HGVS Tools enables rapid forward and reverse translation between protein, cDNA, and genomic HGVS variant descriptions. In addition, it provides reasonable rules for inferring transcripts from ambiguous identifiers, automating the process of concordant, unambiguous transcript selection.
You may construct a variant object directly from an HGVS string, using Chromosome names, HGNC Gene Symbols, or Ensembl Transcript or Protein IDs.
>>> from hgvs_tools import Variant
>>> v1 = Variant('FGFR3:p.R248C')
>>> v2 = Variant('9:g.22125504G>C')
>>> v3 = Variant('ENST00000003084:c.1431_1433delTTC')>>> v1.g.hgvs
ENST00000352904:g.1803564C>T
>>> v1.c.hgvs
ENST00000352904:c.742C>T
>>> v1.p.hgvs
ENSP00000231803:p.R248C>>> v1.g.ucsc
chr4:1803564-1803564
>>> v1.g.ensembl
4:1803564-1803564>>> v1.g.info
{'edit_type': 'substitution', 'strand': '1', 'ref': 'C', 'start': '1803564', 'chromosome': '4', 'alt': 'T',
'id': 'ENST00000352904', 'stop': '1803564'}
>>> v1.c.info
{'alt': 'T', 'stop': '742', 'edit_type': 'substitution', 'id': 'ENST00000352904', 'ref': 'C', 'predicted': False,
'start': '742'}
>>> v1.p.info
{'predicted': False, 'start': '248', 'edit_type': 'substitution', 'alt': 'C', 'stop': '248', 'ref': 'R',
'id': 'ENSP00000231803'}>>> from hgvs_tools import Variant
>>> v = Variant('FGFR3:p.R248C', reference_assembly=37)
>>> print(v)
('ENST00000352904:g.1803564C>T', 'ENST00000352904:c.742C>T', 'ENSP00000231803:p.R248C')