Hello.

I know when I use msaPrettyPrint() function, this write the aligned sequences in fasta file ;

C:/Users/SEBASTIEN/AppData/Local/Temp/RtmpMTD00Y/seq21e072f6414e.fasta

Is there a way to change the ouput directory?

Thanks for all the contributions in this thread! The problem is that TeX cannot handle spaces and some special characters in paths, especially on Windows. That may lead to problems with temporary files, but also if the path to the current working directory has some "illegal" characters in it. In case such a problem occurs, use a different working directory the path to which does not have any spaces or other illegal characters. In case this occurs with temporary files, use the 'file' argument to redirect the temporary files. I think this sums up all the previous suggestions. By the way, this is also mentioned in Section 7.8 of the package vignette (page 33 in the current version).

Have you looked at the help page for the function you are using? In particular the 'file' argument?

I'm trying this 

# #
bdir = "E:/DOCTORAT/workspace/alignement_prot_ribo_all"
workdir = file.path(bdir,"one_file_per_ptne/")
outdir = file.path(bdir,"alignements")

myFiles = list.files(path = workdir,full.names = TRUE)
for (i in 1:66){
  newdir = substr(basename(myFiles[i]), start = 1 ,stop = 6)
  output = file.path(outdir, newdir)
  dir.create(output,showWarnings = FALSE)
  current_seq <- readAAStringSet(myFiles[i])
  current_align <- msa(current_seq)
  fasta_file = paste(outdir,'/',newdir,".aln",sep="")
  pdf_file = paste(outdir,"/" ,newdir,".pdf",sep="")
  msaPrettyPrint(current_align, output="pdf", showNames="none", askForOverwrite=FALSE, verbose=FALSE,
                  file = output, alFile = fasta_file)
}

But there are errors on alFile and file:

Error in msaPrettyPrint(current_align, output = "pdf", showNames = "none",  : 
  The parameter alFile has an invalid argument

If i remove alFile:

Error in msaPrettyPrint(current_align, output = "pdf", showNames = "none",  : 
  The file name suffix and output type do not match!

___________________________________________________________________________________________________

EDIT: Solution for specifying output files names

It's working now, we have to specify both .pdf and .fasta in file name 

  fasta_file = paste(outdir,'/',newdir,".fasta",sep="")
  pdf_file = paste(output,"/",newdir,".pdf",sep="")
  print(pdf_file)
  msaPrettyPrint(current_align, output="pdf", showConsensus = "none", askForOverwrite=FALSE, verbose=FALSE,
                  file = pdf_file, alFile = fasta_file )
}

But my loop is broken with an error:

 Error in texi2dvi(texfile, quiet = !verbose, pdf = identical(output, "pdf"),  : 
  unable to run 'pdflatex' on 'E:/DOCTORAT/workspace/alignement_prot_ribo_all/alignements/L1_all.tex' In addition: Warning message:
running command '"pdflatex" -interaction=nonstopmode "E:/DOCTORAT/workspace/alignement_prot_ribo_all/alignements/L1_all.tex"' had status 1 

If i open tex file with texmaker, the compliation is working... So i don't know whats going wrong

PROBLEM SOLVED:

I have resolved my problems.

1. Save tex file with msaPrettyPrint()

2. Construct pdf with texi2pdf()

bdir = "E:/DOCTORAT/workspace/alignement_prot_ribo_all"
workdir = file.path(bdir,"one_file_per_ptne/")
outdir = file.path(bdir,"alignements")

myFiles = list.files(path = workdir,full.names = TRUE)
for (i in 1:66){
  newdir = substr(basename(myFiles[i]), start = 1 ,stop = 6)
  output = file.path(outdir, newdir)
  dir.create(output,showWarnings = FALSE)
  current_seq <- readAAStringSet(myFiles[i])
  current_align <- msa(current_seq)
  fasta_file = paste(outdir,'/',newdir,".fasta",sep="")
  tex_file = paste(outdir,"/",newdir,".tex",sep="")
  print(pdf_file)
  msaPrettyPrint(current_align, output="tex", showConsensus = "none", askForOverwrite=FALSE, verbose=FALSE,
                  file = tex_file, alFile = fasta_file )
  texi2pdf(tex_file, clean=TRUE)
}

Hi all,

I have tried the solution, but I receive the following error:
 

Error in .normarg_input_filepath(filepath) :
  'filepath' must be a character vector with no NAs


Unsure of where to go from here...

Could you please specify what are these three parameters stand for?
what should be included in bdir, workdir and outdir?

bdir = "E:/DOCTORAT/workspace/alignement_prot_ribo_all"
workdir = file.path(bdir,"one_file_per_ptne/")
outdir = file.path(bdir,"alignements")