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 <[EMAIL PROTECTED]>
To: joseph <[EMAIL PROTECTED]>
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
<[EMAIL PROTECTED]>
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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