Metadata-Version: 2.4
Name: genomic-config
Version: 0.1.6
Summary: A simple handler for configuration files detailing genomic datasets
Author-email: Chris Finan <c.finan@ucl.ac.uk>
License-Expression: GPL-3.0-or-later
Project-URL: Homepage, https://cfinan.gitlab.io/genomic-config
Project-URL: Repository, https://gitlab.com/cfinan/genomic-config
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Requires-Python: <3.14,>=3.9
Description-Content-Type: text/markdown
License-File: LICENSE.txt
Requires-Dist: bx-python
Provides-Extra: dev
Requires-Dist: pytest; extra == "dev"
Requires-Dist: pytest-dependency; extra == "dev"
Requires-Dist: flake8; extra == "dev"
Requires-Dist: bump2version; extra == "dev"
Requires-Dist: build; extra == "dev"
Requires-Dist: twine; extra == "dev"
Dynamic: license-file

# Getting Started with genomic-config
__version__: `0.1.6`

The genomic-config package provides an interface to configuration files that provide the locations for various genomic based files that might exist on a system. It can be used by external programs and Python code to provide a central point to locate the files. Currently, it only supports `ini` files but will be expanded to incorporate other configuration file types in the future.

genomic-config provides access to:

1. Reference genome assemblies (fasta files)
2. Reference genotype files (i.e. 1000 genomes)
3. Chain files for liftovers
4. Sample lists
5. variant annotation/mapping VCF files
6. mappings between chromosome synonyms
7. Providing access to a chromosome sort order

There is [online](https://cfinan.gitlab.io/genomic-config/index.html) documentation.

## Installation instructions
Can be installed using either pip or conda.

Using pip:

```
pip install genomic-config
```

Using conda:

```
conda install -c cfin -c bioconda genomic-config
```

## Next steps...
If you have cloned the repository, after installation, you may want to run the tests:

1. Run the tests using ``pytest ./tests`` - If you have installed using conda, you will need to clone the repository using git to run the tests.
2. [Setup](https://cfinan.gitlab.io/genomic-config/config_files.html) your configuration file.
