bios2mds (version 1.2.3)

export.fasta: Writes a MSA file in FASTA format

Description

Writes a multiple sequence alignment (MSA) file in FASTA format.

Usage

export.fasta(x, outfile = "alignment.fa", ncol = 60, open = "w")

Arguments

x

an object of class 'align', obtained from import.fasta or import.msf, or an element list from the extract.cluster function return.

outfile

a string of characters or string vector to indicate the name of the MSA file(s) to be written. If x is an object of class 'align', default is "alignment.fa". If x is an element list, for each element in x, default is the element name, followed by the ".alignement.fa" extension.

ncol

an integer value indicating the number of characters per line for the sequences in outfile.Default is 60.

open

a character value indicating the opening mode for outfile. This should be either of "w" to write into a new file, or "a" to append at the end of an already existing file. Default is "w".

Value

Produces a FASTA file for an 'align' object or a FASTA file for each cluster in list.

Details

Initially, FASTA (for FAST-ALL) was the input format of the FASTA program, used for protein comparison and searching in databases. Presently, FASTA format is a standard format for biological sequences.

The FASTA formatted file of a single sequence displays:

• a single-line description beginning with a greater-than (>) symbol. The following word is the identifier.

• followed by any number of lines, representing biological sequence.

For multiple alignments, the FASTA formatted sequences are concatenated to create a multiple FASTA format.

See Also

write.fasta function from seqinr package.

Examples

# NOT RUN {
# reading of the multiple sequence alignment of human GPCRS in FASTA format:
wd <- tempdir()
#wd <- getwd()
file1 <- file.path(wd,"alignment.fa")
aln <- import.fasta(system.file("msa/human_gpcr.fa", package = "bios2mds"))
export.fasta(aln,file1)
# }