fa.read {ftrCOOL}

Fasta File Reader (fa.read)

Description

This function reads a FASTA file. Each sequence starts with '>' in the file. This is a general function which can be applied to all types of sequences (i.e., protein/peptide, dna, and rna).

Usage

fa.read(file, legacy.mode = TRUE, seqonly = FALSE, alphabet = "aa")

Arguments

file

The address of the FASTA file.

legacy.mode

comments all lines which start with ";".

seqonly

if it is set to true, the function will return sequences with no description.

alphabet

is a vector which contains amino acid, RNA, or DNA alphabets.

Value

a string vector such that each element is a sequence.

References

https://cran.r-project.org/web/packages/rDNAse/index.html

Examples

fileLNC<-system.file("extdata/Athaliana_LNCRNA.fa",package="ftrCOOL")
sequenceVectLNC<-fa.read(file=fileLNC,alphabet="dna")

filePrs<-system.file("extdata/proteins.fasta",package="ftrCOOL")
sequenceVectPRO<-fa.read(file=filePrs,alphabet="aa")