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VirVarDP

Virus variant detection pipeline

Author

Dechun Lin

Citation

Please cite the following article when using VirVarDP:

Lin, D., Li, L., Xie, T., et al. (2018). Codon usage variation of Zika virus: The potential roles of NS2B and NS4A in its global pandemic. Virus research 247, 71-83. Article Link

Introduction

A pipeline based on python to detect synonnymous or non-synonnymous substitutions within homologous gene of Virus complete genome

This lists the basic information for using VirVarDP.

Requirements

  • A UNIX based operating system.

  • python 2.7

  • python packages: biopython, scipy, pandas, statsmodels

  • megacc

Installation

Download VirVarDP from GitHub. You'll need to add VirVarDP's bin directory to your $PATH.:

git clone https://github.com/lindechun/VirVarDP.git
/your/path/to/VirVarDP/VirVarDP.py -h

You will nedd to install all the dependencies packages by pip or conda.

Basic test data set

See /your/path/to/VirVarDP/data/ for test data set.

Usage

$ python ../bin/VirVarDP.py -h
usage: VirVarDP.py [-h] [-v] [-i FALIST] [-r REFERENCE] [-I INFO]
                   [-l GENELENGTH] [-t SET_TABLE] [-g GROUPCOLUMNS] [-G GAP]
                   [-j ORDERGENES] [-p PREFIX] [-o OPATH]

The flow of Virus variant detection pipeline

optional arguments:
  -h, --help       show this help message and exit
  -v, --version    show program's version number and exit
  -i FALIST        a list file consists of individual Genes, based codon align
                   (megacc)
  -r REFERENCE     which sample id regard as reference
  -I INFO          sample info table
  -l GENELENGTH    eachGene.length.txt
  -t SET_TABLE     Genetic Code Table, default is 1
  -g GROUPCOLUMNS  the columns of info table, which is the groups of sample
  -G GAP           The gaps before specific gene. eg: '**:40,**:50'
  -j ORDERGENES    The order of genes
  -p PREFIX        Output file prefix
  -o OPATH         Path of Output File

See /your/path/to/VirVarDP/test/demo_*.sh for example of variant calling about 100 Zika sequences.

$ cat demo_python_flow.sh
python ../bin/VirVarDP.py -i data.list -r LC002520 -I ../data/SampleInfo.txt -l ../data/eachGene.length.txt -j "C,prM,E,NS1,NS2A,NS2B,NS3,NS4A,NS4B,NS5" -g Lineage -o results -G 'NS4B:69' -p Zika