ProForma notation file format

[veitveit]

Files containing sequences that are annotated according to the nomenclature:

Suggestions:
Extension: .ptm.fasta or just .proteoforms
Format name: Proteoform format, PTM format

[trishorts]

.pf .pfm .pForm

[sgibb]

PTM often stands for post translational modification so it is maybe misleading.

.ptm.fasta would be ok, .proteoforms is very long.

What about .ptf or .ptf.fasta?

[stefanks]

Yes, it would be great to have a file format for storing proteoforms: it could be used downstream for proteoform database searches, etc.

Each fasta entry has a header and a sequence. I believe that the only requirement for a header is that it start with a > character.

I propose the following rules for our files:

1. Header starting with > character
2. Every header is unique in a file, so it could act as a key
3. Sequence in our format

A complete specification doesn't need much more than this!

I like .pf .ptf .pfm

[rfellers]

I like the shorter file extensions without .fasta, but don't have a favorite. Should we allow line breaks in the middle of a ProForma string like a typical FASTA file does?