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cole-trapnell-lab / garnett

Automated cell type classification
MIT License
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Syntax error '(' at or near line when running check_markers() #48

Closed a-solovyev12 closed 3 years ago

a-solovyev12 commented 4 years ago

Hello,

When running the check_markers() function, I am getting the following error: 

Marker file error. Illegal character '('
Error in self$errorfunc(errtoken) : 
  Marker file error. Syntax error '(' at or near line number 1
Calls: check_markers -> parse_input -> <Anonymous> -> <Anonymous>

Marker file used has brackets in the names of corresponding cell types, e.g. 

>CD16-negative natural killer cell (NK CD16-)
expressed: ENSG00000188404, ENSG00000150045, ...

>CD16-positive natural killer cell (NK CD16+)
expressed: ENSG00000150045, ENSG00000180644, ..., etc.

This marker file was generated as a part of an automated pipeline, and there are no checks for specific aspects of cell type naming. I was wondering if brackets are causing any specific problems? Otherwise I can't see a reason why they should be considered illegal characters. Please let me know what you think.

Many thanks, Andrey

hpliner commented 4 years ago

Hi Andrey, This is definitely a bug related to the automated monocle3-to-garnett functionality. You are correct that the issue here are the parentheses. I'm going to leave this open to be fixed when I get a chance, but in the meantime, go ahead and just open the marker text file that's generated by monocle3 and delete or replace the parentheses.

Hopefully I can get to a better fix in the next few weeks.

Thanks for the report!

hpliner commented 3 years ago

I believe this is fixed in the latest version of monocle3. Reinstall and give it a try!