biomedsheets 0.2

Python 3 library for accessing and managing BioMedical sheets

BioMed Sheets

This project contains the documentation for the BioMedical sample sheets project. Further, it contains the implementation of a Python API for I/O and comfortable access to the sample sheets and some CLI tools.

Installation

It’s best to start a new virtualenv

$ virtualenv -p python3 venv
$ source venv/bin/activate
$ pip install -r requirements_dev.txt
$ pip install -e .

Use python setup.py install if you want to copy the files instead of creating a link only.

Building Documentation

After installation (requirements_dev.txt contains the appropriate Sphinx version)

$ cd docs
$ make clean html

Now, open docs/build/html/index.html.

Running Tests

$ py.test

BioMed Sheets Changelog

v0.2

• Auto-deployment to pypi

• Fixing shortcuts to father/mother during cohort loading

• Cleanup code (according to Flake 8)

• Adding more tests, replacing examples by TSV files

• Removing protein pools

• Adding Sphinx-based ocumentation

• Restructuring requirements txt files

• Configurable entity name generation. This allows to use secondary id only for naming, e.g.

• Fixing requirements*.txt files for always using SSH

• Fixing sample naming for germline sample sheets

• Adding versioneer integration

v0.1.1

• First actual release, versioning done using versioneer

• Everything is new!