peroba: A Python repository from Quadram Institute Bioscience

Leonardo de Oliveira Martins¹
_{1. Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ, UK}

Introduction

peroba is a tool for continuous updating of outbreak information as new sequences are incorporated. It is being developed as a phylogenetic tracking tool to aggregate samples sequenced at the QIB with global information from COG-UK and GISAID. Therefore you will not find any real data here (all COG-UK data are available online however). If you find any report/results/data here, it is from randomised/simulated data (due to privacy reasons) and cannot be used or interpreted.

This tool may not be very useful yet for general phylogenetic analyses, you may need to have access to the COGUK consortium or at least be familiar with it to make sense of some variables. If you are looking for more stable COGUK-related tools, please have a look at https://github.com/COG-UK (for instance civet or phylo reports) and https://cov-lineages.org/. Peroba is under active testing and development, it is being employed at the QIB but we hope others may find it useful.

peroba is the name of an endangered Brazilian timber tree. But if you like acronyms it stands for Phylogenetic Epidemiology with ROBust Assignment.

Modules

peroba is composed of four modules, that should be run in order:

peroba_database: This script collects information from several sources and generates a set of perobaDB files.
peroba_subsample: creates a table with several selections of samples from the perobaDB database
peroba_backbone: This script selects a set of "global" sequences from perobaDB to be analysed together with the local ones (NORW). It finds local sequences within the database, but the user should also include other local sequences.
peroba_report: once the user finishes the analysis (i.e. has a phylogenetic tree using suggestions from peroba_backbone), this script will estimate ancestral states and generate a PDF report.

Installation

Before installing peroba, you will need to download and copy the shapefiles for plotting the maps, which we cannot distribute here due to copyright issues.

Requirements

conda
texlive
linux
python > 3.6
internet access to download shapefiles

Download shapefiles

Shapefiles can be downloaded however, and the postcode shapefiles are kindly provided by OpenDoorLogistics (please check their license terms):

wget https://www.opendoorlogistics.com/wp-content/uploads/Data/UK-postcode-boundaries-Jan-2015.zip
unzip  UK-postcode-boundaries-Jan-2015.zip -d postcodes
cp postcodes/Distribution/Districts.* ${perobadir}/peroba/data/

Where ${perobadir} is the root directory of your peroba installation. The directory ${perobadir}/peroba/data should already exist when you cloned this repo.

Likewise, the adm2 location correspond to NUTS 2 regions, and can be downloaded from GADM:

wget https://biogeo.ucdavis.edu/data/gadm3.6/shp/gadm36_GBR_shp.zip
unzip gadm36_GBR_shp.zip -d adm2
cp adm2/gadm36_GBR_2.* ${perobadir}/peroba/data/

You will also need to download by hand the Sars-cov2 sequence and metadata files, which is not covered here. I have never tried, but it might work to download the publicly available data on COG-UK.

Generate a conda environment

This software depends on several other packages, installable through conda or pip. The suggested installation procedure is to create a conda environment (to take care of dependencies) and then installing the python package:

conda update -n base -c defaults conda # probably not needed, but some machines complained about it
conda env create -f environment.yml  
conda activate peroba
python setup.py install # or "pip install ."

Since this software is still under development, these two commands are quite useful:

conda env update -f environment.yml # update conda evironment after changing dependencies
pip install -e . # installs in development mode (modifications to python files are live)

There are two system packages that might need to be installed outside conda, libGL and texlive:

apt-get install libgl1-mesa-glx texlive-full

ete3 complains about missing lbGL which is safer to install system-wise; To test it, type from PyQt5 import QtGui in a python console and see if you are good to go. And texlive is for the PDF report generation (texlive-full is a monster, but you won't need to worry about missing fonts again :D )

The report generation relies on the Eisvogel latex template for pandoc, which is included here (it's released under a BSD 3-clause). The complete list of dependencies is described in the file environment.yml. Please let me know if there are missing dependencies, although peroba is under active development and its behaviour may change without notice.

Instructions

You can find a tutorial on using the software here.

Caveats

When interpreting any result, please remember that not all sequences pass the sequencing quality control. Those that do may be excluded from COGUK phylogenetic analysis, which means we won't have metadata (in particular sequence_name, which allows mapping between tree, sequence, and epi data) information from them. We minimise this by using local information whenever possible, but still the reasons for exclusion remain.

This is not a general-purpose software. It is being released publicly in the hope that other researchers can build upon it.

License

SPDX-License-Identifier: GPL-3.0-or-later

peroba 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 (http://www.gnu.org/copyleft/gpl.html).

quadram-institute-bioscience/peroba