R/AESNN3.R

In ftrCOOL: Feature Extraction from Biological Sequences

#' Learn from alignments (AESNN3)
#'
#' This function replace each amino acid of the sequence with a three-dimensional vector. Values are taken from the three hidden units of the neural network trained on structure alignments.
#' The AESNN3 function can be applied to encode peptides of equal length.
#'
#' @references Lin K, May AC, Taylor WR. Amino acid encoding schemes from protein structure alignments: multi-dimensional vectors to describe residue types. J Theor Biol (2002).
#'
#' @note This function is provided for sequences with the same lengths.
#' Users can use 'txt' option in outFormat parameter for sequences with different lengths.
#' Warning: If outFormat is set to 'mat' for sequences with different lengths, it returns an error.
#' Also, when output format is 'txt', label information is not shown in the text file.
#' It is noteworthy that 'txt' format is not usable for machine learning purposes.
#'
#'
#' @param seqs is a FASTA file with amino acid sequences. Each sequence starts
#' with a '>' character. Also, seqs could be a string vector. Each element of the vector is a peptide/protein sequence.
#'
#' @param label is an optional parameter. It is a vector whose length is equivalent to the number of sequences. It shows the class of
#' each entry (i.e., sequence).
#'
#'
#' @param outFormat (output format) can take two values: 'mat'(matrix) and 'txt'. The default value is 'mat'.
#'
#' @param outputFileDist shows the path and name of the 'txt' output file.
#'
#' @return The output depends on the outFormat parameter which can be either 'mat' or 'txt'. If outFormat is 'mat', the function returns a feature
#' matrix for sequences with the same length such that the number of columns is (sequence length)*(5)
#' and the number of rows is equal to the number of sequences.
#' If the outFormat is 'txt', the output is written to a tab-delimited file.
#'
#' @export
#'
#' @examples
#'
#' ptmSeqsADR<-system.file("extdata/",package="ftrCOOL")
#' ptmSeqsVect<-as.vector(read.csv(paste0(ptmSeqsADR,"/ptmVect101AA.csv"))[,2])
#' mat<-AESNN3(seqs = ptmSeqsVect,outFormat="mat")


AESNN3<-function(seqs,label=c(),outFormat="mat",outputFileDist=""){


  path.pack=system.file("extdata",package="ftrCOOL")

  if(length(seqs)==1&&file.exists(seqs)){
    seqs<-fa.read(seqs,alphabet="aa")
    seqs_Lab<-alphabetCheck(seqs,alphabet = "aa",label)

    seqs<-seqs_Lab[[1]]
    label<-seqs_Lab[[2]]
  }
  else if(is.vector(seqs)){

    seqs<-sapply(seqs,toupper)
    seqs_Lab<-alphabetCheck(seqs,alphabet = "aa",label)
    seqs<-seqs_Lab[[1]]
    label<-seqs_Lab[[2]]

  }
  else {
    stop("ERROR: Input sequence is not in the correct format. It should be a FASTA file or a string vector.")
  }
  numSeqs<-length(seqs)
  lenSeqs<-sapply(seqs, nchar)
  zIndexAD<-paste0(path.pack,"/AESNN3.csv")
  zIndex<-read.csv(zIndexAD,header = FALSE)
  row.names(zIndex)<-zIndex[,1]
  zIndex<-zIndex[,-1]
  zIndex<-as.matrix(zIndex)
  zIndex<-type.convert(zIndex)
  zIndex<-t(zIndex)


  if(outFormat=="mat"){
    if(length(unique(lenSeqs))>1){
      stop("ERROR: All sequences should have the same length in 'mat' mode. For sequences with different lengths, please use 'txt' for outFormat parameter")
    }
    featureMatrix<-matrix(0, nrow = numSeqs, ncol = (lenSeqs[1]*3))


    nameP1<-rep((1:(lenSeqs[1])),each=3)
    nameP1<-paste0("aa",nameP1)
    nameP2<-paste("AESNN3",rep(c(1,2,3),lenSeqs[1]),sep = "")
    colnames(featureMatrix)<-paste(nameP1,nameP2)
    for(n in 1:numSeqs){
      seq<-seqs[n]
      chars<-unlist(strsplit(seq,split = ""))
      featureVector<-zIndex[,chars]
      featureVector<-as.vector(featureVector)
      featureMatrix[n,]<-featureVector
    }

    if(length(label)==numSeqs){
      featureMatrix<-as.data.frame(featureMatrix)
      featureMatrix<-cbind(featureMatrix,label)
    }
    row.names(featureMatrix)<-names(seqs)
    print(featureMatrix)
    #return(featureMatrix)
  }
  else{
    nameSeq<-names(seqs)
    for(n in 1:numSeqs){
      seq<-seqs[n]
      chars<-unlist(strsplit(seq,split = ""))
      featureVector<-zIndex[,chars]
      vect<-as.vector(featureVector)
      temp<-c(nameSeq[n],vect)
      temp<-paste(temp,collapse = "\t")
      write(temp,outputFileDist,append = TRUE)

    }
  }

}