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

[Haruo Suzuki]

Dear Dr. Lobry,

Thank you for your reply.
I would be most grateful if you could provide an example code to do the job.

uco(ec999[[1]], index="rscu") # it worked for a single gene (vector)
uco(ec999, index="rscu") # it did not work for all genes (list) and generated NA..
uco(unlist(ec999), index="rscu") # for a concatenation of all genes

I would like to compute RSCU values for Global codon usage like Table 1 in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2671203/

Yours sincerely,
Haruo Suzuki

On Apr 22, 2018, at 22:28, Jean Lobry <jean.lobry at univ-lyon1.fr> wrote:

> 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
>>> 
>> .
>