samanfrm / adrtarget Goto Github PK

How to solve this error?

FileNotFoundError: [WinError 3] The system cannot find the path specified: '/usr/local/bin/python3'

it happened after this command
virtualenv -p /usr/local/bin/python3 py3 #creates virtual environment py3 using python v3.7

Hi @samanfrm

This is Chloe again.
While I was looking at V1_compounds_FDA.csv data

I see these data between numbers (pic below)

do I need to get rid of these rows before running openFDAoutput2modelformat.py?
It seems these data cause problem while running the script.

also do you mind providing these csv output files as well?

data/v1_compounds_FDA_model_format_SOC_ocr_prob.csv
data/v1_compounds_FDA_model_format_SOC_ocr_bool.csv
data/v1_compounds_FDA_model_format_HLGT_ocr_prob.csv
data/v1_compounds_FDA_model_format_HLGT_ocr_bool.csv

Thanks a lot!

Hi @samanfrm,

Thank you so much for pushing your code! very impressed with your work.

While I was trying to replicate the work, I encountered request error from openFDA.

I followed python openFDAapi.py 0 2134 [openFDA api key] [local path] this command (using the API key) but got this error. As an alternative, I also queried smaller chunks of compounds but still an erro. Can you please take a look to see what I need to do to fix this issue?

Thank you so much in advance!

Hello this is Chloe,

Hope you had a good Thanksgiving.
I came across a question regarding the data that goes in ADR_target.ipynb
For step: Determine associations for each replicate run individually

I'm hold up on this part:
Q) where/how would I get the "features_ADRs_predictions.csv file for i == 0?
I have Features_ADRs_predictions.csv for different seed from RF model (R_modeling script) but what should I put or where should I get the features_ADRs_predictions.csv for i == 0?

Thank you for helping :)