[Seqinr-forum] Query regarding running "Online Synonymous Codon Usage Analyses with the ade4 and seqinR packages"

[Jean lobry]

>  The code is running fine and I can reproduce the output as
>  same as yours. It seems that the data is accessible.

Perfect.

>  Yes, these are absolutely those genomes that I intend to
>  work with. I want to consider only all the CDS (or Open
>  Reading Frame) for the statistical observation.

OK, let's make one more baby step: can you compute the table
of codon counts with the following code?

######
library(seqinr)
choosebank("refseqViruses")
#
# Now we want all to extract all complete CDS from
# these genomes:
#
query("herpcds", "TID=548681 AND T=CDS AND NO K=PARTIAL")
n <- herpcds$nelem
n # there are 4887 CDS
mnemo.cds <- getName(herpcds)
head(mnemo.cds) # just to see what they look like
#
# We pre-allocate a table for codon counts:
#
tabcod <- matrix(0, nrow = n, ncol = 64)
rownames(tabcod) <- mnemo.cds # cds names
colnames(tabcod) <- words()   # codon names
head(tabcod) # this empty for now
#
# Now we loop over all CDS to compute codon usage (this
# may take a while)
#
pb <- txtProgressBar(min = 1, max = n, initial = 1, style = 3)
for(i in 1:n){
   setTxtProgressBar(pb, i) # to show progression
   tabcod[i, ] <- uco(getSequence(herpcds$req[[i]]))
}
close(pb)
head(tabcod) # shouldn't be empty now
#
# We save this table on disk for further usage
#
save(tabcod, file = "tabcod.RData")
######

Best,
-- 
Jean R. Lobry            (lobry at biomserv.univ-lyon1.fr)
Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I,
43 Bd 11/11/1918, F-69622 VILLEURBANNE CEDEX, FRANCE
allo  : +33 472 43 27 56     fax    : +33 472 43 13 88
http://pbil.univ-lyon1.fr/members/lobry/