Package: biomedsheets
BioMed SheetsThis 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.InstallationIt's best to start a new virtualenv$ virtualenv -p python3 venv
$ source venv/bin/activate
$ pip install -r requirements/dev.txt
$ pip install -e .Usepython setup.py installif you want to copy the files instead of creating a link only.Building DocumentationAfter installation (requirements_dev.txtcontains the appropriate Sphinx version).$ cd docs
$ make clean htmlNow, opendocs/build/html/index.html.Running Tests$ py.testBioMed Sheets Changelog0.11.7(2023-02-22)Bug FixesMANIFEST.in file for CHANGELOG.md (#32) (c093555)0.11.6(2023-02-22)Bug Fixesimplementing release-please (#30) (2076440)v0.11.5Fixing consistency check for Duo Cases (#26).v0.11.4Fixing issues with ResourceAdapter (#21).v0.11.3Fixing warnings in the tests (#19).v0.11.2Updating/modernizing dependencies.v0.11.1Adding property to shortcut sheets that indicates available kwargs.v0.11.0Adding custom option to join pedigrees by fields such asfamilyId.v0.10.0Adding functionality for filtering pedigrees.v0.9.1Fixing sorting bug.v0.9.0Sorting donors for picking the index in germline sample sheets.v0.8.1Fixing mapping ofUnknownvalues.v0.8.0Changed 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.v0.7.1Removing superflous print.v0.7.0Allowing to specifybioSampleandtestSamplein germline TSV
files.Fixing some tests.v0.6.2Proper merging with recentruamel.yamlupdates.v0.6.1Interpreting#in TSV files in more locations.v0.6.0Allowing to comment out lines in TSV files by prefixing them with#.v0.5.6Fixing bug in computing index (for real).v0.5.5Fixing bug in computing index.v0.5.4Fixingsetup.pyto work with pip v10.tv0.5.3Fixing packaging to use base and not test dependencies.v0.5.2Removing some hard (transitive) dependencies.v0.5.1Fixing manifest so the package contains the JSON file.v0.5Allow cancer sheets for use in germline calling.Only warn if index has no NGS library, no error.v0.4Fixin TSV I/O.Bumping ruamel.yaml version.Fixing cancer sheet iteration.Allowing cancer-only samples in cance case sheets.Fixingfloat-related bug.Fixing bug in reference resolving (+tests)v0.3.1Fixingsetup.pyto work with pip v10.v0.3Adding 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.v0.2Auto-deployment to pypiFixing shortcuts to father/mother during cohort loadingCleanup code (according to Flake 8)Adding more tests, replacing examples by TSV filesRemoving protein poolsAdding Sphinx-based ocumentationRestructuring requirements txt filesConfigurable entity name generation. This allows to use secondary id
only for naming, e.g.Fixingrequirements*.txtfiles for always using SSHFixing sample naming for germline sample sheetsAdding versioneer integrationv0.1.1First actual release, versioning done using versioneerEverything is new!