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.
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
v0.11.0
Adding custom option to join pedigrees by fields such as familyId.
v0.10.0
Adding functionality for filtering pedigrees.
v0.9.1
Fixing sorting bug.
v0.9.0
Sorting donors for picking the index in germline sample sheets.
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!
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