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
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Release files for bionorm 0.7.11
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| bionorm-0.7.11.tar.gz | 33.8 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| bionorm-0.7.11-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 71.2 kB
Release files / bionorm-0.7.11.tar.gz
| Download URL | bionorm-0.7.11.tar.gz |
|---|---|
| Size | 33.8 kB |
| Tags | Source |
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Release files / bionorm-0.7.11-py3-none-any.whl
| Download URL | bionorm-0.7.11-py3-none-any.whl |
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| Size | 37.4 kB |
| Tags | Python 3 |
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