Data and script for extracting rate of gene gain/loss and pseudogenes from the branches of an ML tree.
The script is designed with special parameters and inputs for the Figure S2A and B in the manuscript :
Title: Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica.
Authors: Zhemin Zhou, Inge Lundstrøm, Alicia Tran-Dien, Sebastián Duchêne, Nabil-Fareed Alikhan,
Martin J. Sergeant, Gemma Langridge, Anna K. Fotakis, Satheesh Nair, Hans K. Stenøien,
Stian S. Hamre, Sherwood Casjens, Axel Christophersen, Christopher Quince, Nicholas R. Thomson,
François-Xavier Weill, Simon Y. W. Ho, M. Thomas P. Gilbert, Mark Achtman
Copyright Zhemin Zhou, Mark Achtman (2017)
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.
Folder structure:
temporalFreq.py: A script to generate the matrix used for the curve plot in Figure S2.
events.onBranch: The input for temporalFreq.py. This input is generated based on Additional Data 12 and 13.
ParatyphiC.island.mat: The matrix that is used to generat Figure S2A.
ParatyphiC.pseudogene.mat: The matrix that is used to generat Figure S2B.
Requirements:
pip packages:
dendropy
numpy
Commands to generate the matrices :
python temporalFreq.py events.onBranch island FA1062AA HA1701AA Br_437 1400 > ParatyphiC.island.mat
python temporalFreq.py events.onBranch pseudogene FA1062AA HA1701AA Br_437 1400 > ParatyphiC.pseudogene.mat
Usage:
python temporalFreq.py <input.file> <y.category> <start.tip> <end.tip> <MRCA.branch> <year.range> > <output.filt>
input.file: specialized input file. Example: "events.onBranch"
y.category: the category of events to be recorded.
start.tip: the first strain in the target sub-lineage.
end.tip: the last strain in the target sub-lineage.
MRCA.branch: the name of the branch before the MRCA of the sub-lineage. Events before the MRCA will not be recorded.
year.range: The range of the tip-to-root year (X axis)
output.file: The output is redirected from standard output.
zheminzhou/TemporalCurve
The script is designed as part of the supplementary data for the manuscript: https://www.biorxiv.org/content/early/2017/02/03/105759
Python