R/TorsionAngle.R

In ftrCOOL: Feature Extraction from Biological Sequences

#' Torsion Angle (TorsionAngle)
#'
#' The inputs to this function are phi and psi angles of each amino acid in the sequence. We use the output of SPINE-X software to obtain the angles.
#' Further, the TA function replaces each amino acid of the sequence with a vector. The vector contain two elements: The phi and psi angles.
#'
#' @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 the outFormat is set to 'mat' for sequences with different lengths, it returns an error.
#' It is noteworthy that 'txt' format is not usable for machine learning purposes.
#'
#' @param dirPath Path of the directory which contains all output files of SPINE-X. Each file belongs to a sequence.
#'
#' @param outFormat It can take two values: 'mat' (which stands for matrix) and 'txt'. The default value is 'mat'.
#'
#' @param outputFileDist It shows the path and name of the 'txt' output file.
#'
#'
#' @return The output is differnet depending on the outFormat parameter ('mat' or 'txt').
#' If the outFormat is set to 'mat', it returns a feature matrix for sequences with the same lengths.
#' The number of rows is equal to the number of sequences and the number of columns
#' is (length of the sequence)*2.
#' If the outFormat is set to 'txt', all binary values will be writen in a 'txt' file.
#' Each row belongs to a sequence.
#'
#'
#' @export
#'
#' @examples
#'
#' dir = tempdir()
#' ad<-paste0(dir,"/ta.txt")
#'
#' PredTorsioNdir<-system.file("testForder",package="ftrCOOL")
#' PredTorsioNdir<-paste0(PredTorsioNdir,"/TorsioNdir/")
#' mat<-TorsionAngle(PredTorsioNdir,outFormat="txt",outputFileDist=ad)
#'
#' unlink("dir", recursive = TRUE)

TorsionAngle<-function(dirPath,outFormat="mat",outputFileDist=""){


  VectorSimple<-readTorsionDir(dirPath)
  lens<-lapply(VectorSimple, length)

  if(outFormat=="mat"){
    if(length(unique(lens))==1){
      simpleMatrix=matrix("",ncol = lens[[1]],nrow = length(VectorSimple))
      colnames(simpleMatrix)<-paste0("pos",1:lens[[1]])
      for(i in 1:nrow(simpleMatrix)){
        simpleMatrix[i,]=VectorSimple[[i]]
      }
      return(simpleMatrix)
    }
    else{
      stop("ERROR all sequences should be in the same lengths in 'mat' mode. Use 'txt' mode for outFormat parameter")
    }
  } else {
    for(i in 1:length(VectorSimple)){
      temp<-VectorSimple[[i]]
      tempName<-paste0("sequence",i)
      temp<-c(tempName,temp)
      vect<-paste(temp,collapse = "\t")
      write(vect,outputFileDist,append = TRUE)
    }

  }

}