The goal is to build an embedding space for bacterial sequences and use them as an index of dense vector to perform fast queries using faiss
panspace is a library based on tensorflow and faiss index.
It provides commands for creating FCGR from kmer counts, train an autoencoder,
extract Encoder and Decoder from a trained model, and create and query an Index
of embeddings.
git clone git@github.com:pg-space/panspace.git
cd panspace
mamba env create -n panspace -f condaenv.yaml
mamba activate panspace
panspace --help
Usage: panspace [OPTIONS] COMMAND [ARGS]...
🐱 Welcome to panspace, a tool for Indexing and Querying a pan-genome in an embedding space
╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --install-completion Install completion for the current shell. │
│ --show-completion Show completion for the current shell, to copy it or customize the installation. │
│ --help Show this message and exit. │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Commands ──────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ data-curation Find outliers and mislabaled samples. │
│ docs Open documentation webpage. │
│ fcgr Create FCGRs from fasta file or from txt file with kmers and counts. │
│ index Create and query index. Utilities to test index. │
│ stats-assembly N50, number of contigs, avg length, total length. │
│ trainer Train Autoencoder/Metric Learning. Utilities. │
│ utils Extract info from text or log files │
│ what-to-do 🐱 If you are new here, check this step-by-step guide │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯panspace is developed by Jorge Avila