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)))