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/gendiscalpyThis 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 euclidianUsage 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')
