Tool to retrieve location information of genetic variants
Switch branches/tags
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
MutationInfo
abstracts
biopython_mapper
docker
docs
test
web
.gitignore
LICENSE
README.md
setup.py

README.md

DOI

MutationInfo

MutationInfo is a python package to extract the position, the reference and the alternative sequence of a genomic variant. It accepts variants in dbSNP rs format or in HGVS format.

The main purpose of MutationInfo is to simplify the process of locating a variant in a dataset (i.e. of sequences or variants) that is aligned in a human reference genome (for example hg19 or hg38). It mainly wraps a collection of existing tools with a simple interface.

Example:

from MutationInfo import MutationInfo
mi = MutationInfo()

mi.get_info('rs53576')
{'chrom': '3', 'source': 'UCSC', 'genome': 'hg19', 
 'offset': 8804371L, 'alt': 'G', 'ref': 'A'}

mi.get_info('NM_006446.4:c.1198T>G')
{'chrom': '12', 'source': 'NC_transcript', 'genome': 'GRCh37.p13', 
 'offset': 21355487, 'alt': 'G', 'ref': 'T'}

Documentation

The documentation is here: http://mutationinfo.readthedocs.io/en/latest/

License

MIT License (MIT)

Contact

Alexandros Kanterakis