R help - Mar 2013 - Transpose a big data file and write to a new file

Dear all:

I have a big data file of 60000 columns and 60000 rows like that:

AA AC AA AA .......AT
CC CC CT CT.......TC
..........................
.........................

I want to transpose it and the output is a new like that
AA CC ............
AC CC............
AA CT.............
AA CT.........
....................
....................
AT TC.............

The keypoint is  I can't read it into R by read.table() because the
data is too large,so I try that:
c<-file("silygenotype.txt","r")
geno_t<-list()
repeat{
  line<-readLines(c,n=1)
  if (length(line)==0)break  #end of file
  line<-unlist(strsplit(line,"\t"))
geno_t<-cbind(geno_t,line)
}
 write.table(geno_t,"xxx.txt")

It works but it is too slow ,how to optimize it???

Thank you

Yao He
?????????????????????????
Master candidate in 2rd year
Department of Animal genetics & breeding
Room 436,College of Animial Science&Technology,
China Agriculture University,Beijing,100193
E-mail: yao.h.1988 at gmail.com
??????????????????????????

Hi Yao He,

this doesn't sound like R to me. I'd go for perl (or awk).

See e.g. here:
http://stackoverflow.com/questions/1729824/transpose-a-file-in-bash

HTH

Claudia

Am Wed, 6 Mar 2013 22:37:14 +0800
schrieb Yao He <yao.h.1988 at gmail.com>:
> Dear all:
> 
> I have a big data file of 60000 columns and 60000 rows like that:
> 
> AA AC AA AA .......AT
> CC CC CT CT.......TC
> ..........................
> .........................
> 
> I want to transpose it and the output is a new like that
> AA CC ............
> AC CC............
> AA CT.............
> AA CT.........
> ....................
> ....................
> AT TC.............
> 
> The keypoint is  I can't read it into R by read.table() because the
> data is too large,so I try that:
> c<-file("silygenotype.txt","r")
> geno_t<-list()
> repeat{
>   line<-readLines(c,n=1)
>   if (length(line)==0)break  #end of file
>   line<-unlist(strsplit(line,"\t"))
> geno_t<-cbind(geno_t,line)
> }
>  write.table(geno_t,"xxx.txt")
> 
> It works but it is too slow ,how to optimize it???
> 
> Thank you
> 
> Yao He
> ?????????????????????????
> Master candidate in 2rd year
> Department of Animal genetics & breeding
> Room 436,College of Animial Science&Technology,
> China Agriculture University,Beijing,100193
> E-mail: yao.h.1988 at gmail.com
> ??????????????????????????
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html and provide commented,
> minimal, self-contained, reproducible code.


-- 
Claudia Beleites
Spectroscopy/Imaging
Institute of Photonic Technology 
Albert-Einstein-Str. 9
07745 Jena
Germany

email: claudia.beleites at ipht-jena.de
phone: +49 3641 206-133
fax:   +49 2641 206-399