Sequence columns

[TomSmithCGAT]

PD output sometimes includes Annotated Sequence but not sequence. Some functions, e.g

camprotR/R/ptm.R

Line 153 in 6058ca4

add_PTM_positions <- function(obj, proteome_fasta, master_protein_col = "Master.Protein.Accessions",

need the 'unannotated' sequence.

We should include a function to create unannotated sequence...
obj$Sequence <- toupper(sapply(strsplit(obj$Annotated.Sequence, '\\.'), '[[', 2))

And add some checks to ensure more sensible error thrown if annotated sequence column is provided.