So my problem is the following, I am reading through a text file using readlines, and have to go line by line until there is a trigger, and then I have to read the following line using read.fortran().
The problem is that read.fortran() only read text files, and I need to read a line (a string). At the moment I have solved this problem with a disastrous function which writes a file and then I read the file.
read.fortran.string <- function(x_string, x_format, x_file, col.names){
# Disastrous function to be changed
if (missing(x_file)){
x_file = r'(C:\Users\your_user\Documents\tempfolder\line.txt)'
}
write(x_string,x_file)
df = read.fortran(x_file, x_format)
if (!missing(col.names)){
colnames(df) <-col.names
}
return(df)
}
I was expecting that someone will point to a different solution in which:
Do not require to hardcode a path
Do not require having to have writing permission
I believe that
read.fortran(textConnection(x_string), x_format)
will do what you want (untested!)
Related
I tried PGP encrypting a file in ChoPGP library. At the end of the process it shows embedded file name along with the whole original file name path.
But I thought it will show only the filename without the whole path. Which I intend to work on and figure out a way to do so?
Doing the following:
using (ChoPGPEncryptDecrypt pgp = new ChoPGPEncryptDecrypt())
{
pgp.EncryptFile(#"\\appdevtest\c$\appstest\Transporter\test\Test.txt",
#"\\appdevtest\c$\appstest\Transporter\test\OSCTestFile_ChoPGP.gpg",
#"\\appdevtest\c$\appstest\Transporter\pgpKey\PublicKey\atorres\atorres_publicKey.asc",
true,
true);
}
which will result in:
But I would like to only extract the Test.txt in the end something
like this:
Looking at this line from the ChoPGP sources: https://github.com/Cinchoo/ChoPGP/blob/7152c7385022823013324408e84cb7e25d33c3e7/ChoPGP/ChoPGPEncryptDecrypt.cs#L221
You may find out that it uses internal function GetFileName, which ends up with this for the FileStream: return ((FileStream)stream).Name;.
And this one, according to documentation, Gets the absolute path of the file opened in the FileStream..
So you should either make fork of ChoPGP and modify this line to extract just filename, or submit a pull request to the ChoPGP. Btw, it's just a wrapper around the BouncyCastle so you may use that instead.
Using QMake, I read some boiler plate code, make modifications and write the modified code to a file.
However, I get very strange results. I have simplified the problem down to the following:
# Open boiler plate file
interfaceBoilerPlateCode = $$cat($$boilerPlateFile, blob)
# Make sure we read the right content
message("Content read: $$interfaceBoilerPlateCode")
# Write the read text into a file
output = $$system(echo $$interfaceBoilerPlateCode >> $$targetFile) # Doesnt work
output = $$system(echo "Howde" >> $$targetFile) # This works
The file being read is a plain text file containing only the string "Howde".
The contents of the file get read correctly.
However, when I try and write the contents of the file to another target file, I get no output (literally: no errors/warnings but no new file generated). However, if I use echo with just a string defined in the code itself (as in the last line of snippet above), a new file gets generated with the string "Howde" inside it.
What is going on? What am I doing wrong that the penultimate line does not generate a new file?
Use write_file. Instead of:
$$system(echo $$content >> $$file_path)
use
write_file($$file_path, $$content)
I am writing a CGI script in Perl with a section of embedded R script which produces a graph. The original data filename is unknown as it has been uploaded by the CGI script and is stored in a Perl variable called $filename.
My question is that I now would like to open that file in R using read.table(). I am using Statistics::R and so I have tried:
my $R = Statistics::R->new();
$R->set('filename',$filename);
my $out1 = $R->run(
q`rm(list=ls())`,
# Fetch data
q`setwd("/var/www/uploads")`,
q`peakdata<-read.table(filename, sep="",col.names=c("mz","intensity","ionsscore","matched","query","index","hit"))`,
q`attach(peakdata)` ...etc
I can get this to work ONLY if I change $filename into something static and known like 'data.txt' before trying to open the file in read.table - is there a way for me to open a file with a variable for a name?
Thank you in advance.
One possible way to do this is by doing a little more work in Perl.
This is untested code, to give you some ideas:
my $filename = 'fileNameIGotFromSomewhere.txt'
my $source_dir = '/var/www/uploads';
my $file = "$source_dir/$fielname";
# make sure we can read it
unless ( -r $file ) {
die 'can read that data file: $!";
}
Then instead of $R->set, you could interpolate the file name into the R program. Where you've used the single-quote operator, use the double-quote operator instead:
So instead of:
q`peakdata<-read.table(filename, sep="",col.names= .... )`
Use:
qq`peakdata<-read.table($filename, sep="",col.names= .... )`
Now this looks like it would be inviting problems similar to SQL/Code Injections, so that's why I put int the logic to insure that the file exists and is readable. You might be able to think other checks to add to safeguard your use of user-supplied info.
I was trying to write a file using R and in order to distinguish each file, i tried to add a different suffix each time in a function.
For example......
counts <- function(counts_file)
{
..............................
..............................
name <- substr(counts_file,1,5)
file <- paste(name,".cpm.csv")
write.csv(countpermillion, file)
}
But when i run the function counts("JKNC1.bam.tsv"), the output file created is like this
JKNE3 .cpm.csv i.e there is a gap between the JKNEE3 and .cpm.csv. What am i doing wrong here?
Thanks
Upendra
The default separator is a space. paste(name,".cpm.csv",sep="") should do what you want here. Alternately, you could use
paste0(name,".cpm.csv")
The documentation for this can be found by typing ?paste at the console.
I am bit new to R and have a question about a program I am trying to write. I am hoping to take in files (as many as a user pleases) with a while loop (eventually using read.table on each) but it keeps breaking on me.
Here is what I have so far:
cat("Please enter the full path for your files, if you have no more files to add enter 'X': ")
fil<-readLines(con="stdin", 1)
cat(fil, "\n")
while (!input=='X' | !input=='x'){
inputfile=input
input<- readline("Please enter the full path for your files, if you have no more files to add enter 'X': ")
}
if(input=='X' | input=='x'){
exit -1
}
When I run it (from the commandline (UNIX)) I get these results:
> library("lattice")
>
> cat("Please enter the full path for your files, if you have no more files to add enter 'X': ")
Please enter the full path for your files, if you have no more files to add enter 'X': > fil<-readLines(con="stdin", 1)
x
> cat(fil, "\n")
x
> while (!input=='X' | !input=='x'){
+ inputfile=input
+ input<- readline("Please enter the full path for your files, if you have no more files to add enter 'X': ")
+ }
Error: object 'input' not found
Execution halted
I am not quite sure how to fix the problem, but I am pretty sure that it is probably a simple problem.
Any suggestions?
Thanks!
when you first run the script input doesnt exist. Assign
input<-c()
say before your while statement or put
inputfile=input
below input<- readline....
I'm not exactly sure what the underlying problem is for your issue. It may be that you're inputting the directory path incorrectly.
Here's a solution I've used a few times. It makes it much easier for the user. Basically, your code will not require user input, all it requires is that you have a certain naming convention for your files.
setwd("Your/Working/Directory") #This doesn't change
filecontents <- 1
i <- 1
while (filecontents != 0) {
mydata.csv <- try(read.csv(paste("CSV_file_",i,".csv", sep = ""), header = FALSE), silent = TRUE)
if (typeof(mydata.csv) != "list") { #checks to see if the imported data is a list
filecontents <- 0
}
else {
assign(paste('dataset',i, sep=''), mydata)
#Whatever operations you want to do on the files.
i <- i + 1
}
}
As you can see, the naming convention for the files is CSV_file_n where n is any number of input files (i took this code out of one of my programs, in which I load csv's). One of the problems I kept having was Error messages popping up when my code looked for a file that wasn't there. With this loop, those messages won't arise. If it assigns the contents of a non-existant file to mydata.csv, it merely checks to see if mydata.csv is a list. If it is, it continues operating. If not, it stops. If you're worried about differentiating between your data from different files within the code, just insert any relevant information about the file in a constant location within the file itself. For example, in my csv's, My 3rd column always contained the name of the image from which I gathered the information contained in the rest of the csv.
Hope this helps you a bit, even though I see you've already got a solution :-). It's really just an option if you want your program to be more autonomous.