TF Regression Error about garnet HOT 9 CLOSED

@iamjli is run_new_garnet.py your code?

from garnet.

It's my file modified from Divya's code :

from GarNet import *
expression = "./Garnet_input_liver_DEGs.txt"
options = {}
df = "./DNase_output_garnet_genes.txt"
df_reg = TF_regression(df, expression, options)
df_reg.to_csv('./DNase_output_TF_regression.txt', sep='\t', header=True, index=False)

from garnet.

aha!

df = "./DNase_output_garnet_genes.txt"

is you're problem I bet. df stands for dataframe which is different from a filename. You'll need to load the dataframe from the file, probably with a pd.read_csv("./Garnet_input_liver_DEGs.txt")

from garnet.

Ok, with this code:
df = pd.read_csv("./DNase_output_garnet_genes.txt", sep='\t')

I get this error:
06:55:15 - GarNet: INFO - Performing linear regression on 3 transcription factor expression profiles...
Traceback (most recent call last):
File "run_new_garnet.py", line 19, in
df_reg = TF_regression(df, expression, options)
File "/home/nlpm/.local/lib/python3.6/site-packages/GarNet/garnet.py", line 371, in TF_regression
return imputed_TF_features_dataframes
NameError: name 'imputed_TF_features_dataframes' is not defined

My path is:
/home/nlpm/Jeff_Carroll_Htt_ASO/OmicsIntegrator/results/new_garnet

from garnet.

Hmm. Looks like a typo in the garnet source code. Weird that you're the first to find it.

Try

pip install --user --upgrade garnet

(confirm that it installs version 0.2.21)

And then try this again.

from garnet.

Mmm. You'll need to be in a virtual environment. @iamjli and @divyaramamoorthy can advise you on that (i'll be in soon too), but here are the commands you should be able to run and will work:

From your working directory:

python3 -m venv venv
source venv/bin/activate
pip install garnet

from garnet.

I got the code to run with the upgraded garnet. It works without a printed error now, but I get a file with only the header and no actual data inside.

from garnet.

That one will be harder to debug from here. I'll be in around noon to help, unless this is urgent and I can come in right now..?

from garnet.

Not urgent, see you later

from garnet.