microseq (version 2.1.6)

readFasta: Read and write FASTA files

Description

Reads and writes biological sequences (DNA, RNA, protein) in the FASTA format.

Usage

readFasta(in.file)
writeFasta(fdta, out.file, width = 0)

Value

readFasta returns a tibble with the contents of the (gzipped) FASTA file stored in two columns of text. The first, named Header, contains the headerlines and the second, named Sequence, contains the sequences.

writeFasta produces a (gzipped) FASTA file.

Arguments

in.file

url/directory/name of (gzipped) FASTA file to read.

fdta

A tibble with sequence data, see ‘Details’ below.

out.file

Name of (gzipped) FASTA file to create.

width

Number of characters per line, or 0 for no linebreaks.

Author

Lars Snipen and Kristian Hovde Liland.

Details

These functions handle input/output of sequences in the commonly used FASTA format. For every sequence it is presumed there is one Header-line starting with a ‘>’. If filenames (in.file or out.file) have the extension .gz they will automatically be compressed/uncompressed.

The sequences are stored in a tibble, opening up all the possibilities in R for fast and easy manipulations. The content of the file is stored as two columns, Header and Sequence. If other columns are added, these will be ignored by writeFasta.

The default width = 0 in writeFasta results in no linebreaks in the sequences (one sequence per line).

See Also

readFastq.

Examples

if (FALSE) {
# We need a FASTA-file to read, here is one example file:
fa.file <- file.path(file.path(path.package("microseq"),"extdata"),"small.ffn")

# Read and write
fdta <- readFasta(fa.file)
ok <- writeFasta(fdta[4:5,], out.file = "delete_me.fasta")

# Make use of dplyr to copy parts of the file to another file
readFasta(fa.file) %>% 
  filter(str_detect(Sequence, "TGA$")) %>% 
  writeFasta(out.file = "TGAstop.fasta", width = 80) -> ok
}