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Python 3 library for accessing and managing BioMedical sheets

Project description

BioMed Sheets

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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

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!

Project details


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Filename, size & hash SHA256 hash help File type Python version Upload date
biomedsheets-0.6.2.tar.gz (122.3 kB) Copy SHA256 hash SHA256 Source None Aug 16, 2018

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