[Feature request] Alternative protein separator

[jspaezp]

Hello there!

I was wondering if you would consider viable a config option to change the separator of the proteins field. Right now it separates the last protein column with tabs Prot1\tProt2, which breaks many tools that expect a consistent number of tabs per line (pandas, polars, duckdb ...) or silently drops the non-first.

What I am suggesting is a protein_column_separator config option that defaults to "\t", but could be assigned to something like ":::", where your protein column would end up with fields like so Prot1:::Prot2.

Let me know what you think!
-Kindest wishes-Sebastian

[jke000]

Yes, I'll add in that parameter to allow the user to specify the delimiter in the Percolator pin output. I would not have chosen that same protein delimiter when the rest of the file also uses a tab but that's how it's expected in the Percolator pin tsv format. I'm going to close this issue with this comment but am confirming that I will add in this parameter within the hour and in the 2024.01.1 maintenance release that I also hope to push out today.

[jspaezp]

Thanks Jimmy! You rock!

[jke000]

I just created the 2024.01 rev. 1 release. I named the new parameter pinfile_protein_delimiter which allows you to change the Percolator pin file protein field delimiter to some other character or string.

[gessulat]

Wow, this is amazing. Thank you for this super quick response!