fasta2DNAbin: Read large DNA alignments into R

Description

The function fasta2DNAbin reads alignments with the fasta format (extensions ".fasta", ".fas", or ".fa"), and outputs a DNAbin object (the efficient DNA representation from the ape package). The output contains either the full alignments, or only SNPs. This implementation is designed for memory-efficiency, and can read in larger datasets than Ape's read.dna.

The function reads data by chunks of a few genomes (minimum 1, no maximum) at a time, which allows one to read massive datasets with negligible RAM requirements (albeit at a cost of computational time). The argument chunkSize indicates the number of genomes read at a time. Increasing this value decreases the computational time required to read data in, while increasing memory requirements.

Usage

fasta2DNAbin(file, quiet=FALSE, chunkSize=10, snpOnly=FALSE)

Value

an object of the class DNAbin

Arguments

file

a character string giving the path to the file to convert, with the extension ".fa", ".fas", or ".fasta".

Can also be a connection (which will be opened for reading if necessary, and if so closed (and hence destroyed) at the end of the function call).

quiet

a logical stating whether a conversion messages should be printed (FALSE, default) or not (TRUE).

chunkSize

an integer indicating the number of genomes to be read at a time; larger values require more RAM but decrease the time needed to read the data.

snpOnly

a logical indicating whether SNPs only should be returned.

Author

Thibaut Jombart t.jombart@imperial.ac.uk

Examples

Run this code

if (FALSE) {
## show the example file ##
## this is the path to the file:
myPath <- system.file("files/usflu.fasta",package="adegenet")
myPath

## read the file
obj <- fasta2DNAbin(myPath, chunk=10) # process 10 sequences at a time
obj
}