bionorm normalizes and validates genomic data files prior to further processing
or inclusion in a data store such as that of the
Legume Federation.
Python 3.6 or greater is required. This package is tested under Linux and MacOS using Python 3.7.
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)"
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
Installation puts a single script called bionorm in your path. The usage format is:
bionorm [GLOBALOPTIONS] COMMAND [COMMANDOPTIONS][ARGS]
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). |
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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