Virus variant detection pipeline
Dechun Lin
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
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.
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A UNIX based operating system.
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python 2.7
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python packages: biopython, scipy, pandas, statsmodels
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.
See /your/path/to/VirVarDP/data/ for test data set.
$ 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