Astra: Scalable HMM-based Sequence Search and Retrieval

Overview

Astra is a Python package designed to facilitate bioinformatic workflows involving Hidden Markov Models (HMMs). It serves as a wrapper around PyHMMER and HMMER, as well as a compendium of downloadable HMM databases. It automates the process of downloading and searching with custom or pre-installed HMM databases. Astra aims to streamline bioinformatic analyses, allowing for greater flexibility and ease of use. I intend to make Astra into a capable command-line tool as well as a python library.

Features

(Just what I've implemented so far! This list will grow!)

• Initialize: Download and install HMM databases directly from various sources with a simple command.
• Search: Perform advanced HMM searches on sequence data with customizable options.

Installation

To install the package, use pip:

pip install astra-hmm

The distribution is named astra-hmm because astra was already taken on PyPI; the command and the importable package are both still astra.

To install from a clone:

pip install -e .

Dependencies (all installed automatically via pip):

• pyhmmer >= 0.10
• pandas >= 2.0
• tqdm
• requests
• platformdirs

Python 3.9 or newer. No external binaries are required — HMMER itself comes bundled with PyHMMER.

Usage

Initialization

This is not necessary if you have locally installed HMMs. You can specify those without ever running 'Astra initialize'.

If you would like to view the available HMM databases for install:

Astra initialize --show_available

To initialize and download one of these databases:

Astra initialize --hmms database_name

Or to install them all (takes quite a bit of time!):

Astra initialize --hmms all_prot

Search

To perform an HMM search:

Astra search --prot_in your_fasta_file --installed_hmms database_name  --cut_ga --outdir example_output

Combined Search

To perform an HMM search using custom HMM files:

Astra search --prot_in your_fasta_file --hmm_in custom_db --installed_hmms pre_installed_db --cut_ga --outdir example_output

Contributing & License

Contributions are welcome! Especially if you have database suggestions. Feel free to raise an issue if you'd like to add a database to the installable list. Feature requests will be considered and implemented if I have the time and ability.

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MIT License

Copyright (c) 2023 Jacob West-Roberts

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.