In gnomAD website (https://gnomad.broadinstitute.org/), you can write a gene name (such as BRCA1 or P53) in the search box and you can obtain information for a subset of variants as a csv file.
I was wondering if there is a way to do this in a more programmatic way with Python, R or bash or any other API.
Hello,
There's this available in github https://github.com/furkanmtorun/gnomad_python_api
You need to replace line 10 in both python scripts with the following lines. It seems to be working.
from pandas.io.json._json import dumps, loads, read_json, to_json
from pandas.io.json._normalize import json_normalize
Have a great day!
Aysima
Thanks Aysima. Furkan was saying that it is not working anymore. So, I wrote one based on Python selenium. I am attaching it here just in case someone needs it in future.
To perform an automated search inside the gnomAD website using gene names in Python, you can use the `requests` and `beautifulsoup4` libraries. Here's an example program that demonstrates how to do this:
```python
import requests
from bs4 import BeautifulSoup
# Define the base URL and search query parameters
base_url = "https://gnomad.broadinstitute.org/gene/"
search_params = {"dataset": "gnomad_r3", "query": ""}
# Define a list of gene names to search for
gene_names = ["BRCA1", "BRCA2", "TP53"]
# Loop over each gene name and perform the search
for gene_name in gene_names:
# Update the search query parameters with the current gene name
search_params["query"] = gene_name
# Send a GET request to the gnomAD website with the search parameters
response = requests.get(base_url, params=search_params)
# Parse the HTML response using BeautifulSoup
soup = BeautifulSoup(response.content, "html.parser")
# Extract the variant table from the HTML response
table = soup.find("table", {"class": "datatable"})
# Print the gene name and the first 10 rows of the variant table
print(gene_name)
for row in table.find_all("tr")[1:11]:
cols = row.find_all("td")
print(f"{cols[0].text}\t{cols[1].text}\t{cols[2].text}\t{cols[3].text}")
```
The program defines a base URL and search query parameters for the gnomAD website, and then loops over a list of gene names. For each gene name, it updates the search query parameters with the current gene name, sends a GET request to the gnomAD website with the search parameters, parses the HTML response using BeautifulSoup, extracts the variant table from the HTML response, and prints the gene name and the first 10 rows of the variant table.
It assumes that the variant table on the gnomAD website has four columns: "Variant", "AC", "AN", and "AF". If the variant table has different columns or a different format, you may need to modify the program accordingly.
Hope it helps
Credit AI tool
Thanks Mohammad. Indeed, my script attached above is doing something in similar lines.
Chuck A Arize Are you sure? Because the official web site says:
https://gnomad.broadinstitute.org/help/how-do-i-query-a-batch-of-variants-do-you-have-an-api
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