[R] Importing data from text file with mixed format

jim holtman
2009-10-25T17:19:09Z

try this:

> # read in the file
> x <- readLines(textConnection("#begin text file
+ Timepoint 1
+ ObjectNumber     Volume     SurfaceArea
+ 1                      5.3          9.7
+ 2                      4.9          8.3
+ 3                      5.0          9.1
+ 4                      3.5          7.8
+
+ Timepoint 2
+ ObjectNumber     Volume     SurfaceArea
+ 1                      5.1          9.0
+ 2                      4.7          8.9
+ 3                      4.3          8.3
+ 4                      4.2          7.9"))
> # delete blank lines
> blanks <- grep("^\\s*$", x)
> if (length(blanks) > 0) x <- x[-blanks]
> # determine where "Timepoint" occurs in the text vector
> tp <- grep("^Timepoint", x)
> # append length+1 to the result
> tp <- c(tp, length(x) + 3)
> input <- textConnection(x)
> # skip to the first "Timepoint" if not first line
> if (tp[1] != 1) readLines(input, n=tp[1] - 1)
[1] "#begin text file"
> result <- list()
> # repeat for each Timepoint
> for (numLines in diff(tp)){  # repeat for number of lines to read
+     id <- readLines(input, n=1)
+     result[[id]] <- read.table(input, header=TRUE, nrows=numLines - 2)
+ }
> result
$`Timepoint 1`
  ObjectNumber Volume SurfaceArea
1            1    5.3         9.7
2            2    4.9         8.3
3            3    5.0         9.1
4            4    3.5         7.8

$`Timepoint 2`
  ObjectNumber Volume SurfaceArea
1            1    5.1         9.0
2            2    4.7         8.9
3            3    4.3         8.3
4            4    4.2         7.9

> closeAllConnections()


On Sat, Oct 24, 2009 at 11:31 PM, delnatan <delnatan at gmail.com>
wrote:
>
> Hi,
> I'm having difficulty importing my textfile that looks something like
this:
>
> #begin text file
> Timepoint 1
> ObjectNumber ? ? Volume ? ? SurfaceArea
> 1 ? ? ? ? ? ? ? ? ? ? ?5.3 ? ? ? ? ?9.7
> 2 ? ? ? ? ? ? ? ? ? ? ?4.9 ? ? ? ? ?8.3
> 3 ? ? ? ? ? ? ? ? ? ? ?5.0 ? ? ? ? ?9.1
> 4 ? ? ? ? ? ? ? ? ? ? ?3.5 ? ? ? ? ?7.8
>
> Timepoint 2
> ObjectNumber ? ? Volume ? ? SurfaceArea
> 1 ? ? ? ? ? ? ? ? ? ? ?5.1 ? ? ? ? ?9.0
> 2 ? ? ? ? ? ? ? ? ? ? ?4.7 ? ? ? ? ?8.9
> 3 ? ? ? ? ? ? ? ? ? ? ?4.3 ? ? ? ? ?8.3
> 4 ? ? ? ? ? ? ? ? ? ? ?4.2 ? ? ? ? ?7.9
>
> ... #goes on to Timepoint 80
>
> How would I import this data into a list containing data.frame for each
> timepoint?
> I'd like my data to be organized like this:
>
>>myList
> [[1]]
> ? ObjectNumber ? ? Volume ? ? SurfaceArea
> 1 ?1 ? ? ? ? ? ? ? ? ? ? ?5.3 ? ? ? ? ?9.7
> 2 ?2 ? ? ? ? ? ? ? ? ? ? ?4.9 ? ? ? ? ?8.3
> 3 ?3 ? ? ? ? ? ? ? ? ? ? ?5.0 ? ? ? ? ?9.1
> 4 ?4 ? ? ? ? ? ? ? ? ? ? ?3.5 ? ? ? ? ?7.8
>
> [[2]]
> ?ObjectNumber ? ? Volume ? ? SurfaceArea
> 1 1 ? ? ? ? ? ? ? ? ? ? ?5.1 ? ? ? ? ?9.0
> 2 2 ? ? ? ? ? ? ? ? ? ? ?4.7 ? ? ? ? ?8.9
> 3 3 ? ? ? ? ? ? ? ? ? ? ?4.3 ? ? ? ? ?8.3
> 4 4 ? ? ? ? ? ? ? ? ? ? ?4.2 ? ? ? ? ?7.9
>
> -Daniel
> --
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>
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>



--
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem that you are trying to solve?