Metadata-Version: 1.1
Name: VEnCode
Version: 0.2.1
Summary: Package to get VEnCodes as in Macedo and Gontijo, 2019
Home-page: https://github.com/AndreMacedo88/VEnCode
Author: AndrÃ© Macedo and Alisson M. Gontijo
Author-email: andre.lopes.macedo@gmail.com
License: UNKNOWN
Description: Module for VEnCode-related projects based on FANTOM5 databases
        ==============================================================
        
        This module contains classes and functions that perform intersectional genetics-related operations to find VEnCodes using databases provided by the `FANTOM5 consortium`_, namely the CAGE enhancer and transcription start site (TSS) databases.
        
        For more information on the VEnCode technology, please refer to **Macedo and Gontijo, bioRxiv 2019. DOI:10.1101/552984**
        
        Getting started
        ---------------
        
        These instructions are designed to:
        
        - Get you a copy of the project up and running on your local machine for development and testing purposes;
        - Install the VEnCode package in your python library environment for use in your projects.
        
        Prerequisites
        ^^^^^^^^^^^^^
        
        To effectively use this module you will need Python3_ with some external libraries installed in your machine.
        Check the requirements_ file.
        If you install the package with pip, it should resolve the library requirements for you.
        
        Additionally, you will have to download the unannotated TSS files from `FANTOM5 consortium`_ website.
        More specifically, for human, `this file`_ for promoter analysis, and `this one`_ and the `ID-sample name`_ map for enhancers.
        Finally, download the `curated sample category file`_.
        
        Those 4 files are enough to find CAGE-based VEnCodes for human.
        
        Installing
        ^^^^^^^^^^
        1. Make sure you have the prerequisites;
        
        If you want to edit the project:
        
        2. Fork this project;
        3. Put the missing FANTOM5 prerequisite files (only the large TSS files are missing) in the directory called "Files".
        
        If you are a user:
        
        2. Install VEnCode with pip;
        3. Put all the FANTOM5 prerequisite files in a directory of your choice and when creating DataTpm objects remember to pass the argument: files_path=your_dir_path.
        
        Deployment
        -----------------
        To develop your own projects, import objects directly from VEnCode using, for example:
        
        .. code-block:: python
        
            import VEnCode
            object1 = VEnCode.DataTpm(...)
        
        You can see examples of some functions and objects being used at the `VEnCode Capsule`_ hosted in CodeOcean.
        
        Alternatively, you can look at more advanced usage by going to the "Scripts" folder inside the package.
        
        Running the Tests
        -----------------
        Tests for this module can be run in several ways; some examples:
        
        1. In the command-line:
        
        1.1. Run python's standard module "unittest" in the tests directory.
        Basic example in command line:
        
        .. code-block:: console
        
            python -m unittest test_internals
        
        1.2. Install nosetests python package and run nosetests in the "tests" directory.
        Basic example in command line:
        
        .. code-block:: console
        
            nosetests test_internals.py
        
        2. By importing the VEnCode module in python:
        
        .. code-block:: python
        
            from VEnCode import tests
            tests.test_internals_()
        
        Contributing
        ------------
        
        Please read `CONTRIBUTING.rst`_ for details on our code of conduct, and the process for submitting pull requests to us.
        
        Versioning
        ----------
        
        We use SemVer_ for versioning. For the versions available, see:
        
        - The `tags on github`_, or
        - In PyPi_.
        
        Authors
        -------
        
        - `Andre Macedo`_
        - `Alisson M. Gontijo`_
        
        See also the list of contributors_ who participated in this project.
        
        License
        -------
        
        Refer to file LICENSE_.
        
        Acknowledgements
        ----------------
        - Integrative Biomedicine Laboratory @ CEDOC, NMS, Lisbon (supported by FCT: UID/Multi/04462/2019; PTDC/MED-NEU/30753/2017; and PTDC/BIA-BID/31071/2017 and FAPESP: 2016/09659-3)
        - CEDOC: Chronic Diseases Research Center, Nova Medical School, Lisbon
        - The MIT Portugal Program (MITEXPL/BIO/0097/2017)
        - LIGA PORTUGUESA CONTRA O CANCRO (LPCC) 2017.
        - FCT (IF/00022/2012, SFRH/BD/94931/2013, PTDC/BEXBCM/1370/2014)
        - Prof. Dr. Ney Lemke and Ms. Benilde Pondeca for important discussions.
        
        .. Starting hyperlink targets:
        
        .. _FANTOM5 consortium: http://fantom.gsc.riken.jp/5/data/
        .. _this file: https://fantom.gsc.riken.jp/5/datafiles/latest/extra/CAGE_peaks/hg19.cage_peak_phase1and2combined_tpm.osc.txt.gz
        .. _this one: https://fantom.gsc.riken.jp/5/datafiles/latest/extra/Enhancers/human_permissive_enhancers_phase_1_and_2_expression_tpm_matrix.txt.gz
        .. _ID-sample name: https://fantom.gsc.riken.jp/5/datafiles/latest/extra/Enhancers/Human.sample_name2library_id.txt
        .. _curated sample category file: https://github.com/AndreMacedo88/VEnCode/blob/master/VEnCode/Files/sample%20types%20-%20FANTOM5.csv
        .. _Python3: https://www.python.org/
        .. _requirements: https://github.com/AndreMacedo88/VEnCode/blob/master/requirements.txt
        .. _SemVer: https://semver.org/
        .. _tags on github: https://github.com/AndreMacedo88/VEnCode/tags
        .. _PyPi: https://pypi.org/project/VEnCode/#history
        .. _VEnCode Capsule: https://codeocean.com/capsule/7611480/tree
        .. _CONTRIBUTING.rst: https://github.com/AndreMacedo88/VEnCode/blob/master/CONTRIBUTING.rst
        .. _contributors: https://github.com/AndreMacedo88/VEnCode/graphs/contributors
        .. _Andre Macedo: https://github.com/AndreMacedo88
        .. _Alisson M. Gontijo: https://github.com/alissongontijo
        .. _LICENSE: https://github.com/AndreMacedo88/VEnCode/blob/master/LICENSE
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3.6
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
