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 a few 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.

Optionally, if you want to retrieve VEnCodes using the comprehensive FANTOM5 CAGE-seq data, you will have to download the unannotated TSS files from FANTOM5 consortium website. More specifically, for human, download 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:

  1. Fork this project.

  • You are ready. Optionally, if you are using the FANTOM5 data instead of your own:

  1. Put the missing FANTOM5 prerequisite files (only the large TSS files are missing) in the directory called “Files”.

If you are a user:

  1. Install VEnCode with pip:

pip install VEnCode

  • You are good to go. Optionally, if you are using the FANTOM5 data instead of your own:

  1. Put all the FANTOM5 prerequisite files in a directory of your choice and when creating DataTpmFantom5 objects remember to pass the argument: files_path=your_dir_path.

Using the module

There are several ways to use this module:

  1. To develop your own projects, import objects directly from VEnCode using, for example:

import VEnCode
object1 = VEnCode.DataTpm(...)
vencodes = VEnCode.Vencodes(object1, ...)
vencodes.next(amount=2)
vencodes.export("vencodes", ...)

You can see examples of some functions and objects being used at the VEnCode Capsule hosted in CodeOcean.

2. To run the most relevant scripts, use the utility file process.py, which gives easy access to many scripts, for example:

python process.py get_vencodes Hepatocyte --algorithm heuristic

  1. Run any script by going to the “Scripts” folder inside the package and calling the script individually.

Running the Tests

Tests for this module can be run in several ways; some examples:

  1. In the command-line:

1.1. Using the process.py utility file to run all the tests in one go. This is easily done by running the following command inside the VEnCode module:

python process.py run_tests

1.2. Run python’s standard module “unittest” in the tests directory to run each test individually. Basic example in command line:

python -m unittest test_internals

1.3. Another way to run each test individually is to install the nosetests python package and run nosetests in the tests directory. Basic example in command line:

nosetests test_internals.py

  1. By importing the VEnCode module in python:

from VEnCode import tests
tests.run_all_tests()

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:

Authors

See also the list of contributors who participated in this project.

License

Refer to the 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.