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
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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 <mogjibs at 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 at 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.
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 <jdnewmil at 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 <mogjibs at 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 at 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 at 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]]
Hi Mogjib, Does the following solve your issue?> setwd(WD)On Sat, Jun 17, 2017 at 7:26 AM, Mogjib Salek <mogjibs at 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 at 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]]