Library¶

The Mutalyzer class contains all relevant methods. A class instance is created by providing a build name.

>>> from mutalyzer_client import Mutalyzer
>>>
>>> mutalyzer = Mutalyzer('GRCh37')

The hgvs_to_db can be used to convert an HGVS description to a simple format to be used in databases.

>>> mutalyzer.hgvs_to_db('NC_000001.10:g.12783G>A')
('chr1', 12783, 'G', 'A')

To work with VCF files, we recommend to use the PyVCF library.

>>> from vcf import Reader
>>>
>>> reader = Reader(open('data/sample.vcf'))
>>> record = next(reader)

To convert a VCF record to HGVS, use the vcf_to_hgvs method.

>>> mutalyzer.vcf_to_hgvs(record.CHROM, record.POS, record.REF, record.ALT[0])
'NC_000001.10:g.12783G>A'

To convert a VCF record to database format, use the vcf_to_db method.

>>> mutalyzer.vcf_to_db(record.CHROM, record.POS, record.REF, record.ALT[0])
('chr1', 12783, 'G', 'A')