ABGDpy

Primary species delimitation using automatic barcode gap discovery.

This is a Python wrapper for ABGD: https://bioinfo.mnhn.fr/abi/public/abgd/

(you will need a C compiler when building from source)

Quick start

Install using pip:

$ pip install .

Run the GUI:

$ abgdpy-qt

Simple command line tool:

$ abgdpy tests/test.fas

Launch without installing

Before the first time you use the program, you must install any required modules, build the ABGD core and auto-compile the Qt resource files:

$ pip install -r requirements.txt
$ python setup.py build_ext --inplace
$ python setup.py build_qt

You can now launch the GUI:

$ python launcher.py

Packaging

You must first compile the ABGD C module, auto-compile Qt resources, then use PyInstaller on the launcher spec file:

$ pip install pyinstaller
$ python setup.py build_ext --inplace
$ python setup.py build_qt
$ pyinstaller launcher.spec

Module

You may import and use the ABGD module in your python scripts.

To launch the GUI:

>>> import abgdpy.qt
>>> abgdpy.qt.main.show()

More examples to follow soon.

Python interactive example

From the root directory, launch the Python interpreter:

$ python -i

Initialize an analysis on your file:

>>> a = abgd.BarcodeAnalysis('tests/test.fas')

Browse and change parameters:

>>> a.param.keys()
>>> a.param.general.keys()
>>> a.param.general.all = True

Run the analysis:

>>> abgd.launch(a)

You can find the results inside the folder a.results. Save them in a new directory:

>>> print(a.results)
>>> a.fetch('./my_results')

Acknowledgements

N Puillandre, A Lambert, S Brouillet and G Achaz ABGD,
Automatic Barcode Gap Discovery for primary species delimitation,
Mol Ecol. 2011.

• Original C code by G. Achaz
• Code update by Sophie Brouillet
• BIONJ by Olivier Gascuel