R/extractClassyFire.R

In JustinZZW/ImmsTools: Some tools for ion mobility mass spectrometry data processing

#' @title extractClyssyFire
#' @author Zhiwei Zhou
#' \email{zhouzw@@sioc.ac.cn}
#' @description extract sdf file exported from ClassyFire
#' @param filename the sdf file name
#' @importFrom magrittr '%>%'
#' @export


extractClassyFire <- function(filename){
  temp <- readr::read_lines(filename)

  idx.kegg.id <- which(temp=='$$$$') + 1
  idx.kegg.id <- c(1, idx.kegg.id)
  idx.inchikey <- which(temp=='> <InChIKey>') + 1
  idx.smiles <- which(temp=='> <SMILES>')+1
  idx.kingdom <- which(temp== '> <Kingdom>')+1
  idx.superclass <- which(temp=="> <Superclass>") + 1
  idx.class <- which(temp=="> <Class>") + 1
  idx.subclass <- which(temp=="> <Subclass>") + 1

  if (length(idx.kegg.id) != length(idx.inchikey)) {
    less.num <- length(idx.kegg.id) - length(idx.inchikey)
    NA.num <- rep(NA, less.num)
    idx.inchikey <- which(temp=='> <InChIKey>') + 1
    idx.inchikey <- c(idx.inchikey, NA.num)
  }

  if (length(idx.kegg.id) != length(idx.smiles)) {
    less.num <- length(idx.kegg.id) - length(idx.smiles)
    NA.num <- rep(NA, less.num)
    idx.smiles <- which(temp=='> <SMILES>') + 1
    idx.smiles <- c(idx.smiles, NA.num)
  }

  if (length(idx.kegg.id) != length(idx.kingdom)) {
    less.num <- length(idx.kegg.id) - length(idx.kingdom)
    NA.num <- rep(NA, less.num)
    idx.kingdom <- which(temp=='> <Kingdom>') + 1
    idx.kingdom <- c(idx.kingdom, NA.num)
  }

  if (length(idx.kegg.id) != length(idx.superclass)) {
    less.num <- length(idx.kegg.id) - length(idx.superclass)
    NA.num <- rep(NA, less.num)
    idx.superclass <- which(temp=="> <Superclass>") + 1
    idx.superclass <- c(idx.superclass, NA.num)
  }


  if (length(idx.kegg.id) != length(idx.class)) {
    less.num <- length(idx.kegg.id) - length(idx.class)
    NA.num <- rep(NA, less.num)
    idx.class <- which(temp=="> <Class>") + 1
    idx.class <- c(idx.class, NA.num)
  }

  if (length(idx.kegg.id) != length(idx.subclass)) {
    less.num <- length(idx.kegg.id) - length(idx.subclass)
    NA.num <- rep(NA, less.num)
    idx.subclass <- which(temp=="> <Subclass>") + 1
    idx.subclass <- c(idx.subclass, NA.num)
  }

  temp_result <- data.frame(kegg.id=temp[idx.kegg.id],
                            inchikey=temp[idx.inchikey],
                            smiles=temp[idx.smiles],
                            kingdom=temp[idx.kingdom],
                            superclass=temp[idx.superclass],
                            class=temp[idx.class],
                            subclass=temp[idx.subclass],
                            stringsAsFactors = F)

  # replace no character with NA
  idx.na <- apply(temp_result, 2, function(x){
    temp <- which(nchar(x)==0)
  })

  if (length(idx.na)==0) {
    idx.na <- lapply(1:7, function(i)(return(NULL)))
  }

  for (i in 1:7) {
    if (length(idx.na[[i]]) > 0 ) {
      temp_result[idx.na[[i]],i] <- NA
    }
  }

  temp_result

  # temp <- readr::read_lines(filename)
  #
  # idx.kegg.id <- which(temp=='$$$$') + 1
  # idx.kegg.id <- c(1, idx.kegg.id)
  # idx.inchikey <- which(temp=='> <InChIKey>') + 1
  #
  # if (length(idx.kegg.id) == length(idx.inchikey)) {
  #   idx.inchikey <- which(temp=='> <InChIKey>')+1
  #   idx.smiles <- which(temp=='> <SMILES>')+1
  #   idx.kingdom <- which(temp== '> <Kingdom>')+1
  #   idx.superclass <- which(temp=="> <Superclass>") + 1
  #   idx.class <- which(temp=="> <Class>") + 1
  #   idx.subclass <- which(temp=="> <Subclass>") + 1
  # } else {
  #   less.num <- length(idx.kegg.id) - length(idx.inchikey)
  #   NA.num <- rep(NA, less.num)
  #
  #   idx.inchikey <- which(temp=='> <InChIKey>') + 1
  #   idx.inchikey <- c(idx.inchikey, NA.num)
  #
  #   idx.smiles <- which(temp=='> <SMILES>') + 1
  #   idx.smiles <- c(idx.smiles, NA.num)
  #
  #   idx.kingdom <- which(temp== '> <Kingdom>') + 1
  #   idx.kingdom <- c(idx.kingdom, NA.num)
  #
  #   idx.superclass <- which(temp=="> <Superclass>") + 1
  #   idx.superclass <- c(idx.superclass, NA.num)
  #
  #   idx.class <- which(temp=="> <Class>") + 1
  #   idx.class <- c(idx.class, NA.num)
  #
  #   idx.subclass <- which(temp=="> <Subclass>") + 1
  #   idx.subclass <- c(idx.subclass, NA.num)
  # }
  #
  #
  #
  # temp_result <- data.frame(kegg.id=temp[idx.kegg.id],
  #                           inchikey=temp[idx.inchikey],
  #                           smiles=temp[idx.smiles],
  #                           kingdom=temp[idx.kingdom],
  #                           superclass=temp[idx.superclass],
  #                           class=temp[idx.class],
  #                           subclass=temp[idx.subclass],
  #                           stringsAsFactors = F)
  #
  # idx.na <- apply(temp_result, 2, function(x){
  #   temp <- which(nchar(x)==0)
  # })
  #
  # for (i in 1:6) {
  #   if (length(idx.na[[i]]) > 0 ) {
  #     temp_result[idx.na[[i]],i] <- NA
  #   }
  # }
  #
  # temp_result
}