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Python 3 library for accessing and managing BioMedical sheets

Project description

BioMed Sheets

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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

Publishing to PyPi

$ python setup.py sdist upload

BioMed Sheets Changelog

v0.8.1

  • Fixing mapping of Unknown values.

v0.8.0

  • 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.

v0.7.1

  • Removing superflous print.

v0.7.0

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

  • Fixing some tests.

v0.6.2

  • Proper merging with recent ruamel.yaml updates.

v0.6.1

  • Interpreting # in TSV files in more locations.

v0.6.0

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

v0.5.6

  • Fixing bug in computing index (for real).

v0.5.5

  • Fixing bug in computing index.

v0.5.4

  • Fixing setup.py to work with pip v10.t

v0.5.3

  • Fixing packaging to use base and not test dependencies.

v0.5.2

  • Removing some hard (transitive) dependencies.

v0.5.1

  • Fixing manifest so the package contains the JSON file.

v0.5

  • Allow cancer sheets for use in germline calling.

  • Only warn if index has no NGS library, no error.

v0.4

  • 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)

v0.3.1

  • Fixing setup.py to work with pip v10.

v0.3

  • 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.

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!

Project details


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biomedsheets-0.8.1.tar.gz (121.6 kB view hashes)

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