Metadata-Version: 2.1
Name: mycotools
Version: 0.30.4
Summary: Bleeding-edge comparative genomics automation and standardization software
Home-page: https://gitlab.com/xonq/mycotools/mycotools
Author: xonq
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: >=3.0,<4
Description-Content-Type: text/markdown
License-File: LICENSE

<p align="center">
    <img
        src="https://gitlab.com/xonq/mycotools/-/raw/master/misc/pictogo.white.png"
    >
</p>

<br /><br />

# NOTE
This software is a beta release (prokaryote is alpha state) - errors are expected. Kindly report them.
If you can find the bug, even better! The goal is to reach a longterm stable
release, 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](https://github.com/xonq/mycotools/blob/master/mycotools/MTDB.md) software that facilitate large-scale fungal 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`, allowing for reliable analyses and format expectations from
  multiple eras
- The `.mtdb` database format enables swift transitions from analyses with datasets of 100,000s genomes to as few as a lineage of interest
- The MycotoolsDB can be adminstered by one administrator and accessed by
  multiple users that integrate via `mtdb -i <DB_DIR>`

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

<br />

Mycotools facilitates routine-complex
tasks like retrieving locus, `gff`, or `fasta` accessions; running and compiling
`fasta`s of MycotoolsDB BLAST/hmmsearches; automated phylogenetic analysis
pipelines from BLAST to Pfam extraction to tree prediction, etc etc. Mycotools
includes sets of utilities that also enable easy acquisition of batches of
sequence data using `ncbiDwnld.py` and `jgiDwnld.py`. Please see the [USAGE
guide](https://github.com/xonq/mycotools/blob/master/mycotools/USAGE.md) for
more information.

<br />

# USAGE
Check out [README.md](https://github.com/xonq/mycotools/blob/master/mycotools/README.md) for install and the [USAGE.md](https://github.com/xonq/mycotools/blob/master/mycotools/USAGE.md) for a guide. 

<br />

# CITING
If Mycotools contribute to your analysis, please cite this git repository (gitlab.com/xonq/mycotools) and mention the Mycotools version in line.

<img align="right" src="https://gitlab.com/xonq/mycotools/-/raw/master/misc/ablogo.png">

<br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br />
