Python 3 library for accessing and managing BioMedical 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 setup.py install if you want to copy the files instead of creating a link only.
After installation (requirements_dev.txt contains the appropriate Sphinx version)
$ cd docs $ make clean html
Now, open docs/build/html/index.html.
Publishing to PyPi
$ python setup.py sdist upload
BioMed Sheets Changelog
- 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 setup.py 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 setup.py 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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