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Python 3 library for accessing and managing BioMedical sheets

Project description

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.


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 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

Publishing to PyPi

$ python sdist upload

BioMed Sheets Changelog


  • Adding property to shortcut sheets that indicates available kwargs.


  • Adding custom option to join pedigrees by fields such as familyId.


  • Adding functionality for filtering pedigrees.


  • Fixing sorting bug.


  • Sorting donors for picking the index in germline sample sheets.


  • Fixing mapping of Unknown values.


  • Changed behaviour in case of no affected donor has library. In this case, the first donor becomes the index. Consequently, the index must have an NGS library.


  • Removing superflous print.


  • Allowing to specify bioSample and testSample in germline TSV files.
  • Fixing some tests.


  • Proper merging with recent ruamel.yaml updates.


  • Interpreting # in TSV files in more locations.


  • Allowing to comment out lines in TSV files by prefixing them with #.


  • Fixing bug in computing index (for real).


  • Fixing bug in computing index.


  • Fixing to work with pip v10.t


  • Fixing packaging to use base and not test dependencies.


  • Removing some hard (transitive) dependencies.


  • Fixing manifest so the package contains the JSON file.


  • Allow cancer sheets for use in germline calling.
  • Only warn if index has no NGS library, no error.


  • Fixin TSV I/O.
  • Bumping ruamel.yaml version.
  • Fixing cancer sheet iteration.
  • Allowing cancer-only samples in cance case sheets.
  • Fixing float-related bug.
  • Fixing bug in reference resolving (+tests)


  • Fixing to work with pip v10.


  • Adding possibility for generic TSV sample sheets.
  • Many updates to make documentation more clear.
  • Various updates, fixing Codacy issues.
  • Adding routines for writing out PED file from germline sample sheets.


  • 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


  • First actual release, versioning done using versioneer
  • Everything is new!

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