[Seqinr-forum] Questions about how to set 'numcode' when I use your package

[Jean Lobry]

Dear Dr. KONG,

the function uco() works only with the standard genetic
code, it doesn't handle variant genetic codes in the
present version of seqinr.

This is for sure something we could improve but do
not expect this in a near future unless you have
a patch to submit.

Thanks for pointing this.

Very best,

Pr. Jean LOBRY


Le 19/03/2019 à 09:49, Simon Penel a écrit :
> Salut Jean,
> 
> je crois que tu es plus à même que moi de répondre à cette question?
> 
> 
> à bientot
> 
> Simon
> 
> 
> 
> -------- Message transféré --------
> Sujet :     Ask for help. Questions about how to set 'numcode' when I 
> use your package
> Date :     Mon, 18 Mar 2019 22:01:09 +0800
> De :     上善若水 <acq116 at qq.com>
> Pour :     simon.penel <simon.penel at univ-lyon1.fr>
> 
> 
> 
> Dear penel,
> I am a researcher in China, now I am carrying  a research on codon 
> evolution . I referred to your package during my research, however, I 
> was not very clearly understand  how to set 'numcode' when I use Seqinr 
> to mesure 'RSCU' in your package,  it is known that codons between 
> nuclear gene and mitochondrial genes are different, so it is important 
> for me to set the 'numcode' , so would you please tell me how to set it?
> My R code is as followings:
> 
> -----------------------------------------
> library(seqinr)
> 
> seqs = read.fasta("x.fasta")
> 
> dat = matrix(0, 236, 64)
> 
> x = uco(seqs[1][[1]], index= 'rscu')
> colnames(dat) <- names(x)
> rownames(dat) <- names(seqs)
> 
> for(i in 1:236){
>    dat[i,] = uco(seqs[i][[1]], index = 'rscu')
> }
> 
> write.csv(dat, '8uuu.csv')
> ------------------------------------------------
> 
> It is very kindly of you to help me, and I am looking forward to hearing 
> from you.
> Sincerely yours
> KONG
> .
>