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
1 maintainer
Release files for utrcalling 1.2.5
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| utrcalling-1.2.5.tar.gz | 1.7 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| utrcalling-1.2.5-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 3.4 MB
Release files / utrcalling-1.2.5.tar.gz
| Download URL | utrcalling-1.2.5.tar.gz |
|---|---|
| Size | 1.7 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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|
|
BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.2 CPython/3.9.12
|
Release files / utrcalling-1.2.5-py3-none-any.whl
| Download URL | utrcalling-1.2.5-py3-none-any.whl |
|---|---|
| Size | 1.7 MB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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|
|
BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.2 CPython/3.9.12
|
