oncokb / oncokb-annotator

Annotates variants in MAF with OncoKB annotation.
GNU Affero General Public License v3.0
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Using clinical data results in encoding error #209

Closed kbrar4013 closed 11 months ago

kbrar4013 commented 11 months ago

Hi,

I'm running MafAnnotator using a shell script and when including the clinical data file in the argument, I'm getting the below error:

Screenshot 2023-11-14 at 1 43 27 PM

Below is my shell script:

Screenshot 2023-11-14 at 1 44 44 PM

I'm unsure what the issue is here; the CSV is written with R. I checked the AnnotatorCore.py file and it looks like read.csv was being called treating the clinical file as tab-delimited, so I changed my CSV to tab-delimited and saved it with .txt extension as you can see in the shell script, and I'm still getting the same error. I'm fairly certain the csv/txt file is encoded as UTF-8, as far as I can tell. Any help would be appreciated.