mpg-age-bioinformatics/AGEpy

Bioinformatics tools for Python

AGEpy

This python package contains Bioinformatics tools developed at the Bioinformatics Core Facility of the Max Planck Institute for Biology of Ageing.

Max Planck Institute for Biology of Ageing
Joseph-Stelzmann-Str. 9b
D-50931 Cologne
Germany

https://bioinformatics.age.mpg.de

Read the Docs

agepy.readthedocs.io

Installation

pip

pip3 install git+https://github.com/mpg-age-bioinformatics/AGEpy.git --user

To install a specific commit use:

pip3 install git+https://github.com/mpg-age-bioinformatics/AGEpy.git@<ash> --user
# eg.
pip3 install git+https://github.com/mpg-age-bioinformatics/AGEpy.git@9b10b76d021652c44f93e8dd3850a7a937e6fcee --user

Alternatively you can also install the package with a symlink, so that changes to the source files will be immediately available to users of the package on your system:

git clone https://github.com/mpg-age-bioinformatics/AGEpy
cd AGEpy
python setup.py develop --user

Be aware that with the develop option you won't be able to properly update once new scripts are added.

Example usage

import AGEpy as age

gtf=age.readGTF("/path/to/file.gtf")

gtf.head()

Help

In bash:

pydoc AGEpy.AGEpy

In python:

help("AGEpy.AGEpy")