vcf_flag_modifier

Python utility to remove flags from a VCF file. It can be used to filter a whole file or optionally only positions in a bed file.

Master	Develop

Contents:

• Docker, Singularity and Dockstore
• Dependencies/Install
  • Package Dependencies
  • Installation
    • Assuming setup of virtualenv as per Setup VirtualEnv
• Usage
• Development Environment
  • Setup VirtualEnv
  • Testing/Coverage (./run_tests.sh)
• Cutting a Release
  • Ensure you increment the version number in setup.py
• Creating a release
  • Preparation
  • Release process
    • Code changes
    • Docker image
    • Cutting the release
• LICENCE

Docker, Singularity and Dockstore

There is a pre-built images containing this codebase on quay.io. The docker image is known to work correctly after import into a singularity image.

Dependencies/Install

Package Dependencies

pip will install the relevant python dependancies, listed here for convenience:

• vcfpy

Installation

Assuming setup of virtualenv as per Setup VirtualEnv

git clone vcf_flag_modifier
source venv/bin/activate # if not already in venv
python setup.py install
python flag_modifier.py -h

Usage

$ python vcf_flag_modifier.py -h
usage: vcf_flag_modifier.py [-h] -f input.vcf[.gz] [-o output.vcf]
                            [-b positions.bed[.gz]] [-a] [-t | -l UMV]

Modify a VCF file, removing provided flags.

optional arguments:
  -h, --help            show this help message and exit
  -f input.vcf[.gz], --vcfin input.vcf[.gz]
                        Path to input VCF file
  -o output.vcf, --vcfout output.vcf
                        path to write output VCF file
  -b positions.bed[.gz], --bedfile positions.bed[.gz]
                        Path to bed file of positions to consider for flag
                        modification Bed file can be `contig start stop` or
                        can include specific changes for each coordinate
                        `contig start stop ref alt`
  -a, --alleles         Path to bed file of positions to consider for flag
                        modification Bed file can be `contig start stop` or
                        can include specific changes for each coordinate
                        `contig start stop ref alt`
  -t, --listflags       Instead of modifying a VCF, list flags avaialble from
                        header
  -l UMV, --flagremove UMV
                        Flag(s) to remove from the passed VCF file
                        (repeatable)

Development Environment

This project uses git pre-commit hooks. As these will execute on your system it is entirely up to you if you activate them. If you want tests, coverage reports and lint-ing to automatically execute before a commit you can activate them by running:

git config core.hooksPath git-hooks

Only a test failure will block a commit, lint-ing is not enforced (but please consider following the guidance).

You can run checks manually without a commit by executing the following in the base of the clone:

./run_all_tests.sh

Setup VirtualEnv

cd $PROJECTROOT
hash virtualenv || pip3 install virtualenv
virtualenv -p python3 venv
source venv/bin/activate

python setup.py develop # so bin scripts can find module

Testing/Coverage (./run_tests.sh)

source venv/bin/activate # if not already in venv
pip install pytest
pip install pytest-cov
run_tests.sh

Cutting a Release

Ensure you increment the version number in setup.py

Creating a release

Preparation

• Commit/push all relevant changes.
• Pull a clean version of the repo and use this for the following steps.

Release process

This project is maintained using HubFlow.

Code changes

1. Make appropriate changes
2. Update setup.py to the correct version (adding rc/beta to end if applicable).
3. Update CHANGES.md to show major items.
4. Check all tests and coverage reports are acceptable.
5. Commit the updated docs and updated module/version.
6. Push commits.

Docker image

1. Use the GitHub tools to draft a release.
2. Build image locally
3. Run example inputs and verify any changes are acceptable
4. Bump version in Dockerfile
5. Push changes

Cutting the release

1. Check state on Travis
2. Generate the release (add notes to GitHub)
3. Confirm that image has been built on quay.io

LICENCE

Copyright (c) 2018-2019 Genome Research Ltd.

Author: CancerIT [email protected]

This file is part of vcf_flag_modifier.

vcf_flag_modifier is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License along with this program. If not, see http://www.gnu.org/licenses/.