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rs509749-manual-liftover.rst

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Manual liftover of NM_001261456.1:c.1762A>G (rs509749) to NM_001261457.1 via GRCh37

http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=509749

import hgvs.dataproviders.uta
import hgvs.variantmapper
import hgvs.parser
hdp = hgvs.dataproviders.uta.connect()
variantmapper = hgvs.variantmapper.VariantMapper(hdp)
hgvsparser = hgvs.parser.Parser()
var_c1 = hgvsparser.parse_hgvs_variant('NM_001261456.1:c.1762A>G')
var_p1 = variantmapper.c_to_p(var_c1, None)
var_c1, var_p1
(SequenceVariant(ac=NM_001261456.1, type=c, posedit=1762A>G),

SequenceVariant(ac=MD5_e999a940ca422ec8cab9bc3cc64e0d7d, type=p, posedit=(Met588Val)))

var_g = variantmapper.c_to_g(var_c1,'NC_000001.10')
var_g

SequenceVariant(ac=NC_000001.10, type=g, posedit=160793560A>G)

txs = hdp.get_tx_for_gene('LY9')
txs
[['LY9', 30, 1998, 'ENST00000263285', 'NC_000001.10', 'genebuild'],

['LY9', 1, 583, 'ENST00000368039', 'NC_000001.10', 'genebuild'], ['LY9', 0, 1648, 'ENST00000392203', 'NC_000001.10', 'genebuild'], ['LY9', 0, 1833, 'ENST00000368037', 'NC_000001.10', 'genebuild'], ['LY9', 211, 1024, 'ENST00000368035', 'NC_000001.10', 'genebuild'], ['LY9', 50, 1616, 'ENST00000341032', 'NC_000001.10', 'genebuild'], ['LY9', 170, 1751, 'ENST00000368041', 'NC_000001.10', 'genebuild'], ['LY9', 1094, 1907, 'ENST00000368040', 'NC_000001.10', 'genebuild'], ['LY9', 114, 2040, 'NM_001261456.1', 'AC_000133.1', 'splign'], ['LY9', 114, 2040, 'NM_001261456.1', 'NC_000001.10', 'blat'], ['LY9', 114, 2040, 'NM_001261456.1', 'NC_000001.10', 'splign'], ['LY9', 114, 2040, 'NM_001261456.1', 'NC_018912.2', 'splign'], ['LY9', 114, 696, 'NM_001033667.2', 'AC_000133.1', 'splign'], ['LY9', 114, 696, 'NM_001033667.2', 'NC_000001.10', 'blat'], ['LY9', 114, 696, 'NM_001033667.2', 'NC_000001.10', 'splign'], ['LY9', 114, 696, 'NM_001033667.2', 'NC_018912.2', 'splign'], ['LY9', 114, 2082, 'NM_002348.3', 'AC_000133.1', 'splign'], ['LY9', 114, 2082, 'NM_002348.3', 'NC_000001.10', 'blat'], ['LY9', 114, 2082, 'NM_002348.3', 'NC_000001.10', 'splign'], ['LY9', 114, 2082, 'NM_002348.3', 'NC_018912.2', 'splign'], ['LY9', 114, 1812, 'NM_001261457.1', 'AC_000133.1', 'splign'], ['LY9', 114, 1812, 'NM_001261457.1', 'NC_000001.10', 'blat'], ['LY9', 114, 1812, 'NM_001261457.1', 'NC_000001.10', 'splign'], ['LY9', 114, 1812, 'NM_001261457.1', 'NC_018912.2', 'splign']]

var_c2 = variantmapper.g_to_c(var_g,'NM_001261457.1',alt_aln_method='splign')
var_p2 = variantmapper.c_to_p(var_c2, None)
var_c2, var_p2
(SequenceVariant(ac=NM_001261457.1, type=c, posedit=1534A>G),

SequenceVariant(ac=MD5_921ebefe79bff479f4bfa17e133fc084, type=p, posedit=(Met512Val)))