## Created by: Lisheng Zhou

## Date: 15JUN2018

## Purpose: Extract chrom/pos from rs #

## dbsnp144, build 38

## =================================================

## ************* NOTE ******************************

## This script should be run in virtualenv with these installed:

# pip install six

# pip install cruzdb

# pip install sqlalchemy

# pip install mysql-python

## *************************************************

from cruzdb import Genome

import sys

fname = "variants_rs.csv"

outfile = open('chrom_pos.table', 'w')

lines = [line.rstrip('\r\n') for line in open(fname, "r")]

for rs in lines:

if rs.startswith("rs"):

var_info = Genome('hg38').snp144.filter_by(name=rs).first()

if var_info is not None:

outputstring = str(var_info.chrom.split("chr")[1]) + "\t" + str(var_info.chromStart+1) + "\n"

outfile.write(outputstring)

else:

outfile.write(str("Caution:"+rs+"\n"))

outfile.close()