Programming

Hi power user,

I have this type of data (distance list):

file1
I want output like this

Which is a distance matrix


I have tried this following R script

Code:

> x <- read.table("/homes/bierdepot/arli/workspace/prak09/bioinf09/DATA/"file1, as.is=TRUE)
> closeAllConnections()
> x.names <- sort(unique(c(x[[1]], x[[2]])))
> x.dist <- matrix(0, length(x.names), length(x.names))
> dimnames(x.dist) <- list(x.names, x.names)
> x.ind <- rbind(cbind(match(x[[1]], x.names), match(x[[2]], x.names)),
+ cbind(match(x[[2]], x.names), match(x[[1]], x.names)))
> x.dist[x.ind] <- rep(x[[3]], 2)
> x.dist

However, the result is like this.
Which is not a distance matrix, but an adjacency matrix. Is there any solution to repair the script, so I could get the distance matrix?
I have about 20.000 lines files of distance list. If I run those script, I will have this message:

[ reached getOption("max.print") -- omitted xxxx rows ]]

How could I get rid of that message?