On Jul 3, 2011, at 6:10 PM, Bansal, Vikas wrote:
So I want to code so that it will give the output like this-
DATA FRAME (Input)
Editing the task so it is reproducible:
dat <- read.table(textConnection(' col3 col9
T .a,g,,
A .t,t,,
A .,c,c,
C .,a,,,
G .,t,t,t
A .c,,g,^!.
A .g,ggg.^!,
A .$,,,,,.,
C a,g,,t,
T ,,,,,.,^!.
T ,$,,,,.,."'), header=TRUE,
stringsAsFactors=FALSE)
output
A C G T
1 0 1 4
4 0 0 2
4 2 0 0
1 5 0 0
0 0 4 3
It's also possible to apply the logic that Gabor Grothendieck offered
at the beginning of this thread:
dat[, "newcol"] <- apply(dat, 1, function(x) gsub("\\,|\\." ,x[1],
x[2]) )
# ... and the obvious repetition for C.G.T
> dat[,"A"] <- nchar( gsub("[^aA]", "", dat[ , "newcol"] ))
> dat
col3 col9 newcol A
1 T .a,g,, TaTgTT 1
2 A .t,t,, AtAtAA 4
3 A .,c,c, AAcAcA 4
4 C .,a,,, CCaCCC 1
5 G .,t,t,t GGtGtGt 0
6 A .c,,g,^!. AcAAgA^!A 5
7 A .g,ggg.^!, AgAgggA^!A 4
8 A .$,,,,,., A$AAAAAAA 8
9 C a,g,,t, aCgCCtC 1
10 T ,,,,,.,^!. TTTTTTT^!T 0
11 T ,$,,,,.,." T$TTTTTTT" 0
I am deeply in debt to Gabor Grothendieck. He taught me all I know
regarding regex. The man is a master at patterns.
--
David Winsemius, MD
West Hartford, CT
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