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Dario Strbenac

2013-Oct-04 12:00 UTC

[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

William Dunlap

2013-Oct-04 16:22 UTC

head link

[R] Tab Separated File Reading Error

> > 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")
> ...[many omitted lines]...
> The line does not contain comment or quote characters. What can you suggest
?
I suggest looking at the lines preceding the one where the error was found, with
both
print and cat:
    print(lines[5933 - (10:0)])
    cat(lines[5933 - (10:0)], sep="\n")

If things are not obvious after looking at them, see if read.table can read just
those lines
    read.table(text=lines[5933 - (10:0)], sep="\t",
stringsAsFactors=FALSE)
If it can, try backing up more than 10 lines.

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com

> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at
r-project.org] On Behalf
> Of Dario Strbenac
> Sent: Friday, October 04, 2013 5:01 AM
> To: r-help at r-project.org
> 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
> ______________________________________________
> R-help at r-project.org mailing list
> 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.

arun

2013-Oct-04 16:38 UTC

head link

[R] Tab Separated File Reading Error

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
______________________________________________
R-help at r-project.org mailing list
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.

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