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Biocommons HGVS example code
Dave Lawrence edited this page Mar 21, 2023
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4 revisions
If you get HGVSDataNotAvailableError
meaning sequences are not available - you may also want to look into using FastaSeqFetcher to provide transcripts
import hgvs
from hgvs.assemblymapper import AssemblyMapper
from cdot.hgvs.dataproviders import JSONDataProvider, RESTDataProvider
hdp = RESTDataProvider() # Uses API server at cdot.cc
# hdp = JSONDataProvider(["./cdot-0.2.14.refseq.grch37.json.gz"]) # Uses local JSON file
am = AssemblyMapper(hdp,
assembly_name='GRCh37',
alt_aln_method='splign', replace_reference=True)
hp = hgvs.parser.Parser()
var_c = hp.parse_hgvs_variant('NM_001637.3:c.1582G>A')
am.c_to_g(var_c)
from cdot.hgvs.dataproviders import JSONDataProvider, RESTDataProvider
import hgvs.parser
import hgvs.assemblymapper
hp = hgvs.parser.Parser()
hdp = RESTDataProvider()
am = hgvs.assemblymapper.AssemblyMapper(hdp,
assembly_name='GRCh37', alt_aln_method='splign',
replace_reference=True)
var_g = hp.parse_hgvs_variant('NC_000007.13:g.36561662C>T')
am.g_to_c(var_g, 'NM_001637.3')