[R] inserting text lines in a dat frame

[jim holtman]

This should do it for you:

x <- read.table(textConnection("    V1    V2 V3
1 chr1 11255 55
2 chr1 11320 29
3 chr1 11400 45
4 chr2 21680 35
5 chr2 21750 84
6 chr2 21820 29
7 chr2 31890 46
8 chr3 32100 29
9 chr3 52380 29
10 chr3 66450 46" ), header=TRUE)
outfile <- '/tempxx.txt'
cat("browser position chr1:1-10000\nrowser hide all\n", file=outfile)
result <- lapply(split(x, x$V1), function(.chro){
    cat(sprintf("track type=wiggle_0 name=sample description=%s_sample
visibility=full\nvariableStep chrom=%s span=1\n",
        as.character(.chro$V1[1]), as.character(.chro$V1[1])),
file=outfile, append=TRUE)
    write.table(.chro[, -1], sep="\t", file=outfile, append=TRUE,
quote=FALSE, col.names=FALSE, row.names=FALSE)
})


On 2/6/08, joseph <jdsandjd at yahoo.com> wrote:
>
> Hi Jim
> yes, this exactly want I want. However,  I need one more step to get rid of
> the first column so that the final file looks like this:
> browser position chr1:1-10000
> browser hide all
> track type=wiggle_0 name=sample description=chr1_sample visibility=full
> variableStep chrom=chr1 span=1
> 11255  55
> 11320  29
>  11400  45
> track type=wiggle_0 name=sample description=chr2_sample visibility=full
> variableStep chrom=chr2 span=1
> 21680 35
> 21750 84
> 21820 29
> track type=wiggle_0 name=sample description=chr3_sample visibility=full
> variableStep chrom=chr3 span=1
> 32100 29
> 32170 45
> 32240 45
>  Thank you very much
> ----- Original Message ----
> From: jim holtman <jholtman at gmail.com>
> To: joseph <jdsandjd at yahoo.com>
> Cc: r-help at r-project.org
> Sent: Wednesday, February 6, 2008 2:37:38 AM
> Subject: Re: inserting text lines in a dat frame
>
> Try this and see if it is what you want:
>
> x <- read.table(textConnection("    V1    V2 V3
> 1 chr1 11255 55
> 2 chr1 11320 29
> 3 chr1 11400 45
> 4 chr2 21680 35
> 5 chr2 21750 84
> 6 chr2 21820 29
> 7 chr2 31890 46
> 8 chr3 32100 29
> 9 chr3 52380 29
> 10 chr3 66450 46" ), header=TRUE)
> cat("browser position chr1:1-10000\nrowser hide all\n", file='tempxx.txt')
> result <- lapply(split(x, x$V1), function(.chro){
>     cat(sprintf("track type=wiggle_0 name=sample description=%s_sample
> visibility=full\nvariableStep chrom=%s span=1\n",
>         as.character(.chro$V1[1]), as.character(.chro$V1[1])),
> file="tempxx.txt", append=TRUE)
>     write.table(.chro, sep="\t", file="tempxx.txt", append=TRUE,
> col.names=FALSE, row.names=FALSE)
> })
>
>
>
> On Feb 5, 2008 11:22 PM, joseph <jdsandjd at yahoo.com> wrote:
> >
> >
> >
> >
> >
> > Hi Jim
> >  I am trying to prepare a bed file to load as accustom track on the UCSC
> > genome browser.
> > I have a data frame that looks like the one below.
> > > x
> >      V1    V2 V3
> > 1 chr1 11255 55
> > 2 chr1 11320 29
> > 3 chr1 11400 45
> > 4 chr2 21680 35
> > 5 chr2 21750 84
> > 6 chr2 21820 29
> > 7 chr2 31890 46
> > 8 chr3 32100 29
> > 9 chr3 52380
> >  29
> > 10 chr3 66450 46
> > I would like to insert the following 4 lines at the beginning:
> > browser position chr1:1-10000
> > browser hide all
> > track type=wiggle_0 name=sample description=chr1_sample visibility=full
> > variableStep chrom=chr1 span=1
> > and then insert 2 lines before each chromosome:
> > track type=wiggle_0 name=sample description=chr2_sample visibility=full
> > vriableStep chrom=chr2 span=1
> > The final result should be tab delimited file that looks like this:
> > browser position chr1:1-10000
> > browser hide all
> > track type=wiggle_0 name=sample description=chr1_sample visibility=full
> > variableStep chrom=chr1 span=1
> > chr1 11255 55
> > chr1 11320 29
> > chr1 11400 45
> > track type=wiggle_0 name=sample description=chr2_sample visibility=full
> > variableStep chrom=chr2 span=1
> > chr2 21680 35
> > chr2 21750 84
> > chr2 21820 29
> > track type=wiggle_0 name=sample description=chr3_sample visibility=full
> > variableStep chrom=chr3
> >  span=1
> > chr3 32100 29
> > chr3 32170 45
> > chr3 32240 45
> > Any kind of help or guidance will be much appreciated.
> > Joseph
> >
> > ________________________________
> > Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it
> > now.
>
>
>
> --
> Jim Holtman
> Cincinnati, OH
> +1 513 646 9390
>
> What is the problem you are trying to solve?
>
>
> ________________________________
> Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it
> now.


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

What is the problem you are trying to solve?