Metadata-Version: 2.1
Name: gtdb_precurate
Version: 1.0.2
Summary: Automatic pre-curation of GTDB trees.
Home-page: https://github.com/Ecogenomics/gtdb_precurate
Author: Aaron Mussig
Author-email: aaronmussig@gmail.com
Maintainer: Aaron Mussig
Maintainer-email: aaronmussig@gmail.com
License: GPL3
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: dendropy>=4.1.0
Requires-Dist: typer[all]

# GTDB Precurate

[![PyPI](https://img.shields.io/pypi/v/gtdb_precurate.svg)](https://pypi.python.org/pypi/gtdb_precurate)

`gtdb_precurate` is an internally used tool used that provides automatic pre-curation of GTDB trees.

## Installation

gtdb_precurate is available on PyPI and can be installed with pip:

```bash
pip install gtdb_precurate
```

## Usage

After a successful install, the `gtdb_precurate` command should be available.

The following positional arguments are required:

* `metadata` - This is the path to the metadata file, it should contain a header as the first line.
    The only requirement is that it has the following columns: `formatted_accession` and `ncbi_wgs_formatted`.
* `red_dict` - This is the path to the RED dictionary output by PhyloRank.
* `red_decorated_tree` - This is the path to the scaled RED decorated output by PhyloRank.
* `out_directory` - This is the path to the directory where the output files will be written.

The following optional arguments are available:

* `--min-bootstrap` - This is the minimum bootstrap value to consider a node to be supported. Default: 95.0.
* `--debug` - This enables debug logging. Default: False.

