[R] Tab Separated File Reading Error

[arun]

Hi,
Try:
annoTranscripts<- read.csv("matched.txt", sep = '\t', stringsAsFactors = FALSE,quote="",header=FALSE)
 str(annoTranscripts)
'data.frame':    367274 obs. of  12 variables:
 $ V1 : chr  "comp103529_c0_seq1" "comp129123_c0_seq1" "comp129123_c0_seq1" "comp129124_c0_seq1" ...
 $ V2 : chr  "XM_003723822" "XM_778057" "EU116908" "XM_786928" ...
 $ V3 : chr  "PREDICTED: Strongylocentrotus purpuratus neuromedin-U receptor 2-like (LOC100888633), mRNA" "PREDICTED: Strongylocentrotus purpuratus 60S ribosomal protein L30-like (LOC577852), mRNA" "Barentsia elongata putative ribosomal protein L30 mRNA, complete cds" "PREDICTED: Strongylocentrotus purpuratus 60S ribosomal protein L29-1-like (LOC587182), mRNA" ...
 $ V4 : int  91 392 69 149 149 451 399 203 193 185 ...
 $ V5 : int  136 479 203 209 209 541 463 451 456 472 ...
 $ V6 : int  15 16 40 20 20 24 20 71 83 85 ...
 $ V7 : int  0 11 4 0 0 5 1 10 4 9 ...
 $ V8 : num  2e-38 0e+00 6e-26 2e-70 2e-70 ...
 $ V9 : int  1 22 210 135 135 131 189 205 196 185 ...
 $ V10: int  136 499 410 343 343 669 650 650 649 653 ...
 $ V11: int  576 159 27 1 1 1 21 23 140 22 ...
 $ V12: int  441 627 227 209 209 538 483 468 593 487 ...
 dim(annoTranscripts)
[1] 367274     12
A.K.




----- Original Message -----
From: Dario Strbenac <dstr7320 at uni.sydney.edu.au>
To: "r-help at r-project.org" <r-help at r-project.org>
Cc: 
Sent: Friday, October 4, 2013 8:00 AM
Subject: [R] Tab Separated File Reading Error

Hello,

I have a seemingly simple problem that a tab-delimited file can't be read in.

> annoTranscripts <- read.table("matched.txt", sep = '\t', stringsAsFactors = FALSE)
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  : 
  line 5933 did not have 12 elements

However, all lines do have 12 columns.

> lines <- readLines("matched.txt")
> tabsPosns <- gregexpr("\t", lines)
> table(sapply(tabsPosns, length))

    11 
367274 

> system("wc -l matched.txt")
367274 matched.txt

You can obtain the file from https://dl.dropboxusercontent.com/u/37992150/matched.txt

The line does not contain comment or quote characters. What can you suggest ?

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
[3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
[5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8  
[7] LC_PAPER=C                 LC_NAME=C                
[9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods  
[7] base    

loaded via a namespace (and not attached):
[1] tools_3.0.1

--------------------------------------
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
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