgrade pip
pip install .
Options
Note that pyJellyfish has an option to manually specify which Jellyfish version one wishes to build against. This can be done by running pip install with specific arguments:
source $HOME/.virtualenvs/km/bin/activate
pip install . --config-settings="--build-option='--jf-version=2.3.0'"
For building pyJellyfish distributions, use the build command:
source $HOME/.virtualenvs/km/bin/activate
pip install build
python -m build --config-setting="--build-option='--jf-version=2.3.0'"
Requirements
- Python 3.8.0 or later
2 maintainers
Release files for pyjellyfish 1.3.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| pyjellyfish-1.3.1.tar.gz | 2.9 MB | Details |
Release files / pyjellyfish-1.3.1.tar.gz
| Download URL | pyjellyfish-1.3.1.tar.gz |
|---|---|
| Size | 2.9 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
f9ec8f126b82f2fd85d717b7fb8c80ee8095958d8da748b35e7dcbba5b3fd5de
|
|
BLAKE2b-256 checksum How to use checksums |
b45c6d5ec10777e04f17ec35f3691e042925e34f2cabbea584f65de3e0c703be
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.12.2
|
