Metadata-Version: 2.1
Name: CONGA
Version: 2.1.4
Summary: Combined Open and Narrow searches via Group Analysis
Home-page: https://github.com/freejstone/CONGA
Author: Jack Freestone
Author-email: jfre0619@uni.sydney.edu.au
License: UNKNOWN
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.9.0, <=3.9.16
Description-Content-Type: text/x-rst
License-File: LICENSE

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CONGA: Combined Open and Narrow searches via Group Analysis
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A tool for discovering peptides with unaccounted for PTMs
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CONGA is a tool for discovering peptides in mass spectrometry data with rigourous FDR control. It is designed to allow for unexpected post-translational modifications as well as chimeric spectra. CONGA takes three inputs: (1) the set of top-scoring PSMs from a traditional, narrow-window search against a concatenated target-decoy database, (2) the set of top-k PSMs (or fewer if less than k PSMs exist) from an open search, again against a concatenated target-decoy database, and (3) the pairs of target and decoy peptide sequences from the database. Ideally, an additional option is set which specifies the isolation window used. Given this, CONGA will return a discovery list of peptides.

Documentation
=============

You can find documentation on how to use CONGA over on `readtheddocs <https://open-groupwalk.readthedocs.io/en/latest/>`_. Alternatively you can find the same documentation under docs/pages in this respository.

Paper
=====

A link to the biorXiv paper will eventually go here.

Installation
============

To install, first create a virtual environment using conda:

``conda create --name conga_env python=3.9``

Then activate this virtual environment:

``conda activate conga_env``

Next download the latest release using `pip`:

``pip install CONGA``

Alternatively you can download the latest release from Github, and install using pip in the same directory as setup.py using:

``pip install .``

Please see the documentation, specifically the tutorial, on how to run CONGA.

Releasing
---------

Releases are published automatically when a tag is pushed to GitHub.

.. code-block:: bash

   # Set next version number
   export RELEASE=x.x.x

   # Create tags
   git commit --allow-empty -m "Release $RELEASE"
   git tag -a $RELEASE -m "Version $RELEASE"

   # Push
   git push upstream --tags

