biomedsheets

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

• MANIFEST.in file for CHANGELOG.md (#32) (c093555)

0.11.6 (2023-02-22)

Bug Fixes

• implementing release-please (#30) (2076440)

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 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!