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@gmail.com>
To: joseph <jdsandjd@yahoo.com>
Cc: r-help@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@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 

Mobile. 
Try 
it
> 
now.



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

What 
is 
the 
problem 
you 
are 
trying 
to 
solve?






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