Hi,
Le 10/10/2013 21:07, Juan Antonio Balbuena a écrit :
Hello,
I need to handle in R 10M trees produced with the program evolver of
PAML. With a smaller number of trees one could create a multi-phylo
object with ape as
tree.m <- read.tree("filename.tre")
but this is impractical in this case because it takes all the RAM
memory. I've tried something like
library(ape)
con = file("evolver.out", open="r") # where evolver.out contains 10M
trees
lin = readLines(con)
for (i in 1:length(lin)) {
+ tree <- read.tree(lin[i])
Replace the line above by:
tree <- read.tree(text = lin[i])
This may work if PAML has actually written one tree per line (ie, each
tree ends with a '\n').
HTH,
Emmanuel
+ # my additional syntax mrca analysis etc. here
+ }
But it doesn't work:
Error in file(file, "r") : cannot open the connection
In addition: Warning messages:
1: closing unused connection 3 (evolver.out)
2: In file(file, "r") :
cannot open file '((((S6: 0.33544, (S1: 0.02314, S10: 0.02314):
0.31230): 0.53388, S5: 0.86932): 0.04830, (S4: 0.51901, (S7: 0.05901,
S2: 0.05901): 0.46000): 0.39861): 0.08238, (S3: 0.30236, (S8: 0.13236,
S9: 0.13236): 0.17000): 0.69764);': No such file or directory
I would very much appreciate your help. Note that computing efficiency
is key here.
Thank you very much for your attention.
Juan A. Balbuena
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