[ERROR] import_fusion 'Series' object has no attribute 'DIR'

[emiuga]

Hello,

I wonder if someone knows what could be the issue/solution here.
I'm trying to look into the code 'pyfocus/models/convert.py' , but I'm not familiar with python.

The script I use:
focus import WEIGHTS/GTEx.Whole_Blood.pos fusion --tissue Whole_Blood --name GTEx --assay rnaseq --output fusion

Which print this:
Starting log...
[2022-04-11 12:29:08 - INFO] Preparing weight database
[2022-04-11 12:29:08 - INFO] Starting import from FUSION database WEIGHTS/GTEx.Whole_Blood.pos
[2022-04-11 12:29:08 - INFO] Querying mygene servers for gene annotations
[2022-04-11 12:29:15 - INFO] Starting individual model conversion
[2022-04-11 12:29:15 - ERROR] 'Series' object has no attribute 'DIR'
[2022-04-11 12:29:15 - INFO] Finished importing prediction models

Thanks a lot,
Emilio

[quattro]

Hi Emilio @emiuga , can you post what version of FOCUS you're using? The latest is v 0.8.01.

[emiuga]

Hi Nicholas @quattro, thanks for your reply!
I'm using v0.8.
I re-installed in a new conda environment (python3.10) using pip, but get the same error.
In case it helps, pandas version is 1.4.1.
Best,
Emilio

[quattro]

Hi Emilio, the latest is 0.8.01, can you confirm that is the version you have installed?

[emiuga]

Hi Nicholas,
I updated to latest version: pip install pyfocus==0.8.01 --user
Also pip install mygne and rpy2
Unfortunately I get same error.

[quattro]

Hi @emiuga , yes I see the issue now. It looks like older pos files don't always have the DIR column. In the past this was inferred based on the relative path for the pos file itself. We'll work on pushing out a fix that addresses this. Thanks!

[emiuga]

Thanks @quattro !
I was able to import FUSION db by adding DIR column into the .pos file.
This was also the case for latest versions (GTEx v8) FUSION prediction models.
Best,
Emilio

[rodrigoduarte88]

Thank you for this thread!

I wasn't sure when I read the thread first, but just to clarify for future users with the same problem: the DIR column corresponds to the path to the pos file.

Example below:

WGT ID CHR P0 P1 DIR
gtex_blood/INTS11.wgt.RDat INTS11 1 1246965 1260067 /users/me/Rodrigo/projectX/fusion_weights
gtex_blood/ANKRD65.wgt.RDat ANKRD65 1 1353800 1357149 /users/me/Rodrigo/projectX/fusion_weights