[Seqinr-forum] read.fasta fails to read a gzipped compressed file from a ftp server

[Jean Lobry]

Dear Haruo Suzuki,

I think that the option index = "rscu" of the uco() function
should do the job.

Best,

JLO

Le 22/04/2018 à 14:44, Haruo Suzuki a écrit :
> Dear Dr. Lobry:
> 
> Thank you for your speedy response. The problem was solved by using gzcon().
> 
> I was wondering if there is any easy way to compute Relative Synonymous Codon Usage (RSCU) for a group of genes.
> 
> Based on Examples for `dotchart.uco` at https://cran.r-project.org/web/packages/seqinr/seqinr.pdf
> absolute codon frequencies and relative codon frequencies for a collection of all genes can be computed as follows:
> 
>      # Load dataset:
>      data(ec999)
>      # Compute codon usage for all coding sequences:
>      ec999.uco <- sapply(ec999, uco, index="eff")
>      # Compute absolute codon frequencies
>      af <- rowSums(ec999.uco)
>      # Compute relative codon frequencies
>      rf <- af / sum(af)
>      # How to compute Relative Synonymous Codon Usage (RSCU) values for the collection of all genes (average gene)?
> 
> Yours sincerely,
> Haruo Suzuki
> 
> On Apr 22, 2018, at 3:23, Jean Lobry <jean.lobry at univ-lyon1.fr> wrote:
> 
>> Found it!
>>
>> just use gzcon() to encapsulate the thing, this is explained at:
>>
>> http://seqinr.r-forge.r-project.org/src/mainmatter/getseqflat.pdf
>>
>> Here is it:
>>
>> --------------------- BEGIN
>> $ R --quiet
>>> library(seqinr)
>>> filename <- "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/008/865/GCF_000008865.1_ASM886v1/GCF_000008865.1_ASM886v1_rna_from_genomic.fna.gz"
>>> ld <- read.fasta(file = gzcon(url(filename)))
>>> head(names(ld))
>> [1] "lcl|NC_002695.1_rrna_1" "lcl|NC_002695.1_trna_2" "lcl|NC_002695.1_trna_3"
>> [4] "lcl|NC_002695.1_rrna_4" "lcl|NC_002695.1_rrna_5" "lcl|NC_002695.1_trna_6"
>>
>> ----------------------- END
>>
>> Best,
>>
>> JLO
>>
>> Le 21/04/2018 à 20:02, Jean Lobry a écrit :
>>> Dear all,
>>> I was able to reproduce the well documented faulty behaviour as follows:
>>> -------------------------- BEGIN ------------------------------------
>>> $ R --quiet
>>>> library("seqinr")
>>>> filename <- "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/008/865/GCF_000008865.1_ASM886v1/GCF_000008865.1_ASM886v1_rna_from_genomic.fna.gz"  > ld <- read.fasta(file = filename)
>>> Error in substr(lines, 1L, 1L) :
>>>    chaîne de charactères multioctets incorrecte à '<aa><89><b4>b<68><8d><a4>c0<ed><B$<97>    O<eb>3:<d2>ڀR 46<a4>L<9b><91>d<ba><b2>9<a6><c4>k!<d2>z<a6>G<8d>4<bb> פa0>2H[<ac>X<d2>VP<b0>a<d2>tj<84><e6><99>&<95><8e><86>Kt<ac>OHZ:@<d7>.
>>> |Sэ<e8><81>#<e9><ae><9a><9f>ab><bb>b<ac>ab>W<d7>W<8c><95><93><8d><d5><d0>/<8c><d5>]6<?<fb><cd><f5>ա<8d>\e5><86>a<b2>Qw<b0>Q<b4><90>` <8e>#-M<a8><9d<f5><db><9a>
>>>                                                   z
>>> d$|<8a>4r<dc>¥<d7><f3><eb><e7><ae>a<d7>p<8c>+\??<c2>5<e8><8e>p<f9><d6><e1>!<aa><94>"`E2<a1>iR<ab><88><e6><89>' De plus : There were 27 warnings (use warnings() to see them)
>>>> sessionInfo()
>>> R version 3.4.1 (2017-06-30)
>>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>>> Running under: macOS Sierra 10.12.6
>>> Matrix products: default
>>> BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
>>> LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
>>> locale:
>>> [1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>> other attached packages:
>>> [1] seqinr_3.4-5
>>> loaded via a namespace (and not attached):
>>> [1] compiler_3.4.1 ade4_1.7-8
>>>> q()
>>> Save workspace image? [y/n/c]: n
>>> -------------------------- END ------------------------------------
>>> Rings a bell to me, I'll post a solution asap.
>>> Best,
>>> JLO
>>> -------- Message transféré --------
>>> Sujet :     Re: Error in library(help=seqinr)
>>> Date :     Sun, 22 Apr 2018 02:21:23 +0900
>>> De :     Haruo Suzuki <haruo at sfc.keio.ac.jp>
>>> Pour :     Simon Penel <simon.penel at univ-lyon1.fr>
>>> Copie à :     jean.lobry at univ-lyon1.fr
>>> Dear Simon,
>>> The `read.fasta` function of seqinr package failed to load the gzipped FASTA file directly from the ftp site, simply by specifying a full URL, as shown in attachment.
>>> Yours sincerely,
>>> Haruo Suzuki
>>> _______________________________________________
>>> Seqinr-forum mailing list
>>> Seqinr-forum at lists.r-forge.r-project.org
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/seqinr-forum
>>
> 
> .
>