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AssemblyMapper confusion

Open LeoWelter opened this issue 3 years ago • 0 comments

I'm trying to follow the examples but stumble upon something I don't understand.

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

import hgvs.variantmapper
#vm = variantmapper = hgvs.variantmapper.VariantMapper(hdp)
am37 = easyvariantmapper = hgvs.variantmapper.AssemblyMapper(hdp, assembly_name='GRCh37')

gives me:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
/tmp/ipykernel_1535/4195112627.py in <module>
      4 import hgvs.variantmapper
      5 #vm = variantmapper = hgvs.variantmapper.VariantMapper(hdp)
----> 6 am37 = easyvariantmapper = hgvs.variantmapper.AssemblyMapper(hdp, assembly_name='GRCh37')

AttributeError: module 'hgvs.variantmapper' has no attribute 'AssemblyMapper'

How should I map for example NC_000005.10:g.131741696A>G to any transcript on that position I wanted to use am37.relevant_transcripts(var_g)

LeoWelter avatar Nov 25 '21 11:11 LeoWelter