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

      readFASTA(file, checkComments=TRUE, strip.desc=TRUE)
      writeFASTA(x, file="", width=80)

### Arguments

`file` | Either a character string naming a file or a connection open for reading or writing. If `""` (the default for `writeFASTA`), then the function writes to the standard output connection (the console) unless redirected by `sink`.
`checkComments` | Whether or not comments, lines beginning with a semi-colon should be found and removed.
`strip.desc` | 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`.
`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

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

### Examples

    f1 <- system.file("extdata", "someORF.fa", package="Biostrings")
    ff <- readFASTA(f1, strip.desc=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 2.8.18 Index]