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bogdanlab / focus

FOCUS: Fine-mapping Of CaUsal gene Sets
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error in creating the weight database #49

Closed ruthchia closed 1 year ago

ruthchia commented 1 year ago

Hi, I was trying to create the weight database using the CMC and GTEXv8 FUSION weights and encountered the error below. Although a .db file was created, I am not able to use the database that I created to run the finemapping portion of the analysis. Can you please offer guidance on this?

===================================
             FOCUS v0.802
===================================
focus import
    /data/ALS_50k/BrainBankSeq_May2021/MSA/Analysis.TWAS/fusion_twas/WEIGHTS/CMC.BRAIN.RNASEQ.pos
    fusion
    --tissue brain_dorsolateral_prefrontal_cortex
    --name CMC
    --assay rnaseq
    --output fusion

Starting log...
[2023-01-22 20:29:43 - INFO] Preparing weight database
[2023-01-22 20:29:43 - INFO] Starting import from FUSION database /data/ALS_50k/BrainBankSeq_May2021/MSA/Analysis.TWAS/fusion_twas/WEIGHTS/CMC.BRAIN.RNASEQ.pos
[2023-01-22 20:29:43 - INFO] Querying mygene servers for gene annotations
[2023-01-22 20:29:57 - INFO] Starting individual model conversion
[2023-01-22 20:29:57 - ERROR] 'Series' object has no attribute 'DIR'
[2023-01-22 20:29:57 - INFO] Finished importing prediction models

FYI, the FOCUS tool was installed in a container with the following pyfocus dependencies:

apt-get install -y python3-pip r-base
pip install numpy==1.23.1
pip install pyfocus mygene rpy2

I am guessing this error may have something to do with python packages/versions installed in the container. Can you tell me what specific versions are compatible with the current FOCUS tool?

thanks! Ruth

quattro commented 1 year ago

Hi @ruthchia , please see the discussion in this thread: https://github.com/bogdanlab/focus/issues/40

Please let me know if that fixes the issue.

ruthchia commented 1 year ago

Hi @quattro, Brilliant! thanks for pointing me to the thread. The error is resolved!

Just one quick question: if my GWAS summary stats are of a different hg build from the weighted database, but my SNP IDs are in rsid format, do I still need to update the position to the same build as in the .db or would it just use the rsids for the analysis?

thanks!

quattro commented 1 year ago

Hi @ruthchia , rsIDs are used to align genetic data, so it should be fine if builds differ.