pydbsnp
Interface with dbSNP VCF data
Installation
First install the python package via pip3
pip3 install pydbsnp
or
pip3 install --user pydbsnp
Once the python package is installed, download and index the dbSBP VCF data:
pydbsnp-download
pydbsnp-index
For hg19/GRCh37 coordinates:
pydbsnp-download --reference-build GRCh37
pydbsnp-index
Command line usage
pydbsnp-query -h
pydbsnp-query rs689
pydbsnp-query chr11:2160994
pydbsnp-query --reference-build GRCh37 rs689
API
Two classes are provided: Variant and GeneralizedVariant.
An object of the Variant class has an attribute for each relevant field
of the VCF.
from pydbsnp import Variant
v = Variant(id='rs8056814')
print(v.chrom, v.pos, v.id, v.ref, v.alt)
print(v.info)
w = Variant(id='rs8056814', reference_build='GRCh37')
print(w.chrom, w.pos
help(Variant)
An object of the GeneralizedVariant class is similar, but each attribute
is a tuple which may have multiple items. For example, one RSID may map
to two sets of coordinates.
gv = GeneralizedVariant(id='rs8056814')
print(gv.chrom, gv.pos, gv.id, gv.ref, gv.alt)
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