Improve assign peptide type 243

[elena-krismer]

closes #243

[jpquast]

Let me know if I should review this.

[elena-krismer]

@jpquast i'm getting an error from vroom on macos and windows- have you seen this error before? (it's not related to the changes i made)

[jpquast]

Hi Elena,
I had a quick look at the function. I think it is necessary to introduce the protein_id column as you do in order to know which peptides belong to the same protein. However, as I can see you don't have a way to know about the initiator methionine. I think maybe I was not very clear about that. The point was to assign the peptide as fully tryptic if it starts basically at position 2 of the protein and there is no other peptide that starts at 1. In those cases the initiator cysteine is likely completely absent for most of the copies of this protein in the cell. As far as I can tell you check if any of the peptides of the protein don't have a preceding methionine (which could also be in the middle of the protein).
What I would suggest is to also require the start and end column for each protein and then just check if any starts with position 1. If yes keep the original annotation as it is. If not then any peptide starting at position 2 is considered fully-tryptic if it fulfils its C-terminal criterium.

As far as I can tell the output of the function is generally currently wrong:

assign_peptide_type(data, aa_before, last_aa, aa_after, protein_id)
  aa_before last_aa aa_after protein_id      pep_type
1         K       R        T         P1 fully-tryptic
2         S       K        R         P1 fully-tryptic
3         T       Y        T         P2   non-tryptic
4         M       K        R         P2  semi-tryptic

Row 2 should be semi-tryptic since the aa_before is not K/R. Not sure why the function now gets those standard cases wrong.
Row 4 works of course as you expected based on your code, but is conceptually wrong as explained above.

Not sure why vroom fails, but if it still does we can have a look at that.