AssemblyMapper confusion
LeoWelter opened this issue · 1 comments
LeoWelter commented
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)
davmlaw commented
You have the wrong package, the correct path is hgvs.assemblymapper.AssemblyMapper
Fixing this, the code is:
import hgvs.dataproviders.uta
from hgvs.assemblymapper import AssemblyMapper
hdp = hgvs.dataproviders.uta.connect()
am37 = AssemblyMapper(hdp, assembly_name='GRCh37')
hp = hgvs.parser.Parser()
var_g = hp.parse_hgvs_variant("NC_000005.10:g.131741696A>G")
am37.relevant_transcripts(var_g)
Output:
Out[1]: ['NM_001346114.1', 'NM_001346113.1', 'NM_133372.2', 'NM_001008738.2']