DiMHepy is a Python3 module that provide an alternative view of the outputs produced by the software pyani. If you use this tool, please cite our article: https://doi.org/10.1002/mbo3.938
You can simply download the github folder and launch the python file to use my software!
The graphical output below was generated with the command-line:
DiMHepy.py -ia test/dataset5Other/ANIb_alignment_lengths.tab
-ip test/dataset5Other/ANIb_percentage_identity.tab
-oss test/dataset5Other/ds5Other.png
The DiMHepy.py script enables straightforward ANI output rearrangements at the command-line, and uses the pyani module behind the scenes.
You can get a summary of available command-line options with DiMHepy.py -h
$ DiMHepy.py -h
DiMHepy is a software by Luca Triboli, version 1.0
Usage: python3 DiMHepy.py -i pyani_INDIR -o pyani_OUTDIR -oss DiMHepy_outImage [option] [arg]
or python3 DiMHepy.py -ia AlignmentFile -ip PercentageFile -oss DiMHepy_outImage [option] [arg]
Options and arguments (and corresponding environment variables):
-h : print this help message and exit (also --help)
-v : print version number (also --version)
-i arg : insert the INDIR of pyani
-o arg : insert the OUTDIR of pyani
-ia arg : insert the file name of alignment lengths
-ip arg : insert the file name of percentage identity)
-oss arg : insert the file name of the output image
-s : show output png file (only in graphic environment)
-d : display output interactive window (only in graphic environment)
-ignDiag : ignore Diagonal
[…]
To use DiMHepy in its basic version you have to run these command in the command line:
pip3 install numpy
pip3 install scipy
pip3 install matplotlib
pip3 install biopython
pip3 install pandas
pip3 install seaborn
- Numpy http://www.numpy.org/
- Scipy http://www.scipy.org/
- Matplotlib http://matplotlib.org/
- Biopython http://www.biopython.org/
- Pandas http://pandas.pydata.org/
- Seaborn https://github.com/mwaskom/seaborn
- Mummer http://mummer.sourceforge.net/
For the advanced version (using pyani in the background) you have to install pyani and mummer too (https://github.com/widdowquinn/pyani)
pip3 install pyani
sudo apt-get install mummer
Unless otherwise indicated, all code is subject to the following agreement:
(c) University of Trento, department of CIBIO 2018
Author: Triboli Luca
Contact: luca.triboli@studenti.unitn.it
Address:
Triboli Luca,
department of CIBIO,
University of Trento,
Via Sommarive 9,
Trento (Povo),
Italy
Copyright (c) 2018, Triboli Luca
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.