pyhg19

Get the coordinates of a variant from its RSID, or an RSID from its coordinates

Installation

First make sure you have followed the installation procedure for pydbsnp. Then install pyhg19 with pip3:

pip3 install pyhg19

or

pip3 install --user pyhg19

For full functionality, you should appropriately set environment variables PYHG19_PATH, PYHG19_MASKED, PYHG19_BOWTIE2_INDEX. For example, you could add this to your .bash_profile:

export PYHG19_PATH=<path of your choice>
export PYHG19_MASKED=<path of your choice>
export PYHG19_BOWTIE2_INDEX=<path of your choice>

Examples

import pyhg19
rs10_coord = pyhg19.coord('rs10')
print(f'rs10 is on chromosome {rs10_coord.chr} at position {rs10_coord.pos}')

rs10_coord_tuple = pyhg19.coord_tuple('rs10')
print(
    'rs10 is on chromosome {} at position {}'
    .format(rs10_coord_tuple[0], rs10_coord_tuple[1])
)

rs_something = pyhg19.rsid(chr=1, pos=10019)
print(
    'The RSID of the variant on chromosome 1 at position 10019 is {}.'
    .format(rs_something)
)