bionorm 0.2.1

normalize and verify genomic data

normalize and validate genomic data files

Prerequisites

Python 3.6 or greater is required.

Installation

This package is tested under Linux and MacOS using Python 3.7. Install via pip, pipx, or pipenv in the usual way:

pipx install bionorm

Developers

bionorm uses the poetry <https://python-poetry.org> dependency manager. Install poetry in the usual way. Get the version of python you intend to use as first in the path, and 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/ncgr/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]

A listing of commands is available via bionorm --help. Current available commands are:

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.

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