bionorm 0.7.11

normalize, verify, and select genomic data

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

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