Hi,
I just modified the Sequence Data workflow to suggest the
use of readDNAStringSet() and family to read in a FASTA file.
Cheers,
H.
On 10/18/2017 08:03 AM, Martin Morgan wrote:
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://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioconductor.org_help_workflows_sequencing_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=PQf2b4ItE83XXwu2NechRSckpuQ_eISbAf4B017Xrp4&s=zjUnVdFrQnCYVhojezx1OQ3ulJox_FLqiv8GAl_gzsg&e=
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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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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