Can I make the filename pattern case _insensitive_?

Ask for help
1

I’m writing a custom_data section and for the fn: section I need to specify the pattern in a case-insensitive way. I could get around this by copying files around, but I’d rather not. Is there a way to control the options on the pattern-matching that is used behind the scenes?

I tried setting chopt -s nocaseglob but that doesn’t seem to help.

2

Absolutely, see the docs here and here for using custom search patterns with MultiQC modules.

Instead of using fn, use fn_re and define a case-insensitive regular expression.

3

Thanks for the swift response, but I’m not sure it fully resolves my problem.

My pattern is actually provided to me using !ENV. Specifically I’m given the name of a gene and am looking for files with that gene in a particular location in the filename. The problem is that the gene name is provided by the user and the filename comes from a case-insensitive match with a resource. I could process the <gene_name> and create the pattern “[gG][eE][nN][eE]_[nN][aA][mM][eE]” from it and use that in fn_re but I was hoping for a cleaner solution, something like "oh sure, just add case_sensitive_pattern_match: true under the fn_re element…

I understand form your response that this isn’t possible, but perhaps you’d consider it as a future feature…

4

Could you please post your current config, plus a handful of example file names - so that I can have a play and experiment a bit? Thanks!

5

sure. I’ll post the relevant section.

custom_data:
  cell_qc_gene_overlay_0:
    section_name: !ENV "Clustering UMAP (Gene: ${UMAP_GENE_0})"
sp:
  cell_qc_gene_overlay_0:
    fn: !ENV "*.clust.scaled.${UMAP_GENE_0}*.png"

ignore_images: false

Now I’d like to have enviroment settings UMAP_GENE_0="galc" and the file
sample_name.clust.scaled.GALC_1234.png will contain the image

6

Ok, I think I finally figured out a way to do it (after trying several approaches!). You can use a regular expression instead of a glob, then pass a case-insensitive modifier within the regex: (?i)

So, for your example above, I think that this should work:

sp:
  cell_qc_gene_overlay_0:
    fn_re: !ENV "(?i).*\\.clust\\.scaled\\.${UMAP_GENE_0}.*\\.png"

Let me know how you get on with that!

7

That’s great! thanks for teaching me about in-pattern modifers! Exactly what I was looking for.

(for others looking here’s a nice list: Regex Tutorial - Turning Modes On and Off for Only Part of The Regular Expression)

1 Like
8

Also, for the record, in order to limit the insensitivity to the gene-name, I used

fn_re: !ENV ".*\\.clust\\.scaled\\.((?i)${UMAP_GENE_0})..*\\.png"

However, it turns out that in python, this doesn’t actually limit the case-insensitivity as I had hoped. Still, this works!