In [1]:

    

import hgvs.parser
import hgvs.dataproviders.uta
import hgvs.variantmapper


    

In [2]:

    

hp = hgvs.parser.Parser()
hdp = hgvs.dataproviders.uta.connect()
am = hgvs.variantmapper.AssemblyMapper(hdp,
                                           assembly_name='GRCh37',
                                           alt_aln_method='splign')


    

In [3]:

    

g_hgvs = 'NC_000001.10:g.150550916_150550920delGACAAinsCAATACC'
g_var = hp.parse_hgvs_variant(g_hgvs)
c_var = am.g_to_c(g_var, 'NM_182763.2')
p_var = am.c_to_p(c_var)


    

In [4]:

    

g_var, c_var, p_var


    

    
Out[4]:





(SequenceVariant(ac=NC_000001.10, type=g, posedit=150550916_150550920delGACAAinsCAATACC),
 SequenceVariant(ac=NM_182763.2, type=c, posedit=688+399_688+403delTTGTCinsGGTATTG),
 SequenceVariant(ac=NP_877495.1, type=p, posedit=?))

In [5]:

    

[str(v) for v in (g_var, c_var, p_var)]


    

    
Out[5]:





['NC_000001.10:g.150550916_150550920delGACAAinsCAATACC',
 'NM_182763.2:c.688+399_688+403delTTGTCinsGGTATTG',
 'NP_877495.1:p.?']

In [6]:

    

import hgvs.normalizer
hn = hgvs.normalizer.Normalizer(hdp)
hn.normalize(hp.parse_hgvs_variant('NM_021960.4:c.735_736insT'))


    

    
Out[6]:





SequenceVariant(ac=NM_021960.4, type=c, posedit=737dupT)

In [7]:

    

import hgvs.validator
hv = hgvs.validator.Validator(hdp)
try:
    hv.validate(hp.parse_hgvs_variant('NM_021960.4:c.736_740delATGTCinsGGTATTG'))
except Exception as e:
    print(e)


    

    




NM_021960.4:c.736_740delATGTCinsGGTATTG: Variant reference (ATGTC) does not agree with reference sequence (TTGTC)

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