We'll need more information on the packages you're using. Can you post the output of:
> sessionInfo() Finally, is this a Bioconductor question? They have their own support site: https://support.bioconductor.org HTH, William Michels, Ph.D. On Sat, Jun 17, 2017 at 11:05 AM, Jeff Newmiller <jdnew...@dcn.davis.ca.us> wrote: > I suspect you meant > > WD <- "~/Documents/Scripting/R_Studio/Sequences/" > > but I am entirely unfamiliar with the packages you are using, and know > nothing about what is on your hard drive. > > For future reference: > > A) Read the Posting Guide. This is a plain text email list, and your html > formatting gets removed leaving a mess that is not always readable. > > B) Most frequent users of R change their working directory to where their > project files are before they start R. If you are using RStudio, the use of > Projects will take care of this for you. Then you don't have to put in your > whole working path in the script and you can copy/move your R and data > files elsewhere without breaking everything. > -- > Sent from my phone. Please excuse my brevity. > > On June 17, 2017 7:26:42 AM PDT, Mogjib Salek <mogj...@gmail.com> wrote: > >Hi all, > > > >I am learning R by "doing". And this is my first post. > > > >I want to use R: 1- to fetch a DNA sequence from a databank (see > >bellow) > >and 2- store it as FASTA file. > > > >The problem: neither an error is prompted nor the fasta file is > >created. > >Testing the code (see bellow), I notice that everything works until > >the *"write.dna" > >*command - which is not creating the fasta file. > > > >Here is my code: > > > >####Get gene sequence from GenBank and store it as fasta file > >####16 June 2017 > > > >#1- Set the working directory and make sure the right libraries are > >installed > >(make sure 'ape' and 'seqinr' packages are installed) > > > >WD <- "~Documents/Scripting/R_Studio/Sequences/" > >setwd <- (WD) > > > >#2- Fetch a sequence ( bellow, "enter manually the desired DNA ID") > >from > >GenBank and store it as fasta file. > > > > DNAid <- "JF806202" > > > > # Store the sequence in lst (a list) > > lst <- read.GenBank(DNAid, as.character = T) > > > > # convert the sequence to fasta format > > write.dna (lst, file = "DNAseq.fasta", format = "fasta", append = > >FALSE, > > nbcol= 6, colsep= " ", colw= 10) > > > > > >Any help will be appreciated. > >Thank you. > > > >Kelas > > > > [[alternative HTML version deleted]] > > > >______________________________________________ > >R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > >https://stat.ethz.ch/mailman/listinfo/r-help > >PLEASE do read the posting guide > >http://www.R-project.org/posting-guide.html > >and provide commented, minimal, self-contained, reproducible code. > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/ > posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
