autoOncotator

Python programs for automatically annotate vcf (variant call) file with Oncotator by selenium webdriver http://portals.broadinstitute.org/oncotator/

Prerequisite

• Python 3.6

Installation

git clone https://github.com/shanghungshih/autoOncotator.git

Internal Dependencies

1. download firefox

For Mac:

https://www.mozilla.org/zh-TW/firefox/new/

For Linux:

# download firefox
sudo apt install firefox

2. download geckodriver (v0.19.1)

https://github.com/mozilla/geckodriver/releases

# download geckodriver-v0.19.1
wget https://github.com/mozilla/geckodriver/releases/download/v0.19.1/geckodriver-v0.19.1-linux64.tar.gz
 
# unzip 
tar zxvf geckodriver-v0.19.1-linux64.tar.gz
 
# copy geckodriver to /usr/local/bin/
sudo cp geckodriver /usr/local/bin/

3. install selenium (v3.12.0)

# install pip3
sudo apt install python3-pip

# install package selenium
pip3 install selenium==3.12.0

Current Functions

• --vcf - Variant call file, vcf format
• --input_dir - input directory (default: current working directory)
• --output_dir - output directory (default: current working directory)
• --tsv - Generate the input format file for Oncotator, you can defined the name of the file (default: tsv)
• --maf - output file name (default: oncotator.maf.txt)
• --list_id - list all vcf files in specified directory
• --pool_size - Pool size of multi-thread for parallel computing (default: 1)

Quick start

list all vcfs in specified directory (e.g. current working directory)

python3 autoOncotator.py -l .

for running one vcf file

python3 autoOncotator.py -v test_562.mutect2.vcf

for Parallelly running mutiple vcf files (e.g. pool size = 10)

• Notes: 'NO SPACE' between vcf files

python3 autoOncotator.py -p 10 -v test_562.mutect2.vcf,test_553.mutect2.vcf,test_546.mutect2.vcf,test_543.mutect2.vcf,test_556.mutect2.vcf,test_544.mutect2.vcf,test_573.mutect2.vcf,test_548.mutect2.vcf,test_579.mutect2.vcf,test_565.mutect2.vcf