query by gene not retrieving any results

[UndressK]

Hi!

As in your example, I am trying this same line, but I get nothing:
python gnomad_api_cli.py -filter_by=gene_id -search_by="ENSG00000163599" -dataset="gnomad_r2_1"
What am I missing..?
Thank you!

[QianXiaobo]

Hi,
I check the code and guess #7 could answer your question. There are many updates in gnomAD API, for example it does not support gene_name but gene_symbol as a key, so -filter_by=gene_name should be transferred to -filter_by=gene_symbol, and something like this. You can check the code yourself.

Bests,
Xb

[UndressK]

I tried running both the gnomad_api_cli.py and gnomad_api_gui.py and the first thing to note is that the "from pandas.io.json import json_normalize" has to be updated to "from pandas import json_normalize" for them to run. I tried running both again and the outputs folder is empty, no result, no error msg. I am including screenshots of the GUI just running using the default settings.. nothing happens

[QianXiaobo]

It looks like gnomAD api does not support gene_name as key word. Instead you should recode to use gene_symbol. Actually this tool should be updated...