[Bioc-devel] ShortRead readFasta UniProt Incorrect Import

[Martin Morgan]

On 10/18/2017 01:00 AM, Dario Strbenac wrote:
> Good day,
> 
> If I have a FASTA file that contains
> 
>> sp|Q9NYW0|T2R10_HUMAN Taste receptor type 2 member 10 OS=Homo sapiens GN=TAS2R10 PE=1 SV=3
> MLRVVEGIFIFVVVSESVFGVLGNGFIGLVNCIDCAKNKLSTIGFILTGLAISRIFLIWI
> IITDGFIQIFSPNIYASGNLIEYISYFWVIGNQSSMWFATSLSIFYFLKIANFSNYIFLW
> LKSRTNMVLPFMIVFLLISSLLNFAYIAKILNDYKTKNDTVWDLNMYKSEYFIKQILLNL
> GVIFFFTLSLITCIFLIISLWRHNRQMQSNVTGLRDSNTEAHVKAMKVLISFIILFILYF
> IGMAIEISCFTVRENKLLLMFGMTTTAIYPWGHSFILILGNSKLKQASLRVLQQLKCCEK
> RKNLRVT
> 
> readFasta fails to import it with the warning
> 
> proteins <- readFasta('.', "test.fasta")
> 
> Warning message:
> In .Call2("fasta_index", filexp_list, nrec, skip, seek.first.rec,  :
>    reading FASTA file test.fasta: ignored 129 invalid one-letter sequence codes
> 
> Also, the amino acid sequence is incomplete. There are 308 amino acids, but
> 
>> width(proteins)
> [1] 178
> 
> It's undesirable for users that some amino acids are discarded. Hopefully, they notice the warning message before proceeding with the analysis.
> 
> Admittedly, readFasta is in ShortRead, so is designed to work with high througput sequencing reads. But, perhaps it would be better suited to a infrastructure package such as Biobase and generalised to correctly import any FASTA file. There's even a Bioconductor workflow at https://www.bioconductor.org/help/workflows/sequencing/ which has a section titled "DNA/amino acid sequence from FASTA files" and demonstrates the use of readFasta.

See Biostrings::readAAStringSet (and friends).


> 
> I used version 1.34.2 of ShortRead which is the newest one.
> 
> --------------------------------------
> Dario Strbenac
> University of Sydney
> Camperdown NSW 2050
> Australia
> 
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