utrcalling 1.2.5

Package with tools to calculate molecule UTR sizes from RNA sequencing reads.

Requisites

Should download GTF and fasta files from http://ftp.ensembl.org/pub/

Installing

Requirements

Before using this module, you must have the following software installed in your environment:

• Python (tested on 3.9 but should work for later versions)

• BEDTools for generating the UTR reference regions pkl file. To install, visit https://github.com/arq5x/bedtools2. Alternatively, if using Anaconda, run conda install -c bioconda bedtools to install BEDTools in your current environment. Finally, make sure BEDTools is callable on the command-line.

Using pip

This module is currently not available from PyPi.

From source

1. Clone the git repository hosted at: https://github.com/AndreMacedo88/utrcalling

2. Go to the cloned directory in your local machine.

3. Run $ pip install .

Development

1. Clone the git repository hosted at: https://github.com/AndreMacedo88/utrcalling

2. Go to the cloned directory in your local machine.

3. Run $ pip install -e . --use-feature=in-tree-build

This will install the package locally and in editable mode, where changes to the local files will update the package in real-time.

Run Tests

After installation, you can:

• run the individual test files (example for one test file):

python -m unittest tests.test_core

• Run all test files at once:

utrcalling run_tests