How do I make categorical values from integers?

Hi, I have a custom table with MLST results. MLST results include sequence types which appear numerical but are actually strings. Can put in some custom yaml to make it not highlight the values in the report? Thank you for any insights!

File    mlst_scheme     7-gene_ST       locus1  locus2  locus3  locus4  locus5  locus6  locus7
SRR28368091.shovill.skesa.fasta ecoli   21      adk(16) fumC(4) gyrB(12)        icd(16) mdh(9)       purA(7) recA(7)
SRR28368090.shovill.skesa.fasta ecoli   993     adk(10) fumC(7) gyrB(154)       icd(8)  mdh(12)      purA(8) recA(2)

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Hi @lskatz!

Yes you can. You’ll need a table config for that header, then set the scale to False.

Assuming that you’re doing this with Custom content, you can see the docs for custom content config and table config. You can also find an example of a custom content table with an associated config file here.

I hope that helps!

Phil

Thank you for your help!

1 Like

Is it possible to format with s instead of f? I want to treat it like a string. I tried this and it worked but it is still introducing a separator at the thousands digit.

#headers:
#  7-gene_ST:
#    scale: false

This reverts it back to default formatting with a decimal digit

#headers:
#  7-gene_ST:
#    scale: false
#    format: "{:,s}"