{"id":20612720,"url":"https://github.com/datasnakes/orthoevolution","last_synced_at":"2025-04-15T07:09:05.685Z","repository":{"id":19926160,"uuid":"88282824","full_name":"datasnakes/OrthoEvolution","owner":"datasnakes","description":"An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 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image:: https://travis-ci.org/datasnakes/OrthoEvolution.svg?branch=master\n    :target: https://travis-ci.org/datasnakes/OrthoEvolution\n\n.. image:: https://badge.fury.io/py/OrthoEvol.svg\n   :target: https://badge.fury.io/py/OrthoEvol\n\n.. image:: https://readthedocs.org/projects/orthoevolution/badge/?version=latest\n   :target: http://orthoevolution.readthedocs.io/en/latest/?badge=latest\n\n.. image:: https://codecov.io/gh/datasnakes/OrthoEvolution/branch/master/graph/badge.svg\n   :target: https://codecov.io/gh/datasnakes/OrthoEvolution\n\n.. image:: https://badgen.net/github/last-commit/datasnakes/OrthoEvolution\n  :target: https://github.com/datasnakes/OrthoEvolution/commits/master\n\n.. image:: https://img.shields.io/badge/chat-on%20gitter-753A88.svg\n   :target: https://gitter.im/datasnakes/OrthoEvolution\n\n\n\nOrthoEvolution\n====================\nOrthoEvolution is an **easy to use** and comprehensive python package which aids in the **analysis and\nvisualization of comparative evolutionary genetics** related projects such as the **inference of orthologs**.\n\nOverview\n--------------------------\nThis package focuses on **inferring orthologs** using NCBI's blast, various sequence alignment strategies,\nand phylogenetics analyses including PAML, PhyML, ete3, and more tools.\n\nUltimately, the goal of this project is to create a **reusable pipeline** for the\ninference of orthologs in order to ensure reproducibility of data as well as improve\nthe management and analysis of (what can be) large datasets.  The Cookies, Manager, Pipeline,\nand Tools modules act as a framework for our workflow, while the Orthologs\nmodule provides access to specific functions for our various ortholog inference projects.\n\nView our `read the docs \u003chttp://orthoevolution.readthedocs.io/en/master/\u003e`__ and feel free to also\nread `this related paper \u003chttps://www.frontiersin.org/articles/10.3389/fnhum.2014.00283/full\u003e`__ to gain\nmore insight into this project/python package.\n\n\nInstallation\n----------------\nView the below methods for installing this package. Python3.5 and higher is required.\n\nPyPi\n~~~~~~~~~~~~~~~~\n``pip install OrthoEvol``\n\nGitHub\n~~~~~~~~~~~~~~~~\n1. Download the zip file and unzip it or ``git clone https://github.com/datasnakes/OrthoEvolution.git``\n2. ``cd OrthoEvolution``\n3. ``pip install .``\n\nDevelopment Code\n~~~~~~~~~~~~~~~~\n**WARNING** : This code is actively under development and may not be reliable.  Please create an `issue \u003chttps://github.com/datasnakes/OrthoEvolution/issues\u003e`_ for questions about development.\n\n1. Download the zip file and unzip it or ``git clone -b dev-master https://github.com/datasnakes/OrthoEvolution.git``\n2. ``cd OrthoEvolution``\n3. ``pip install .``\n\nExamples\n----------------\nCheck out this `tutorial \u003chttps://github.com/datasnakes/OrthoEvolution/wiki/Tutorial\u003e`__ in our Wiki Docs.\n\nAlso, please view `examples \u003chttps://github.com/datasnakes/OrthoEvolution/examples\u003e`__ of how to utilize this package to build tools.\n\n\nRunning a pre-configured local blast\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n.. code:: python\n\n    from OrthoEvol.Orthologs.Blast import OrthoBlastN\n\n    # Use an existing list of gpcr genes\n    gpcr_blastn = OrthoBlastN(project=\"orthology-gpcr\", method=1,\n                             save_data=True, acc_file=\"gpcr.csv\", \n                             copy_from_package=True)\n\n    # Run blast\n    gpcr_blastn.run()\n\n\nSimple project creation\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n.. code:: python\n\n    from OrthoEvol.Manager.management import ProjectManagement\n\n    ProjectManagement(repo=\"test-repo\", user=None,\n                      project=\"test-[roject\",\n                      research=None,\n                      research_type='comparative_genetics',\n                      new_repo=False, new_user=False, new_project=True,\n                      new_research=False)\n\nSimple blast database downloading\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n.. code:: python\n\n    from OrthoEvol.Tools.ftp import NcbiFTPClient\n\n    ncbiftp = NcbiFTPClient(email='somebody@gmail.com')\n    ncbiftp.getblastdb(database_name='refseq_rna', v5=True)\n\nCreating projects and databases dynamically \n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n.. code:: python\n\n    from OrthoEvol.Manager.management import ProjectManagement\n    from OrthoEvol.Manager.database_dispatcher import DatabaseDispatcher\n    from OrthoEvol.Manager.config import yml\n    from pkg_resources import resource_filename\n    from pathlib import Path\n    import yaml\n\n    # Set up project management\n    pm_config_file = resource_filename(yml.__name__, \"initialize_new.yml\")\n    with open(pm_config_file, 'r') as f:\n        pm_config = yaml.load(f)\n    pm = ProjectManagement(**pm_config[\"Management_config\"])\n\n    # Set up database management\n    db_config_file = resource_filename(yml.__name__, \"databases.yml\")\n    with open(db_config_file, 'r') as f:\n        db_config = yaml.load(f)\n    config = db_config.update(pm_config)\n\n    # Generate main config file for this job\n    config_file = pm.user_log / Path(\"upload_config.yml\")\n    with open(str(config_file), 'w') as cf:\n        yaml.dump(config, cf, default_flow_style=False)\n\n    # Set up database dispatcher and dispatch the functions\n    dd = DatabaseDispatcher(config_file, pm)\n    dd.dispatch(dd.strategies, dd.dispatcher, dd.configuration)\n\n\nTests\n----------------\nTo run tests, type ``pytest tests`` in the OrthoEvolution directory.\n\nFirst, install the ``pytest` package using pip.\n\nContributors\n----------------\nThis package was created by the Datasnakes.\n\n-  Rob Gilmore \\| Github: `@grabear \u003chttps://github.com/grabear\u003e`__ \\|\n   `✉ \u003cmailto:robgilmore127@gmail.com\u003e`__\n-  Shaurita Hutchins \\| Github:\n   `@sdhutchins \u003chttps://github.com/sdhutchins\u003e`__ \\|\n   `✉ \u003cmailto:sdhutchins@outlook.com\u003e`__\n\nIf you would like to contribute to this package, install the package in development mode,\nand check out our `contributing guidelines \u003chttps://github.com/datasnakes/OrthoEvolution/blob/master/CONTRIBUTING.rst\u003e`__.\n\n\nCitations\n----------------\nWe're so thankful to have a resource such as\n`Biopython \u003chttp://biopython.org/wiki/Biopython\u003e`__. They inspired this\npackage.\n\n*Cock, P.J.A. et al. Biopython: freely available Python tools for\ncomputational molecular biology and bioinformatics. Bioinformatics 2009\nJun 1; 25(11) 1422-3 http://dx.doi.org/10.1093/bioinformatics/btp163\npmid:19304878*\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatasnakes%2Forthoevolution","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdatasnakes%2Forthoevolution","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatasnakes%2Forthoevolution/lists"}