pytest ngs fixtures
Project description
pytest-ngsfixtures
About
This is a pytest plugin that enables next generation sequencing pytest fixtures, including fastq files and output files from a variety of bioinformatics applications and tools. There are sequencing fixtures for some common sample layouts, but it’s easy to generate additional sample fixture layouts using fixture factories.
See the pytest-ngsfixtures documentation for more information.
Free software: GNU General Public License v3
Features
ngs data sets of different sizes
predefined sample layouts
factories for generating new sample layouts
result files from a variety of bioinformatics applications and tools
Installation
$ conda install -c percyfal pytest-ngsfixtures
$ pip install pytest-ngsfixtures
Credits
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.
History
0.6.1 (2017-11-22)
Added some fixes that turned out to be necessary for optional performance.
Add fixture that parametrizes over input parameters (#37)
Fix bug that returned wrong number of snakemake targets in application output generation (#36)
Add travis builds (#35)
Fix reference layout error for python 3.5 (#34)
Update option defaults (#32)
Expose fewer predefined fixtures via plugin (#31)
Unify parameter names (#33)
0.6.0 (2017-11-21)
This is a major revision of the code. Several new abstraction classes have been introduced to ease interaction with local test files, along with new factory functions. For backwards compatibility, most factory functions should work as previously. Documentation has been much improved.
Clarify fixture function naming convention (#29)
Expose bulk of factory inner functions (#24)
Create separate module for os-related functions (#27)
Use separate conda build statements to build for different python versions (#23)
0.5.2 (2017-11-16)
Add pool fixtures (#22)
Add safe_copy function (#21)
0.5.1 (2017-10-25)
Change name to pytest-ngsfixtures (#20)
Add bcftools versions 1.4, 1.4.1, 1.5, 1.6
Add bowtie 1.2.1.1
0.5.0 (2017-09-25)
Add star application
Add vsearch application
Add rseqc application
Add snakemake dependency
Update docs
Separate qualimap pe and se output (#12)
Add mapdamage2 (#11)
Fix mapdamage2 missing output (#18)
Use realpath to determine download url (#17)
Rename download_ngsfixtures_data.py to pytest_ngsfixtures_download_data.py
Update versions for samtools
0.4.0 (2017-03-28)
Add picard output data
Add functions for dealing with application fixtures
Move docs to gh-pages
Add pytest_ngsfixtures_add_application.py for templating new applications
Application outputs now implemented as dictionaries for multiple-output applications
0.3.1 (2017-03-03)
Defer download to script, minor bug fixes
Add application_fixtures to config module
Fix sample_alias bug (#4)
Add script download_ngsfixtures_data.py for manual download of data (#5)
0.3.0 (2017-03-02)
Add application data, pool data, and functions for downloading data
Add application data for cutadapt, fastqc, qualimap and samtools
Add pooled sequencing data
Add functionality for downloading large data sets
Improve make targets for easier releases
Minor bug fixes
0.2.0 (2017-02-24)
Add new reference files, test files, and factory functions.
Use snakemake instead of make to generate data files
Add separate test file for factory functions
Add scaffold file with randomly inserted N’s
Improve safe_symlink
Add threads options for running tests
Add Snakefile and rules for generating application files
Add fileset, filetype factory functions
0.1.0 (2017-01-24)
First release on PyPI.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for pytest_ngsfixtures-0.6.1-py2.py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | a93c745b72530ebd223eef39bf89a78a3f3ab855b64f5af156dbc2a9c8ac9b26 |
|
MD5 | 733f2f40028d34986c67463fd3e682c7 |
|
BLAKE2b-256 | 8478c76f5a6a1225bb88a1fd07026421ea90539f5e4afd75017d67c5118535cb |