This is wrapper script of functions from python package hgvs (https://www.ncbi.nlm.nih.gov/pubmed/30129167). hgvs is used to parse, format, validate, normalize, and map biological sequence variants according to recommendations of the Human Genome Variation Society.
To use this script follow instructions.
Clone this repository to your local directory (no need for installation)
Install following packages to your Python2.7 enviroment (python2+ is required for hgvs package)
- hgvs (https://hgvs.readthedocs.io/en/stable/installation.html)
- pandas (http://pandas.pydata.org/pandas-docs/stable/install.html)
Run script as:
python2.7 /path/to/script_directory/Convert_HGVS.py \
input_table.txt \
conversion_direction_tag \ # string "toHGVS" or "fromHGVS"
output_name_prefix # in example "example_output"
Input table should have same header names as examples inputs in git repository