R help - Jul 2008 - How to emulate perl style of reading files ?

I tried the following, obviously it didn't work. Hope you get my point, how
to do it in R ? My objective is to read a large fasta file (but not storing the
entire data into memory) , and compute some sequence composition statistics.
 
while(a <- readLines("test1") != EOF) print(a)
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On 7/3/2008 9:35 AM, Daren Tan wrote:
> I tried the following, obviously it didn't work. Hope you get my point,
how to do it in R ? My objective is to read a large fasta file (but not storing
the entire data into memory) , and compute some sequence composition statistics.
>  
> while(a <- readLines("test1") != EOF) print(a)
The normal way to do this in R is simply

a <- readLines("test1")

and then process all of the lines in a, but if you don't want them all 
in memory at once, you can use some sort of loop as follows.  You need 
to open a connection to the file, then read one line (or a few lines) at 
a time until your condition is met.  For your specific example,

con <- file("test1", "r")
while ( length(a <- readLines(con, 1)) ) print(a)
close(con)

Duncan Murdoch

You use connections -- see the 'R Data Import/Export Manual'.
Something like

con <- file("test1", "r")
while(length(a <- readLines(con, 1))) print(a)
close(con)

On Thu, 3 Jul 2008, Daren Tan wrote:
>
> I tried the following, obviously it didn't work. Hope you get my point,
how to do it in R ? My objective is to read a large fasta file (but not storing
the entire data into memory) , and compute some sequence composition statistics.
>
> while(a <- readLines("test1") != EOF) print(a)
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>
>
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>
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-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
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