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bogdanlab / focus

FOCUS: Fine-mapping Of CaUsal gene Sets
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symbol issue when creating weight database using Predixcan databases #50

Open ruthchia opened 1 year ago

ruthchia commented 1 year ago

Hi @quattro,

I am trying to create the weight database using Predixcan v8 (downloaded from https://predictdb.org/post/2021/07/21/gtex-v8-models-on-eqtl-and-sqtl/). However, I am encountering the same error message as found in an issue you had previously closed (https://github.com/bogdanlab/focus/issues/26). I am not sure what the resolution is for this because I didn't see it in your reply to that thread. Can you please offer some guidance on this?

Thanks!

===================================
             FOCUS v0.802
===================================
focus import
    ./eqtl/mashr/mashr_Whole_Blood.db
    predixcan
    --tissue Whole_Blood
    --name GTEXv8
    --assay rnaseq
    --use-ens-id
    --from-gencode
    --output predixcan_mashr_eqtl_v8

Starting log...
[2023-01-25 16:02:20 - INFO] Preparing weight database
[2023-01-25 16:02:20 - INFO] Starting import from PrediXcan database ./eqtl/mashr/mashr_Whole_Blood.db
[2023-01-25 16:02:21 - INFO] Querying mygene servers for gene annotations
[2023-01-25 16:02:50 - INFO] Starting individual model conversion
[2023-01-25 16:02:53 - INFO] Committed 250 models to db
[2023-01-25 16:02:56 - INFO] Committed 250 models to db
[2023-01-25 16:02:59 - INFO] Committed 250 models to db
[2023-01-25 16:03:02 - INFO] Committed 250 models to db
[2023-01-25 16:03:05 - INFO] Committed 250 models to db
[2023-01-25 16:03:08 - INFO] Committed 250 models to db
[2023-01-25 16:03:11 - INFO] Committed 250 models to db
[2023-01-25 16:03:15 - INFO] Committed 250 models to db
[2023-01-25 16:03:18 - INFO] Committed 250 models to db
[2023-01-25 16:03:21 - INFO] Committed 250 models to db
[2023-01-25 16:03:24 - INFO] Committed 250 models to db
[2023-01-25 16:03:27 - INFO] Committed 250 models to db
[2023-01-25 16:03:30 - INFO] Committed 250 models to db
[2023-01-25 16:03:33 - INFO] Committed 250 models to db
[2023-01-25 16:03:36 - ERROR] 'symbol'
[2023-01-25 16:03:36 - INFO] Finished importing prediction models
quattro commented 1 year ago

Sure thing. Can you see if updating sqlalchemy and pandas corrects this?

ruthchia commented 1 year ago

So, the container already has the latest versions of pandas and alchemy. Here are the version numbers:

Python 3.10.6

pandas.__version__
'1.5.3'

sqlalchemy.__version__
'1.4.46'

Is there something else I should try?

ruthchia commented 1 year ago

HI, checking to see if there is an update to this? thanks, Ruth

charliexbrown commented 1 year ago

Hi @ruthchia, I am having the same issue. Did you manage to solve it? Thanks

neurogenetics1 commented 1 year ago

Hi, I have the same issue, and installing MA-FOCUS did not help solve it. Is there any update, or has a db for PrediXcan models been published yet?

Thanks