Introduction
Python software for simulating celluar/microbial clonal evolution with Gillespie algorithm usage
Installation and Usage
The simpliest installation:
python -m pip install clonalEvolution
Usage in python:
from microbialClonalEvolution import mainView
mainView.run()
Usage from console:
python -m clonalEvolution
# for simply run graphic verion of software
python -m clonalEvolution -h
# to see instructions for command line parametrization
Usage Instructions
General Tab:
file name - used in multiple functions: saving files, plots, parameters; specify name of file (according to windows acceptable characters), data files will have cycle number (name_number.csv/.txt)
file path - used in multiple functions: saving files, plots, parameters; specify absolute path to folder where simulation data should be saved
file description - 'TODO' add description in params/data file about simulation specyfied by user
clone diagram - button, fire the muller plot creation. It is needed to specify path with muller plot data generated from simulaiton
file structure (file-name_muller_plot_'binned'_data.txt):
clone, cells, previous clone
(0, 5000, 0)
mutations histograms - button, fire the VAF plot creation for all clones in specified file. File is needed to be one of generated simulation data
file structure (file-name_cycle.csv/.txt):
,Clone number,Cells number,Mean fitness,Mean mutation number,Driver mutation list,Passener mutation list,Previous clone number
0,0,5000,1,0,[],[],0
Generated tab:
select which files should be saved automaticaly after one cycle specified in parameters (skip). Not all types works for both algorithm versions 'TODO'
Parameters tab:
Plot tab:
Threads tab:
Main controls:
License
GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc. https://fsf.org/ Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
Disclaimer
Cellular/Microbial Clonal Evolution simulations basing on Gillespie algorithm. Copyright (C) 2022 by Jarosław Gil
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.
Author
Jarosław Gil, Silesian Univeristy of Technology, Department of Computer Graphics, Vision and Digital Systems.
1 maintainer
Release files for clonalEvolution 2.3.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| clonalEvolution-2.3.2.tar.gz | 46.8 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| clonalEvolution-2.3.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 96.0 kB
Release files / clonalEvolution-2.3.2.tar.gz
| Download URL | clonalEvolution-2.3.2.tar.gz |
|---|---|
| Size | 46.8 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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No |
| Uploaded via |
twine/4.0.1 CPython/3.9.13
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Release files / clonalEvolution-2.3.2-py3-none-any.whl
| Download URL | clonalEvolution-2.3.2-py3-none-any.whl |
|---|---|
| Size | 49.2 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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No |
| Uploaded via |
twine/4.0.1 CPython/3.9.13
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