gendiscalpy

Python bindings to GenDisCal and addition of phylogenetic tree function

• GenDisCal repo: https://github.com/LM-UGent/GenDisCal
• GenDisCal paper: https://academic.oup.com/bioinformatics/article/36/8/2337/5695704

Installation

This package was created using Python 3.9.

pip install git+https://github.com/MrTomRod/gendiscalpy

This will add two scripts to your PATH:

• install_gendiscal
• gendiscal_tree

Usage in terminal

install_gendiscal

This script downloads the GenDisCal binary and unpacks it to a path of your choosing.

$ install_gendiscal 
Options:
  1: /home/user/PycharmProjects/venvs/gendiscalpy10/bin
  2: /home/user/miniconda3/condabin
  3: /home/user/bin
  4: /usr/bin
  5: /usr/sbin
Please select a path to install GenDisCal to!
1
You chose: /home/user/PycharmProjects/venvs/gendiscalpy10/bin
Installed GenDiscal here: /home/user/PycharmProjects/venvs/gendiscalpy10/bin/GenDisCal

Now, you should be able to run GenDisCal in your terminal. Test with GenDisCal --version.

gendiscal_tree

Create a phylogenetic tree based on GenDisCal a distance matrix. Returns Newick format.

This script uses the upmga algorithm of the biotite package. See wikipedia and biotite docs.

Requires GenDisCal to be in PATH, see also install_gendiscal.

Examples:

gendiscal_tree from_files assembly1.fna assembly2.fna
gendiscal_tree from_files assemblies/*.fna
gendiscal_tree from_files assemblies/*.fna --preset PaSiT6 --method euclidian

Usage as Python class

from gendiscalpy import GenDisCal, GenDisCalTree
from gendiscalpy.install_gendiscal import install

# install GenDisCal to /home/user/bin/GenDisCal
install(path='/home/user/bin')

gdc = GenDisCal()  # bin='/home/user/bin/GenDisCal'

# these commands return pandas.DataFrame objects
table1 = gdc.run('test-data/*.fna')
table2 = gdc.run('test-data/*.fna', preset='PaSiT6', method='euclidian')
distance_matrix = gdc.run('test-data/*.fna', distance_matrix=True)
histogram = gdc.run('test-data/*.fna', histogram=True)

# this command returns a float
val = gdc.compare_two(assembly_1='test-data/FAM3257-i1-1.fna', assembly_2='test-data/FAM13496-i1-1.fna')

# this command returns a string in Newick format
newick = GenDisCalTree.from_files('test-data/*.fna')