tbhgvs contains functions for converting mutations to from genome coordinates to hgvs format.
You can install the package using the following commands:
git clone https://github.com/jodyphelan/tbhgvs.git
cd tbhgvs
python setup.py install
The fisrt thing to do is to download the fasta and gff files (this only needs to be done once!):
tbhgvs-download-files.py
You can make your own script or you can use you can use the tbhgvs-covert.py script as a commands-line tool.
# Example genome -> hgvs format
tbhgvs-convert.py genome --pos 3841083 --ref A --alt C
# Example hgvs -> genome format
tbhgvs-convert.py hgvs --gene alr --mutation p.Leu113Arg
If you would like to make your own script you can use this example as a template.
ref_db = tbhgvs.reference_db()
ref_db.hgvs2genome("p.Ser450Leu","Rv0667")
ref_db.genome2hgvs([{'pos': '761155', 'ref': 'C', 'alt': 'T'}, {'pos': '761156', 'ref': 'G', 'alt': 'A'}])