I just found a problem with rtracklayer's import function when importing amino acid fasta (also the default way of storing amino acid sequences. (E.g. the "Protein-coding transcript translation sequences" at Gencode genes official site)).

Here is an easy to reproduce example:

### Define local output path (here i use ~/Downloads as a tmp dir)
outputPath <- '~/Downloads/'

### Make example data
aaExample <- 'MAAWRAAGLNYINYSNIAARLLRKALKPELRAQAVRRDDSHIKFTKWQNGKPEKAITE'
aaExample <- AAStringSet(aaExample)
names(aaExample) <- 'test'

### Write it to fasta file
writeXStringSet(
    aaExample,
    filepath = paste0(outputPath, '/aa.fasta')
)

### Verify fasta file
rawInput <- readLines(paste0(outputPath, '/aa.fasta'))
nchar(rawInput[[2]]) == nchar(aaExample)

Which is TRUE whereby we verified the produced fasta file is correct. Now let's import it with rtracklayer

imporAA <- rtracklayer::import(paste0(outputPath, '/aa.fasta'))

width(imporAA)

The resulting with is 41 and the import throws the following warning:

Warning message:
    In .Call2("fasta_index", filexp_list, nrec, skip, seek.first.rec,  :
              reading FASTA file ~/Downloads//aa.fasta: ignored 17 invalid one-letter sequence codes

Hope this can be fixed as it would make it much easier to work with AA sequences.

Cheers Kristoffer

You have to tell rtracklayer the type of sequence using the type= argument ("AA" in this case).