R/exportAsTransfacFile.R

In alyst/MotIV: Motif Identification and Validation

# exportAsTransfacFile <- function (x, file)
# { 
  # if (class(x)!="motiv")
  # {stop("motiv must be an object of class motiv.")}

  # transfac <- file (paste(file, "_matched.txt", sep=""), "w") #PWMs found
  # pairs <-   file (paste(file, "_match_pairs.txt", sep=""), "w") #alignments

  # for (i in 1:length(x@input))
  # {
    # writeChar(paste(">\t", names(x@input)[i], "\n", sep=""), pairs, eos=NULL)
    # for (j in 1:length(x@bestMatch[[i]]@aligns))
    # {
      # writeChar(paste(x@bestMatch[[i]]@aligns[[j]]@TF@name, "\t", format(x@bestMatch[[i]]@aligns[[j]]@evalue, digits=5, scientific=T), "\t", x@bestMatch[[i]]@aligns[[j]]@sequence, "\t", x@bestMatch[[i]]@aligns[[j]]@match, "\n", sep=""), pairs, eos=NULL)
      # writeChar(paste("DE\t", x@bestMatch[[i]]@aligns[[j]]@TF@name,"\n", sep=""), transfac, eos=NULL)
      # pwm <- format( round(x@bestMatch[[i]]@aligns[[j]]@TF@pwm,4), digits=4)
      # for (l in 1:dim(x@bestMatch[[i]]@aligns[[j]]@TF@pwm)[2])
      # {
        # writeChar(paste(c(l-1, pwm[(4*l-4+1):(4*l)]), c("\t","\t","\t","\t","\n"), sep=""), transfac, eos=NULL)
      # }
      # writeChar("XX\n", transfac, eos=NULL)
    # }

  # }
  # close(transfac)
  # close(pairs)
  # print(paste(file,"_matched_transfac.txt created.", sep=""))
  # print(paste(file,"_match_pairs.txt created.", sep=""))
# }


# exportAsTransfacFile <- function (x, file)
# { 
  # transfac <- file (file, "w") 
  # for (i in 1:length(x))
  # {
      # writeChar(paste("DE\t", names(x)[i],"\n", sep=""), transfac, eos=NULL)
      # pwm <- format( round(x[[i]],4), digits=4)
      # for (l in 1:dim(pwm)[2])
      # {
        # writeChar(paste(c(l-1, pwm[(4*l-4+1):(4*l)]), c("\t","\t","\t","\t","\n"), sep=""), transfac, eos=NULL)
      # }
      # writeChar("XX\n", transfac, eos=NULL)
  
  # }
  # close(transfac)
# }