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
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
This email message may contain legally privileged and/or...{{dropped:2}}
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
