Skip to main content

normalize, verify, and select genomic data

Project description

bionorm normalizes and validates genomic data files prior to further processing or inclusion in a data store such as that of the Legume Federation.

Prerequisites

Python 3.6 or greater is required. This package is tested under Linux and MacOS using Python 3.7.

Installation for Users

Install via pip or (better yet) pipx:

pipx install bionorm

bionorm contains some long commands and many options. To enable command-line completion for bionorm commands, execute the following command if you are using bash as your shell:

eval "$(_BIONORM_COMPLETE=source_bash bionorm)"

For Developers

If you plan to develop bionorm, you’ll need to install the poetry dependency manager. If you haven’t previously installed poetry, execute the command:

curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python

Next, get the master branch from GitHub

git clone https://github.com/legumeinfo/bionorm.git

Change to the bionorm/ directory and install with poetry:

poetry install -v

Run bionorm with poetry:

poetry run bionorm

Usage

Installation puts a single script called bionorm in your path. The usage format is:

bionorm [GLOBALOPTIONS] COMMAND [COMMANDOPTIONS][ARGS]

Global Options

The following options are global in scope and, if used, must be placed before COMMAND. Not all commands support every global option:

-v, –verbose

Log debugging info to stderr.

-q, –quiet

Suppress logging to stderr.

–no-logfile

Suppress logging to file.

-e, –warnings_as_errors

Treat warnings as fatal (for testing).

Commands

A listing of commands is available via bionorm --help. The currently implemented commands are:

prefix_fasta

Prefix FASTA files for data store standard.

prefix_gff

Prefix and sort GFF3 file for data store standard.

busco

Perform BUSCO checks.

detector

Detect/correct incongruencies among files.

fasta

Check for GFF/FASTA consistency.

generate_readme

Generates a README file with details of genome.

index

Indexes FASTA file.

Each command has its COMMANDOPTIONS, which may be listed with:

bionorm COMMAND --help

Project Status

Latest Release

Python package

Make me NORMAL, please!

GitHub

GitHub repository

License

License terms

Travis Build

Travis CI

Coverage

Codecov.io test coverage

Code Grade

Codacy.io grade

Dependencies

dependabot dependencies

Pre-commit

pre-commit

Issues

Issues reported

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

bionorm-0.7.11.tar.gz (33.8 kB view hashes)

Uploaded Source

Built Distribution

bionorm-0.7.11-py3-none-any.whl (37.4 kB view hashes)

Uploaded Python 3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page