[adegenet-forum] long processing with fasta2bin

[Adrien Bessy]

Hi there,
I would like to calculate Fst on 1292 genes between 5 populations.So I have 1292 fasta files containing around 30 individual sequences.I saw there is a pairwise.fst function that could be what I want. 
But before that I need to use the fasta2bin function in order to read alignments form my fasta files.The problem is that when I apply this function, for a fasta file containing 30 alignments, the processing seems to be very very long.
Here are my script and the results:--------------------------------------------------------------------------------library(adegenet)res <- fasta2DNAbin("/Users/abessy/Documents/SA_without_N/DSPR_without_N/140up_Chr3R_14124163_14125548.fas_without_N.fas")
> source("fasta.R")
Loading required package: ade4


   /// adegenet 2.0.1 is loaded ////////////


   > overview: '?adegenet'
   > tutorials/doc/questions: 'adegenetWeb()' 
   > bug reports/feature resquests: adegenetIssues()






 Converting FASTA alignment into a DNAbin object... 




 Finding the size of a single genome... 



-----------------------------------------------------------------------------------
I tried with the fasta2genlight function and the processing seems to be very very long too, even with using the parallel parameter:-----------------------------------------------------------------------------------library(adegenet)library(parallel)res1<- fasta2genlight("/Users/abessy/Documents/SA_without_N/DSPR_without_N/140up_Chr3R_14124163_14125548.fas_without_N.fas",parallel=TRUE)
> source("fasta.R")
Loading required package: ade4


   /// adegenet 2.0.1 is loaded ////////////


   > overview: '?adegenet'
   > tutorials/doc/questions: 'adegenetWeb()' 
   > bug reports/feature resquests: adegenetIssues()






 Converting FASTA alignment into a genlight object... 


---------------------------------------------------
Have you an idea why it is so long ?I have a iMac. 
I attached my fasta file.
Best wishes
Adrien


 		 	   		  
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