Skip to main content

Bleeding-edge comparative genomics automation and standardization software

Project description



NOTE

This software is a beta release (prokaryote is alpha state) - errors are expected. Kindly raise an issue if the error has not been mentioned. If you can find the bug, even better! The goal is to reach a longterm stable release with well-annotated PEP8 code, though maintaining the software for my use is currently the priority.

PURPOSE

Bring broadscale comparative genomics to the masses.

Mycotools is a compilation of computational biology tools and database (MycotoolsDB) software that facilitate large-scale comparative genomics. MycotoolsDB locally assimilates all NCBI and MycoCosm (Joint Genome Institute) genomes into a database schema with uniform file curation, scalability, and automation as guiding principles.

  • Database initialization is as simple as mtdb u --init <DIR>
  • mtdb u --update brings the database to the current date
  • The MycotoolsDB (MTDB) uniformly curates the numerous iterations of the gff into a consistent standard
  • The .mtdb database format enables swift transitions from analyses with datasets of 100,000s genomes to as few as a lineage of interest
  • Mycotools software suite includes modules to automate routine-complex comparative genomics


CITING

If Mycotools contribute to your analysis, please cite the preprint and mention the version in-line.

Konkel, Z., Slot, J. C. Mycotools: An Automated and Scalable Platform for Comparative Genomics. bioRxiv 2023.09.08.556886; doi: https://doi.org/10.1101/2023.09.08.556886



INSTALL

The installation guide will use miniconda3 as the environment manager. Please reference their install and initialization instructions.


1. Configuring miniconda3

Setup and prioritize channels for your miniconda installation. This step must be completed for new and old installs.

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

2. Installing mycotools

Make sure conda is active, usually by seeing (base) in in your shell. If not, try conda activate base or source activate base.

conda create -n mycotools mycotools -c xonq -y
conda activate mycotools
python3 -m pip install mycotools --upgrade
mtdb -d

NOTE: The conda package is broken on its own, so please explicitly run pip install as noted above to update the mycotools package inside the conda environment.


Determine if you are going to link to an already installed database, or become the administrator of a new one:

3a. USER: Integrate with already initialized MycotoolsDB

To link with an existing database, fill in <PATH> with the database path

mtdb --init <DB_PATH>

3b. ADMINISTRATOR: Initialize a local MycotoolsDB

mtdb update --init <DB_PATH>



USAGE

Once installed, you're good to proceed to the usage guide!



UPDATE

Mycotools is currently in an advanced beta state with frequent updates. It is recommended to run the following in your conda environment if you are having trouble with analyses:

python3 -m pip install mycotools --upgrade

NOTE: Make sure the conda environment is active when updating. I recommend updating with pip because the conda distribution is currently prone to dependency issues and will not update reliably.




A NOTE ON THE CODE

Each standalone script is written with a cli function, designed to handle running the script from the command line, as well as main function(s), which are importable python modules. This enables Mycotools to be a pipelining-friendly software suite, both from a command line and python scripting standpoint.

Code edits should focus on stabilizing existing features and simplifying/decerasing the code base. I try to implement code aligned with principles of the functional programming paradigm and modifications should act in accord with this paradigm, i.e. sparing implementation of new classes, limited necessary abstraction, no hidden state changes, and function-based flow.












Project details


Release history Release notifications | RSS feed

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

mycotools-0.30.61.tar.gz (1.5 MB view details)

Uploaded Source

Built Distribution

mycotools-0.30.61-py3-none-any.whl (178.4 kB view details)

Uploaded Python 3

File details

Details for the file mycotools-0.30.61.tar.gz.

File metadata

  • Download URL: mycotools-0.30.61.tar.gz
  • Upload date:
  • Size: 1.5 MB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.2 CPython/3.11.4

File hashes

Hashes for mycotools-0.30.61.tar.gz
Algorithm Hash digest
SHA256 2ded876e42262557246dddffffe96783f7574094c7b5e79853c64437e7f26ffc
MD5 970e1da8b8283a0c66d13e1f0db1af18
BLAKE2b-256 7f8775d9ce7df3cee9405a959d121ff73dec0f3b5bb80960e4c4f2bb201ff5bd

See more details on using hashes here.

File details

Details for the file mycotools-0.30.61-py3-none-any.whl.

File metadata

  • Download URL: mycotools-0.30.61-py3-none-any.whl
  • Upload date:
  • Size: 178.4 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.2 CPython/3.11.4

File hashes

Hashes for mycotools-0.30.61-py3-none-any.whl
Algorithm Hash digest
SHA256 3693fd6bea7a89376991cc895a124ddced9ade9ba2bb577a67cbf7e425b97e99
MD5 0294ad4597c1f913a3926d9a2f79dd12
BLAKE2b-256 07c8a36d92a75ad434f1d0f13749a88ed57434dc076ee231ee88cd4233506832

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page