KRGDB Parser

0. Purpose

This web scraper obtains KRGDB allele frequencies for target SNPs from dbSNP.

1. Motivation

Direct access to the KRGDB database is not feasible, necessitating indirect checks through dbSNP.

However, using NCBI's Entrez Programming Utilities sometimes results in missing allele frequencies.

(Example: For https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&id=rs761437962&report=XML, only allele frequency for C in the KOREAN study is shown, not for A or T.)

2. Usage

2-1. Environment

• Python3
• Requires requests and beautifulsoup4 libraries:

pip install requests
pip install beautifulsoup4

2-2. How to Use

Basic usage:

python krgdb_parser.py [-h] [-b] [-o OUTPUT] input_arg

Options:

• -h, --help: show the help message
• -b, --batch: process in batch mode
• -o OUTPUT, --output OUTPUT: output file to write results to.
• --store: store every html files in current directory

3. Sample Input and Output

3-1. Output Format

• rs_id: name of the rs
• position: position of the variant
• version: reference version info
• population_size: size of the population (of KRGDB)
• REF: reference allele
• REF frequency: allele frequency of the reference allele
• ALT: alternative allele
• ALT frequency: allele frequency of the alternative allele

ALT and ALT frequency can be shown multiple times.

3-2. Example Case

Example 1:

• Input: python krgdb_parser.py rs12732870
• Output: rs12732870 2920 T 0.8192 A 0.0301 G 0.1507

Example 2 (Using tags):

• Input: python krgdb_parser.py -b -o result.txt file.txt
• Input file file.txt:

rs200949691
rs141478865
rs141265262
rs72648929
rs34936017

• Output file result.txt:

rs200949691	chr1:215647671	(GRCh38.p14)	2930	C	0.9799	G	0.0201
rs141478865	chr2:97211732-97211734	(GRCh38.p14)	0
rs141265262	chr2:99170546	(GRCh38.p14)	2922	C	0.9849	T	0.0151
rs72648929	chr2:178734746	(GRCh38.p14)	2922	C	0.9610	T	0.0390
rs34936017	chr3:10039727	(GRCh38.p14)	2922	A	0.9846	G	0.0154