AlignScape

The AlignScape package takes an MSA as input and uses a self-organizing map to compute the sequence landscape of the input data.

AlignScape can be utilized as a Jupyter Notebook on their local machines or within a Google Colaboratory Notebook, supporting both CPUs and GPUs.

AlignScape Google Colab

AlignScape locally with a Singularity/Apptainer image

Download the image alignscape.sif

The image can be downloaded using the following link on Zenodo platform:

https://zenodo.org/records/10417520

Using the Singularity image

The image can be used as follows:

singularity run --nv alignscape.sif align_scape -h

If you don't have a GPU on your computer, remove the --nv option.

To run AlignScape on a alignment in fasta format, simply run:

singularity run --nv alignscape.sif align_scape -a alignment.fasta --nepochs 100

PLEASE NOTE: Singularity mounts only a part of your file system. To ensure that your fasta file is accessible within the singularity image, you should place it in your home directory or in your home directory hierarchy. This should guarantee its availability for use.

Plotting the U-matrix

singularity run --nv alignscape.sif python3 /usr/local/lib/python3.11/dist-packages/alignscape/plot_umat.py -s somfile.pickle -o outname

AlignScape locally within a conda environment

Create a conda enviroment and install AlignScape on it:

conda create -n alignscape python=3.12
ENV_PATH=$(conda info --envs | grep 'alignscape' | awk '{print $NF}')
cd $ENV_PATH/lib/python3.12/site-packages/
git clone https://github.com/bougui505/alignscape
cd alignscape
git clone https://github.com/bougui505/quicksom

A list of the needed dependencies can be found at apptainer/alignscape.def

Using AlignScape in the conda environment:

conda activate alignscape

To run AlignScape on a alignment in fasta format, simply run

python -m alignscape.align_scape -a alignment.fasta

Plotting the U-matrix

python -m alignscape.plot_umat -s somfile.pickle -o outname

Test

To check AlignScape local installation:

./test_som.sh

Reference

Please cite ...