SMAP Effect Prediction

SMAP effect-prediction was created to predict the effects of naturally occuring sequence variants or CRISPR-cas induced mutations in a given reference gene sequence on the encoded protein. It takes as input a genotyping mastertable generated by SMAP haplotype-window that lists the relative frequency of observed short haplotypes per locus per sample.

Installation

This software is part of the SMAP framework. Please check the SMAP documentation for how to install it as part of SMAP.

From PyPi

python3 -m venv .venv
source .venv/bin/activate
pip install --upgrade pip
pip install smap-effect-prediction

From Git

Either download a release tarball, extract it and change your current working directory to the extracted folder, or clone the git repository:

git clone git@gitlab.com:dschaumont/smap-effect-prediction.git
cd smap-effect-prediction
python3 -m venv .venv
source .venv/bin/activate
pip install --upgrade pip
pip install .

Documentation

Building from a tarball or the git respository

First, install the documentation build dependencies, then build the documentation in the docs directory:

pip install .[docs]
cd docs
sphinx-build -M html . build

Citation

If you use SMAP, please cite "Schaumont et al., (2022). Stack Mapping Anchor Points (SMAP): a versatile suite of tools for read-backed haplotyping. https://doi.org/10.1101/2022.03.10.483555". Source code is available online at https://gitlab.com/truttink/smap/.

Contributions

This package was created using the help of the following people:

• Arne Verstichele (INARI)
• Dries Schaumont and Tom Ruttink (ILVO)
• Kevin Debray (VIB-ILVO)