Closed ichauchcc closed 2 years ago
Hello @ichauchcc,
Thank you for your question. Unfortunately, I was not able to reproduce your error.
from gnomad_db.database import gnomAD_DB
database_location = "test_dir"
db = gnomAD_DB(database_location, genome="Grch38")
db.get_info_from_str("12:132673597:C>T", "AC")
results in 65
as in https://gnomad.broadinstitute.org/variant/12-132673597-C-T?dataset=gnomad_r3
1) Could you check if you have successfully downloaded Grch38 databasa from https://zenodo.org/record/5758663/files/gnomad_db_v3.1.1.sqlite3.gz?download=1? You can try this:
from gnomad_db.database import gnomAD_DB
download_link = "https://zenodo.org/record/5758663/files/gnomad_db_v3.1.1.sqlite3.gz?download=1"
output_dir = "test_dir" # database_location
gnomAD_DB.download_and_unzip(download_link, output_dir)
database_location
, which contains the gnomad_db.sqlite3
fileLet me know if this works.
Best,
Hey Kalin, Thank you for your quick response. Following your common, I reinstall the version 38 database and it worked. Amazing work!
Thank you for your feedback!
Hi, I am trying to run the function using my own data (db_38.get_info_from_str("12:132673597:C>T", "AC")), the output is like: Series([], Name: AC, dtype: object) When I run on the example data, it worked. Any suggestion on how I can fix it? Thanks so much!