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uclahs-cds / pipeline-call-NonCanonicalPeptide

Nextflow pipeline to call non-canonical peptides as custom databases for proteogenomic analysis
https://automatic-adventure-o4l96o9.pages.github.io/
GNU General Public License v2.0
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splitFasta connector `-` or `_`? #25

Closed lydiayliu closed 2 years ago

lydiayliu commented 2 years ago

So far these are the files I'm getting from splitFasta

ACH-000089_fusion-Noncoding.fasta 
ACH-000089_mutation.fasta 
ACH-000089_mutation-Noncoding.fasta 
ACH-000089_Noncoding.fasta

I guess I'm just not a fan of the mixed - and _ naming?

Seems like everything else uses _ ACH-000089_mutation-Noncoding_encoded.fasta ACH-000089_mutation-Noncoding_encoded_decoy.fasta

So the - connecter between data types is a little awkward, but I can be persuaded that it is easier to parse this way...

(also not happy with Noncoding being capitalized but it's my fault that fusion and mutation is lower case loll)

Oops I thought this was a pipeline setting but I think it's actually still a moPepGen thing?

zhuchcn commented 2 years ago

So the - connecter between data types is a little awkward, but I can be persuaded that it is easier to parse this way...

That is my intention, just to make the 'database type` easier to parse. I can't think of any better way. Using other delimiter is just as awkward as dash. Agreed that it's not the prettiest. Any better idea?

Oops I thought this was a pipeline setting but I think it's actually still a moPepGen thing?

It is from moPepGen 😄

lydiayliu commented 2 years ago

Sigh I don't have any better ideas XD I'm just going to capitalize Mutation and Fusion to make myself feel better : P