CODEWITHSUNDEEP
rtextfile-io
Layla
Layla

Reputation: 5446

Read a text file in R line by line

I would like to read a text file in R, line by line, using a for loop and with the length of the file. The problem is that it only prints character(0). This is the code:

fileName="up_down.txt"
con=file(fileName,open="r")
line=readLines(con) 
long=length(line)
for (i in 1:long){
    linn=readLines(con,1)
    print(linn)
}
close(con)

Upvotes: 84

Views: 174007

Answers (6)

Phillip Long
Phillip Long

Reputation: 51

fileName = "up_down.txt"

### code to get the line count of the file
length_connection = pipe(paste("cat ", fileName, " | wc -l", sep = "")) # "cat fileName | wc -l" because that returns just the line count, and NOT the name of the file with it
long = as.numeric(trimws(readLines(con = length_connection, n = 1)))
close(length_connection) # make sure to close the connection
###

for (i in 1:long){

    ### code to extract a single line at row i from the file
    linn_connection_cmd = paste("head -n", format(x = i, scientific = FALSE, big.mark = ""), fileName, "| tail -n 1", sep = " ") # extracts one line from fileName at the desired line number (i)
    linn_connection = pipe(linn_connection_cmd)
    linn = readLines(con = linn_connection, n = 1)
    close(linn_connection) # make sure to close the conection
    ###
    
    # the line is now loaded into R and anything can be done with it
    print(linn)
}
close(con)

By using R's pipe() command, and using shell commands to extract what we want, the full file is never loaded into R, and is read in line by line.

paste("head -n", format(x = i, scientific = FALSE, big.mark = ""), fileName, "| tail -n 1", sep = " ")

It is this command that does all the work; it extracts one line from the desired file.

Edit: R's default behavior is for i to return as normal number when less than 100,000, but begins returning i in scientific notation when it is greater than or equal to 100,000 (1e+05). Thus, format(x = i, scientific = FALSE, big.mark = "") is used in our pipe command to make sure that the pipe() command always receives a number in normal form, which is all that the command can understand. If the pipe() command is given any number like 1e+05, it will not be able to comprehend it and will result in the following error:

head: 1e+05: invalid number of lines

Upvotes: 0

Dirk is no longer here
Dirk is no longer here

Reputation: 368181

Just use readLines on your file:

R> res <- readLines(system.file("DESCRIPTION", package="MASS"))
R> length(res)
[1] 27
R> res
 [1] "Package: MASS"                                                                  
 [2] "Priority: recommended"                                                          
 [3] "Version: 7.3-18"                                                                
 [4] "Date: 2012-05-28"                                                               
 [5] "Revision: $Rev: 3167 $"                                                         
 [6] "Depends: R (>= 2.14.0), grDevices, graphics, stats, utils"                      
 [7] "Suggests: lattice, nlme, nnet, survival"                                        
 [8] "Authors@R: c(person(\"Brian\", \"Ripley\", role = c(\"aut\", \"cre\", \"cph\"),"
 [9] "        email = \"[email protected]\"), person(\"Kurt\", \"Hornik\", role"  
[10] "        = \"trl\", comment = \"partial port ca 1998\"), person(\"Albrecht\","   
[11] "        \"Gebhardt\", role = \"trl\", comment = \"partial port ca 1998\"),"     
[12] "        person(\"David\", \"Firth\", role = \"ctb\"))"                          
[13] "Description: Functions and datasets to support Venables and Ripley,"            
[14] "        'Modern Applied Statistics with S' (4th edition, 2002)."                
[15] "Title: Support Functions and Datasets for Venables and Ripley's MASS"           
[16] "License: GPL-2 | GPL-3"                                                         
[17] "URL: http://www.stats.ox.ac.uk/pub/MASS4/"                                      
[18] "LazyData: yes"                                                                  
[19] "Packaged: 2012-05-28 08:47:38 UTC; ripley"                                      
[20] "Author: Brian Ripley [aut, cre, cph], Kurt Hornik [trl] (partial port"          
[21] "        ca 1998), Albrecht Gebhardt [trl] (partial port ca 1998), David"        
[22] "        Firth [ctb]"                                                            
[23] "Maintainer: Brian Ripley <[email protected]>"                               
[24] "Repository: CRAN"                                                               
[25] "Date/Publication: 2012-05-28 08:53:03"                                          
[26] "Built: R 2.15.1; x86_64-pc-mingw32; 2012-06-22 14:16:09 UTC; windows"           
[27] "Archs: i386, x64"                                                               
R>

There is an entire manual devoted to this.

Upvotes: 52

xiaodai
xiaodai

Reputation: 16004

I suggest you check out chunked and disk.frame. They both have functions for reading in CSVs chunk-by-chunk.

In particular, disk.frame::csv_to_disk.frame may be the function you are after?

Upvotes: 2

Nick Dong
Nick Dong

Reputation: 3736

I write a code to read file line by line to meet my demand which different line have different data type follow articles: read-line-by-line-of-a-file-in-r and determining-number-of-linesrecords. And it should be a better solution for big file, I think. My R version (3.3.2).

con = file("pathtotargetfile", "r")
readsizeof<-2    # read size for one step to caculate number of lines in file
nooflines<-0     # number of lines
while((linesread<-length(readLines(con,readsizeof)))>0)    # calculate number of lines. Also a better solution for big file
  nooflines<-nooflines+linesread

con = file("pathtotargetfile", "r")    # open file again to variable con, since the cursor have went to the end of the file after caculating number of lines
typelist = list(0,'c',0,'c',0,0,'c',0)    # a list to specific the lines data type, which means the first line has same type with 0 (e.g. numeric)and second line has same type with 'c' (e.g. character). This meet my demand.
for(i in 1:nooflines) {
  tmp <- scan(file=con, nlines=1, what=typelist[[i]], quiet=TRUE)
  print(is.vector(tmp))
  print(tmp)
}
close(con)

Upvotes: 4

dvd
dvd

Reputation: 1820

You should take care with readLines(...) and big files. Reading all lines at memory can be risky. Below is a example of how to read file and process just one line at time:

processFile = function(filepath) {
  con = file(filepath, "r")
  while ( TRUE ) {
    line = readLines(con, n = 1)
    if ( length(line) == 0 ) {
      break
    }
    print(line)
  }

  close(con)
}

Understand the risk of reading a line at memory too. Big files without line breaks can fill your memory too.

Upvotes: 167

Layla
Layla

Reputation: 5446

Here is the solution with a for loop. Importantly, it takes the one call to readLines out of the for loop so that it is not improperly called again and again. Here it is:

fileName <- "up_down.txt"
conn <- file(fileName,open="r")
linn <-readLines(conn)
for (i in 1:length(linn)){
   print(linn[i])
}
close(conn)

Upvotes: 46

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