alperyilmaz/dna2vec repository overview

⁠dna2vec

Dna2vec is an open-source library to train distributed representations of variable-length k-mers.

For more information, please refer to the paper: dna2vec: Consistent vector representations of variable-length k-mers⁠

This repo is fork of the original pnpnpn/dna2vec⁠ repo. The upgrades are:

• runs within Docker container
• uses latest versions of packages
• has nworkers argument, so that you can use more than 4 workers
• contains openBLAS but not sure if NumPy or SciPy can utilize it, needs testing

⁠No Installation Required

There's no need to install packages or no need to clone the repository. To run the script just type the following command in terminal

docker run --rm -v $(pwd):/app/data --user 1000 alperyilmaz/dna2vec train_dna2vec.py -c sample_config.yml

The container mounts the working directory, thus files are read in or write out to folders within working directory. Just put your fasta files into a folder and edit config file and then start training.

The sample config file can be as simple as:

inputs: inputs/chr*.fa
k-low: 3
k-high: 5
out-dir: results/

Please refer to hg38-20161219-0153.yml for full blown example. For details about usage, please refer to pnpnpn/dna2vec⁠ repo.

New: You can add nworkers argument to take full advantage of available CPUs.

⁠About speed

This is not systematic testing results, merely my observations at different platforms

⁠License

This software is licensed under the MIT license⁠