Manuscript Example

In [1]:

    

import hgvs
hgvs.__version__


    

    
Out[1]:





'0.3dev-283858cb6466'

In [2]:

    

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


    

    
Out[2]:





(SequenceVariant(ac=NM_182763.2, type=c, posedit=688+403C>T),
 BaseOffsetPosition(base=688, offset=403, datum=1, uncertain=False))

In [3]:

    

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


    

In [4]:

    

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


    

    
Out[4]:





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

In [5]:

    

vm.relevant_transcripts(var_g)


    

    
Out[5]:





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

In [6]:

    

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


    

    
Out[6]:





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

In [7]:

    

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


    

    
Out[7]:





(SequenceVariant(ac=NP_877495.1, type=p, posedit=?),
 SequenceVariant(ac=NP_001184249.1, type=p, posedit=(Ser94Phe)))

In [8]:

    

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

In [9]:

    

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