readFasta: Read and write FASTA files to or from ShortRead objects

In Bioconductor/ShortRead: FASTQ input and manipulation

Read and write FASTA files to or from ShortRead objects

Description

readFasta reads all FASTA-formated files in a directory dirPath whose file name matches pattern pattern, returning a compact internal representation of the sequences and quality scores in the files. Methods read all files into a single R object; a typical use is to restrict input to a single FASTA file.

writeFasta writes an object to a single file, using mode="w" (the default) to create a new file or mode="a" append to an existing file. Attempting to write to an existing file with mode="w" results in an error.

Usage

readFasta(dirPath, pattern = character(0), ...,
    nrec=-1L, skip=0L)
## S4 method for signature 'character'
readFasta(dirPath, pattern = character(0), ...,
    nrec=-1L, skip=0L)
writeFasta(object, file, mode="w", ...)
## S4 method for signature 'DNAStringSet'
writeFasta(object, file, mode="w", ...)

Arguments

dirPath	A character vector giving the directory path (relative or absolute) or single file name of FASTA files to be read.
pattern	The (grep-style) pattern describing file names to be read. The default (character(0)) results in (attempted) input of all files in the directory.
object	An object to be output in fasta format.
file	A length 1 character vector providing a path to a file to the object is to be written to.
mode	A length 1 character vector equal to either ‘w’ or ‘a’ to write to a new file or append to an existing file, respectively.
...	Additional arguments used by methods or, for writeFasta, writeXStringSet.
nrec	See ?readDNAStringSet.
skip	See ?readDNAStringSet.

Value

readFasta returns a DNAStringSet. containing sequences and qualities contained in all files in dirPath matching pattern. There is no guarantee of order in which files are read.

writeFasta is invoked primarily for its side effect, creating or appending to file file. The function returns, invisibly, the length of object, and hence the number of records written. There is a writeFasta method for any class derived from ShortRead.

Author(s)

Martin Morgan

Examples

showMethods("readFasta")

showMethods("writeFasta")

f1 <- system.file("extdata", "someORF.fa", package="Biostrings")

rfa <- readFasta(f1)
sread(rfa)
id(rfa)

sp <- SolexaPath(system.file('extdata', package='ShortRead'))
rfq <- readFastq(analysisPath(sp), pattern="s_1_sequence.txt")

file <- tempfile()
writeFasta(rfq, file)
readLines(file, 8)

writeFasta(sread(rfq), file)  # no 'id's 

Bioconductor/ShortRead documentation built on Nov. 2, 2024, 4:38 p.m.