Package with tools to calculate molecule UTR sizes from RNA sequencing reads.
Project description
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
Clone the git repository hosted at: https://github.com/AndreMacedo88/utrcalling
Go to the cloned directory in your local machine.
Run $ pip install .
Development
Clone the git repository hosted at: https://github.com/AndreMacedo88/utrcalling
Go to the cloned directory in your local machine.
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
Project details
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