liftover_helper

Requirements

Python3

Packages:

pysam

Setup Project

Download repo

git clone https://github.com/color/pytrims.git

cd pytrims

python3 -m venv ./venv

run make

make

run tests to make sure it works

python -m unittest tests/test_pytris.py

Running from commandline

Note: The code is only tested for vcf files not vcf.gz files

python scripts/pytrimp.py fasta_file raw_mutation_file example: python3 scripts/pytrims.py --reference_fasta ../resources-files/b37-resources/b37/GRCh37.p12.fa --input_file /Users/Anju/Downloads/Breast_raw_mutations_data_ExtractWGS_2014_10_13_example.txt

Description and Notes

run tests to make sure it works

python -m unittest tests/test_lib.py