nonStandardSeq {ftrCOOL}

nonStandard sequence (nonStandardSeq)

Description

This function returns sequences which contain at least one non-standard alphabet.

Usage

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

Arguments

file

The address of fasta file which contains all the sequences.

legacy.mode

It comments all lines starting with ";"

seqonly

If it is set to true, the function returns sequences with no description.

alphabet

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

Value

This function returns a string vector. Each element of the vector is a sequence which contains at least one non-standard alphabet.

Examples

filePrs<-system.file("extdata/proteins.fasta",package="ftrCOOL")
nonStandardPrSeq<-nonStandardSeq(file = filePrs,alphabet="aa")

fileLNC<-system.file("extdata/Athaliana_LNCRNA.fa",package="ftrCOOL")
nonStandardNUCSeq<-nonStandardSeq(file = filePrs, alphabet="dna")