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OrthoEvolution

OrthoEvolution is an easy to use and comprehensive python package which aids in the analysis and visualization of comparative evolutionary genetics related projects such as the inference of orthologs.

Overview

This package focuses on inferring orthologs using NCBI's blast, various sequence alignment strategies, and phylogenetics analyses including PAML, PhyML, ete3, and more tools.

Ultimately, the goal of this project is to create a reusable pipeline for the inference of orthologs in order to ensure reproducibility of data as well as improve the management and analysis of (what can be) large datasets. The Cookies, Manager, Pipeline, and Tools modules act as a framework for our workflow, while the Orthologs module provides access to specific functions for our various ortholog inference projects.

View our read the docs <http://orthoevolution.readthedocs.io/en/master/>__ and feel free to also read this related paper <https://www.frontiersin.org/articles/10.3389/fnhum.2014.00283/full>__ to gain more insight into this project/python package.

Installation

View the below methods for installing this package. Python3.5 and higher is required.

PyPi

``pip install OrthoEvol``

GitHub

1. Download the zip file and unzip it or git clone https://github.com/datasnakes/OrthoEvolution.git
2. cd OrthoEvolution
3. pip install .

Development Code

**WARNING** : This code is actively under development and may not be reliable.  Please create an `issue <https://github.com/datasnakes/OrthoEvolution/issues>`_ for questions about development.

1. Download the zip file and unzip it or ``git clone -b dev-master https://github.com/datasnakes/OrthoEvolution.git``
2. ``cd OrthoEvolution``
3. ``pip install .``

Examples
----------------
Check out this `tutorial <https://github.com/datasnakes/OrthoEvolution/wiki/Tutorial>`__ in our Wiki Docs.

Also, please view `examples <https://github.com/datasnakes/OrthoEvolution/examples>`__ of how to utilize this package to build tools.


Running a pre-configured local blast

.. code:: python

from OrthoEvol.Orthologs.Blast import OrthoBlastN

# Use an existing list of gpcr genes
gpcr_blastn = OrthoBlastN(project="orthology-gpcr", method=1,
                         save_data=True, acc_file="gpcr.csv", 
                         copy_from_package=True)

# Run blast
gpcr_blastn.run()

Simple project creation

.. code:: python

    from OrthoEvol.Manager.management import ProjectManagement

    ProjectManagement(repo="test-repo", user=None,
                      project="test-[roject",
                      research=None,
                      research_type='comparative_genetics',
                      new_repo=False, new_user=False, new_project=True,
                      new_research=False)

Simple blast database downloading

.. code:: python

from OrthoEvol.Tools.ftp import NcbiFTPClient

ncbiftp = NcbiFTPClient(email='[email protected]')
ncbiftp.getblastdb(database_name='refseq_rna', v5=True)

Creating projects and databases dynamically

.. code:: python

    from OrthoEvol.Manager.management import ProjectManagement
    from OrthoEvol.Manager.database_dispatcher import DatabaseDispatcher
    from OrthoEvol.Manager.config import yml
    from pkg_resources import resource_filename
    from pathlib import Path
    import yaml

    # Set up project management
    pm_config_file = resource_filename(yml.__name__, "initialize_new.yml")
    with open(pm_config_file, 'r') as f:
        pm_config = yaml.load(f)
    pm = ProjectManagement(**pm_config["Management_config"])

    # Set up database management
    db_config_file = resource_filename(yml.__name__, "databases.yml")
    with open(db_config_file, 'r') as f:
        db_config = yaml.load(f)
    config = db_config.update(pm_config)

    # Generate main config file for this job
    config_file = pm.user_log / Path("upload_config.yml")
    with open(str(config_file), 'w') as cf:
        yaml.dump(config, cf, default_flow_style=False)

    # Set up database dispatcher and dispatch the functions
    dd = DatabaseDispatcher(config_file, pm)
    dd.dispatch(dd.strategies, dd.dispatcher, dd.configuration)


Tests
----------------
To run tests, type ``pytest tests`` in the OrthoEvolution directory.

First, install the ``pytest` package using pip.

Contributors
----------------
This package was created by the Datasnakes.

-  Rob Gilmore \| Github: `@grabear <https://github.com/grabear>`__ \|
   `✉ <mailto:[email protected]>`__
-  Shaurita Hutchins \| Github:
   `@sdhutchins <https://github.com/sdhutchins>`__ \|
   `✉ <mailto:[email protected]>`__

If you would like to contribute to this package, install the package in development mode,
and check out our `contributing guidelines <https://github.com/datasnakes/OrthoEvolution/blob/master/CONTRIBUTING.rst>`__.


Citations
----------------
We're so thankful to have a resource such as
`Biopython <http://biopython.org/wiki/Biopython>`__. They inspired this
package.

*Cock, P.J.A. et al. Biopython: freely available Python tools for
computational molecular biology and bioinformatics. Bioinformatics 2009
Jun 1; 25(11) 1422-3 http://dx.doi.org/10.1093/bioinformatics/btp163
pmid:19304878*