PEPMatch trimms sequence id

[HA1-biocopy]

Hi,
I'm testing pepmatch with my custom fasta file (--proteome_file). However, I noticed that pepmatch trimms the protein's id, e.g. in my file the id follows this syntax: xx|GENE-ID|genome
what pepmatch reports is GENE-ID.1 , why? how can I make it returns back the full id?
thank you

[dmx2]

PEPMatch is mostly built around UniProt proteomes, as that is what most of our users use and the protein ID is typically between pipe (|) characters.

I think there should be a way to just use the entire FASTA header for output. I'll consider this as a feature to add.

[HA1-biocopy]

Hi,

I noticed that adding '.1' as a suffix to the name can introduce complications downstream, especially since the name may already contain other symbols. I’ve tried changing the ID delimiter, but it still gets stripped and the suffix is added.

Do you have any suggestions on how to resolve this issue in the meantime, until the feature is implemented?

For context: we’re testing the tool as part of our evaluation process, with plans to purchase a license if it meets our internal needs.

Thanks in advance for your help!

[dmx2]

I need to update the README, but if you pass sequence_version=False into the Matcher class (or -v if using the command line) and this will drop the '.#' suffix to the IDs. Let me know if that works for you.

[HA1-biocopy]

thank you again for your help
As I'm still actively testing pepmatch, I noticed that the id of the query sequences is not included in the output. Could you please add that as well? or at least have similar format to blast where we can specifiy the columns we need in the output? thank you

[dmx2]

yes, I will make that a part of the output as well

will update when I make the changes.