Re: [R-sig-phylo] most efficient way to read trees from huge text file
Hello Emmanuel,
Yes, trees come one at a line and your solution is apparently working.
Thank you very much,
Juan
> 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
> >
> > ___
> > R-sig-phylo mailing list - R-sig-phylo@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> > Searchable archive at
http://www.mail-archive.com/r-sig-phylo@r-project.org/
> >
>
>
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Re: [R-sig-phylo] most efficient way to read trees from huge text file
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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[R-sig-phylo] most efficient way to read trees from huge text file
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])
+ # 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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