Re: [R] inserting text lines in a dat frame

From: joseph <jdsandjd_at_yahoo.com>
Date: Wed, 6 Feb 2008 09:36:47 -0800 (PST)


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

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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