Possible to use custom species (non-human/non-mouse)?

[slukowski]

Hi Jamie

I'd like to be able to use mouse constant regions (TRAC/TRBC) with the human TRA/TRB genes, but am not able to do so. It wasn't clear whether I could do this by adding custom regions to the additional-genes.fasta in combination with '-xg', and editing the thimble file to list the mouse genes also didn't work.

I thought of creating a custom human/mouse hybrid reference, where I replaced human TRAC and TRBC genes with the mouse versions in the imgt, and also in the 'C-region-motifs.tsv' file. To try and use this, I called the folder 'HUMAN_mCONST' and specified this with the '-s' option. But no luck here either. I couldn't see in your code why this wouldn't work, as it should only be looking for the named folder in the Data directory, but I get the following error:

  File "/data/github/stitchr/Scripts/thimble.py", line 137, in <module>
    raise IOError("No data available for requested species: " + input_args['species'])
OSError: No data available for requested species: HUMAN_mCONST

Would you have any advice on how or if this might be possible?

Thanks!
Sam

[slukowski]

Update: Changing the name to all upper case (HUMAN_mCONST --> HUMAN_MCONST) lets it pass without the error.

This works well now, and the key was to add the mouse TRAC/TRBC genes to the 'additional-genes.fasta' file and specify -'xg' in the command.