manuscript-example.rst

Manuscript Example

import hgvs
hgvs.__version__

'0.3dev-283858cb6466'

Parse an HGVS string into a Python structure

import hgvs.parser 
hp = hgvs.parser.Parser()
var_c1 = hp.parse_hgvs_variant('NM_182763.2:c.688+403C>T')
var_c1, var_c1.posedit.pos.start

(SequenceVariant(ac=NM_182763.2, type=c, posedit=688+403C>T),

BaseOffsetPosition(base=688, offset=403, datum=1, uncertain=False))

Open the UTA public data source for mapping and validation

import hgvs.dataproviders.uta
hdp = hgvs.dataproviders.uta.connect()

Project transcript variant NM_182763.2:c.688+403C>T to GRCh37 primary assembly using splign alignments

import hgvs.variantmapper
vm = hgvs.assemblymapper.AssemblyMapper(
    hdp, assembly_name='GRCh37', alt_aln_method='splign')
var_g = vm.c_to_g(var_c1)
var_g

SequenceVariant(ac=NC_000001.10, type=g, posedit=150550916G>A)

Project genomic variant to a new transcript

vm.relevant_transcripts(var_g)

['NM_182763.2', 'NM_021960.4', 'NM_001197320.1']

var_c2 = vm.g_to_c(var_g,'NM_001197320.1')
var_c2

SequenceVariant(ac=NM_001197320.1, type=c, posedit=281C>T)

Infer protein changes for these transcript variants

var_p1 = vm.c_to_p(var_c1)
var_p2 = vm.c_to_p(var_c2)
var_p1, var_p2

(SequenceVariant(ac=NP_877495.1, type=p, posedit=?),

SequenceVariant(ac=NP_001184249.1, type=p, posedit=(Ser94Phe)))

Format the results by “stringification”

print("""mapped {var_c1} ({var_p1})
    to {var_c2} ({var_p2})
   via {var_g}""".format(
        var_c1=var_c1, var_p1=var_p1,
        var_c2=var_c2, var_p2=var_p2,
        var_g=var_g))

mapped NM_182763.2:c.688+403C>T (NP_877495.1:p.?)

to NM_001197320.1:c.281C>T (NP_001184249.1:p.(Ser94Phe))

via NC_000001.10:g.150550916G>A

Validate a variant

import hgvs.validator
import hgvs.exceptions
vr = hgvs.validator.Validator(hdp=hdp)
try:
    vr.validate( hp.parse_hgvs_variant('NM_001197320.1:c.281C>T') )
    vr.validate( hp.parse_hgvs_variant('NM_001197320.1:c.281A>T') )
except hgvs.exceptions.HGVSError as e:
    print(e)

NM_001197320.1:c.281A>T: Variant reference does not agree with reference sequence