pydbsnp 0.1.9

Interface with dbSNP VCF data

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 rs231361
pydbsnp-query chr8:118184783
pydbsnp-query --reference-build GRCh37 rs231361
pydbsnp-query rs231361 chr8:118184783 rs7903146

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)
x = Variant('chr16', 75218429)
print(x)
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)