readFASTA {Biostrings}R Documentation

Functions to read/write 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

  fasta.info(file, use.descs=TRUE)
  readFASTA(file, checkComments=TRUE, strip.descs=TRUE)
  writeFASTA(x, file="", append=FALSE, width=80)

Arguments

file Either a character string naming a file or a connection. If "" (the default for writeFASTA), then the function writes to the standard output connection (the console) unless redirected by sink.
use.descs TRUE or FALSE. Whether or not the description lines should be used to name the elements of the returned integer vector.
checkComments Whether or not comments, lines beginning with a semi-colon should be found and removed.
strip.descs Whether or not the ">" marking the beginning of the description lines should be removed. Note that this argument is new in Biostrings >= 2.8. In previous versions readFASTA was keeping the ">".
x A list as one returned by readFASTA.
append TRUE or FALSE. If TRUE output will be appended to file; otherwise, it will overwrite the contents of file. See ?cat for the details.
width The maximum number of letters per line of sequence.

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

An integer vector (for fasta.info) or a list (for readFASTA) with one element for each sequence in the file. For readFASTA, the elements are in two parts, one the description and the second a character string of the biological sequence.

Author(s)

R. Gentleman, H. Pages

See Also

read.BStringSet, read.DNAStringSet, read.RNAStringSet, read.AAStringSet, write.XStringSet, read.table, scan, write.table

Examples

  f1 <- system.file("extdata", "someORF.fa", package="Biostrings")
  fasta.info(f1)
  ff <- readFASTA(f1, strip.descs=TRUE)
  desc <- sapply(ff, function(x) x$desc)
  ## Keep the "reverse complement" sequences only
  ff2 <- ff[grep("reverse complement", desc, fixed=TRUE)]
  writeFASTA(ff2, file.path(tempdir(), "someORF2.fa"))

[Package Biostrings version 2.12.9 Index]