readFASTA {Biostrings}R Documentation

A function to read FASTA formatted files

Description

FASTA is a simple file format for biological sequence data. A file may contain one or more sequences, for each sequence there is a description line which begins with a >.

Usage

readFASTA(file, checkComments = TRUE)

Arguments

file The name of the file to be read from.
checkComments Whether or not comments, lines beginning with a semi-colon should be found and removed.

Details

FASTA is a widely used format in biology. It is a relatively simple markup. I am not aware of a standard. It might be nice to check to see if the data that were parsed are sequences of some appropriate type, but without a standard that does not seem possible.

There are many other packages that provide similar, but different capabilities. The one in the package seqinr seems most similar but they separate the biological sequence into single character strings, which is too inefficient for large problems.

Value

A list with one element for each sequence in the file. The elements are in two parts, one the description and the second a character string of the biological sequence.

Author(s)

R. Gentleman

See Also

read.table, scan

Examples

f1 = system.file("Exfiles/fastaEx", package="Biostrings")
ff = readFASTA(f1)

[Package Biostrings version 1.4.0 Index]