Bug in rtracklayer::import of amino acid fasta sequences
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@kvittingseerup-7956
Last seen 7 months ago
European Union

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

rtracklayer fasta import Biostrings • 1.3k views
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@michael-lawrence-3846
Last seen 2.3 years ago
United States

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

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0
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Is there in practice any difference between that and using Biostrings::readAAStringSet() ? Would you recomend using Biostrings::readDNAStringSet() or rtracklayer::import() for DNA fasta files?

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1
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It's just there for completeness (rtracklayer also provides 2bit import) and is a simple wrapper around Biostrings, which is probably the better way to go.

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