Metadata-Version: 2.1
Name: mycotools
Version: 0.5.11
Summary: A compilation of bioinformatic and computation biology inspired python tools
Home-page: https://gitlab.com/xonq/mycotools/mycotools
Author: xonq
Author-email: konkelzach@protonmail.com
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

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        src="https://gitlab.com/xonq/mycotools/-/raw/master/misc/pictogo.white.png"
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# 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://gitlab.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>`

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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://gitlab.com/xonq/mycotools/-/blob/master/mycotools/USAGE.md) for
more information.

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

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

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