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
0.11.7 (2023-02-22)
Bug Fixes
0.11.6 (2023-02-22)
Bug Fixes
v0.11.5
- Fixing consistency check for Duo Cases (#26).
v0.11.4
- Fixing issues with ResourceAdapter (#21).
v0.11.3
- Fixing warnings in the tests (#19).
v0.11.2
- Updating/modernizing dependencies.
v0.11.1
- Adding property to shortcut sheets that indicates available kwargs.
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
Unknownvalues.
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
bioSampleandtestSamplein germline TSV files. - Fixing some tests.
v0.6.2
- Proper merging with recent
ruamel.yamlupdates.
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.pyto 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.pyto 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*.txtfiles 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!
1 maintainer
Metadata
1 maintainer
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