Metadata-Version: 2.4
Name: mycotools
Version: 1.0.0
Summary: Comparative genomics automation and standardization software
Author-email: Zachary Konkel <konkelzach@protonmail.com>
License: Copyright 2023 Zachary Konkel
        
        Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
        
        1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
        
        2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
        
        3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
        
        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
        
Project-URL: Homepage, https://github.com/xonq/mycotools
Project-URL: Bug Tracker, https://github.com/xonq/mycotools/issues
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)
Classifier: Operating System :: POSIX :: Linux
Requires-Python: <4,>=3.0
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: biopython
Requires-Dist: pandas
Requires-Dist: requests
Requires-Dist: scipy
Requires-Dist: openpyxl
Requires-Dist: tqdm
Requires-Dist: cryptography
Requires-Dist: ete3
Requires-Dist: pyqt5
Dynamic: license-file

<p align="center">
    <img
        src="https://github.com/xonq/mycotools/blob/master/misc/pictogo.white.png"
    >
</p>
<br /><br />

# PURPOSE
Bring broadscale comparative genomics to the masses. Taxonomy-agnostic, with
automated data acquisition operational with
prokaryote, animal, plant, and fungal genome data.

Mycotools is a compilation of computational biology tools and database
([MycotoolsDB/MTDB](https://github.com/xonq/mycotools/wiki/MycotoolsDB)) software
that facilitate large-scale comparative genomics. MycotoolsDB dereplicates and locally
assimilates NCBI and MycoCosm (Joint Genome Institute) genomes into a database schema with uniform file curation, scalability, and automation as guiding principles. 

- Database initialization: `mtdb u --init <DIR>`
- Database updating: `mtdb u --update`
- The MycotoolsDB (MTDB) uniformly curates GenBank/MycoCosm and local `gff` formats into a consistent standard
- The `.mtdb` database format is a uniform input for analyses with 100,000s to as few as a single genome
- Mycotools [software suite](https://github.com/xonq/mycotools/wiki/Usage) includes modules to automate routine-complex
  comparative genomics, such as phylogenetic analysis

<p align="center">
    <img
        src="https://github.com/xonq/mycotools/blob/master/misc/mtdb.png"
    >
</p>

<br />

# INSTALL

Please review the [wiki](https://github.com/xonq/mycotools/wiki/Install) for installation and usage information!

<br />

# 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

---


