--- a
+++ b/scripts/template1.R
@@ -0,0 +1,828 @@
+require(data.table)
+
+cbindPad <- function(...){
+  args <- list(...)
+  n <- sapply(args,nrow)
+  mx <- max(n)
+  pad <- function(x, mx){
+    if (nrow(x) < mx){
+      nms <- colnames(x)
+      padTemp <- matrix(NA, mx - nrow(x), ncol(x))
+      colnames(padTemp) <- nms
+      if (ncol(x)==0) {
+        return(padTemp)
+      } else {
+        return(rbind(x,padTemp))
+      }
+    }
+    else{
+      return(x)
+    }
+  }
+  rs <- lapply(args,pad,mx)
+  return(do.call(cbind,rs))
+}
+
+numbo <- 3
+
+
+if (numbo <= 0) {
+  str2 <- paste("clust_", numbo, ".txt", sep = "")
+}
+setwd("/media/hdd0/unraiddisk1/student/neilm/primestmp/clusters")
+
+res <- try(read.table(str2),silent = TRUE)
+if (!inherits(res, 'try-error')) {
+  b <- read.table(str2)
+  b <- b[,2, drop = F] 
+  b[] <- lapply(b, as.character)
+  b[] <- lapply(b, tolower)
+  
+  l <- as.data.frame(matrix(0, ncol = 1, nrow = (nrow(b))))
+  
+  
+  for (i in 1:nrow(b)) {
+    if (length( unlist(strsplit(unlist(strsplit (b[i,1], "[^[:alnum:]<>=./]")), "(?=[<>=./])", perl = TRUE))) > ncol(l)) {
+      l <- as.data.frame(matrix(0, ncol = length( unlist(strsplit(unlist(strsplit (b[i,1], "[^[:alnum:]<>=./]")), "(?=[<>=./])", perl = TRUE))), nrow = (nrow(b))))
+    }
+    
+  }
+  n <- 1
+  for (i in 1:nrow(b)) {
+    
+    n <- as.numeric(as.numeric(ncol(l)) - as.numeric(length( unlist(strsplit(unlist(strsplit (b[i,1], "[^[:alnum:]<>=./]")), "(?=[<>=./])", perl = TRUE)))))
+    l[i,] <- c( unlist(strsplit(unlist(strsplit (b[i,1], "[^[:alnum:]<>=./]")), "(?=[<>=./])", perl = TRUE)), rep("IGNORE", times = as.numeric(n)))
+  }
+  
+  l <- cbind(l, rep(0, times = nrow(l)))
+  names(l)[ncol(l)] <- "wc"
+  for (i in 1:nrow(l)) {
+    l[i,ncol(l)] <- length(grep("IGNORE", l[i,]))
+  }
+  
+  
+  row1 <- unlist(strsplit(unlist(strsplit(b[which.max(l$wc),1], "[^[:alnum:]<>=./]")), "(?=[<>=./])", perl = TRUE))
+  
+  l <- l[1:(ncol(l)-1)]
+  d <- as.data.frame(matrix(.Machine$double.xmax, ncol = ncol(l), nrow = nrow(l)), stringsAsFactors = F)
+  listo <- rep(.Machine$double.xmax, times = nrow(l))
+  
+  results <- rep('IGNORE', times = ncol(l))
+  n <- 1
+  k <- 1
+  g <- 1
+  p <- 0
+  s <- 1
+  check <- 0
+  ignorecheck <- 0
+  switch01 <- 0
+  while (n <= length(row1)) {
+    while (k <= length(row1)) {
+      p <- 0 
+      if (n > 0) {
+        if (k > 0) {
+          for (i in 1:nrow(l)) {
+            if (i > 0) {
+              for (v in 1:ncol(l)) {
+                for (w in 1:ncol(l)) {  
+                  if (s == 1) {  
+                    if ( ((paste(l[i, v:w], collapse = ' ')) == (paste(row1[n:k], collapse = ' '))) ){
+                      if (w < listo[i]) {  
+                        p <- p + 1
+                        listo[i] <- w
+                        if (n == 1 & v > 1) {
+                          check <- check + 1
+                        }
+                      }
+                    }
+                  }else {
+                    if ( ((paste(l[i, v:w], collapse = ' ')) == (paste(row1[n:k], collapse = ' '))) ){
+                      if (v > d[i,s-1]) {
+                        if (w < listo[i]) {
+                          p <- p + 1
+                          listo[i] <- w
+                        }
+                      }
+                    }
+                  } 
+                } 
+              }
+            }    
+          }
+        }
+      }
+      if (p >= nrow(b)) {
+        results[g] <- paste(row1[n:k], collapse = ' ')
+        if (k == length(row1)) {
+          n <- k
+        }
+        if (k < length(row1)) {
+          k <- k + 1
+        }
+        d[,s] <- listo
+        listo <- rep(.Machine$double.xmax, times = nrow(l))
+        ignorecheck <- ignorecheck + 1
+        switch01 <- 1
+      }
+      if ((p < nrow(b))) {
+        if (n < length(row1)) {
+          if (switch01 == 0) {
+            n <- k + 1
+            k <- n
+          }
+          if (switch01 == 1) {
+            n <- k
+          }
+          g <- g + 2
+          if (d[1,s] != .Machine$double.xmax) {
+            s <- s + 1
+          }
+          listo <- rep(.Machine$double.xmax, times = nrow(l))
+          switch01 <- 0 
+        }
+      }
+      if (n == length(row1)) {
+        n <- n + 1
+        k <- k + 1
+      }
+    }
+  }
+  if (ignorecheck > 0) {
+    results <- unlist(strsplit(results, " "))
+    
+    results <- as.data.frame((results))
+    results <- cbind(results, rep("f", times = nrow(results)))
+    colnames(results)[ncol(results)] <- "tf"
+    results[] <- lapply(results, as.character)
+    results <- results[complete.cases(results),]
+    
+    for (i in 2:nrow(results)) {
+      if (results[i,1] == "IGNORE") {
+        if (results[i,1] == results[(i-1),1]) {
+          results[i,2] <- "t"
+        }
+      }
+    }
+    
+    igcheck <- 0
+    results <- subset(results, tf == "f")  
+    results <- as.data.frame(results[,-(ncol(results))])
+    colnames(results)[1] <- "Template"
+    results <- as.character(results[,1])
+    if (length(results) < ncol(l)) {
+      for (i in (length(results)+1):(ncol(l))) {
+        results[i] <- "IGNORE"
+        igcheck <- 1
+      }
+    }
+    
+    if (check > 0) {
+      results <- c("IGNORE", results)
+    }
+    
+    seq <- as.data.frame(t(as.data.frame(results)))
+    seq <- seq[,(1:(ncol(l)))]
+    seq [] <- lapply(seq, as.character)
+    l[] <- lapply(l, as.character)
+    
+    p <- list(as.character(print(seq[1,])))
+    p <- as.data.frame(p)
+    colnames(p)[1] <- "col1"
+    p <- cbind(p, rep("f", times =nrow(p)))
+    colnames(p)[2] <- "tf"
+    p[,2] <- sapply(p[,2], as.character)
+    for (i in 2:nrow(p)) {
+      if ((trimws(p[i,1], which = "both")) == "IGNORE") {
+        if (p[i,1] == p[(i-1),1])
+          p[i,2] <- "t"
+      }
+    }
+    
+    
+    p <- subset(p, tf == "f")
+    p <- as.character(print(p[,1]))
+    p <- paste(p,collapse=" ")
+    w <- strsplit(p, "IGNORE")
+    w <- as.data.frame(w[[1]])
+    colnames(w)[1] <- "col1"
+    w <- subset(w, col1 != " ")
+    w <- subset(w, col1 != "")
+    w <- as.character(w[,1])
+    w <- gsub(" ","", w)
+    
+    
+    non2 <- as.data.frame(matrix(0, ncol = ncol(l), nrow = nrow(l)), stringsAsFactors = F)
+    d2 <- as.data.frame(matrix("f", ncol = length(w), nrow = nrow(l)), stringsAsFactors = F)
+    
+    non2[] <- lapply(non2, as.numeric)
+    
+    g <- 1 
+    
+    for (j in 1:nrow(l)) {
+      if (j > 0) {
+        for (i in 1:length(w)) {
+          if (i > 0) {
+            for (k in 1:ncol(l)) {
+              for (m in 1:ncol(l)) {
+                if ( (gsub(" ","",paste(l[j,k:m],collapse=" ")) == w[i]) & (d2[j,i] == "f") ){
+                  d2[j,i] <- "t"
+                  if (g == 1) {
+                    non2[j, g] <- k
+                    non2[j, g+1] <- m
+                    g <- g + 2
+                  }else if ((k > as.numeric(non2[j, (g-1)])) & (m > as.numeric(non2[j, (g-1)]))) {
+                    non2[j, g] <- k
+                    non2[j, g+1] <- m
+                    g <- g + 2
+                  }
+                }
+              }
+            }
+          }
+        }
+      }
+      g <- 1
+    }
+    
+    non3 <- as.data.frame(matrix("IGNORE", ncol = ncol(l), nrow = nrow(l)), stringsAsFactors = F)
+    
+    g <- rep(1, times = nrow(non2))
+    f <- 1
+    
+    
+    for (m in 1:nrow(non2)) {
+      q <- as.character(print(non2[m,]))
+      q <- paste(q,collapse=" ")
+      q <- unlist(strsplit(q, " "))
+      x <- 1
+      while (x <= length(q)) {
+        if (q[x] == "0") {
+          q <- q[-x]
+        }else {
+          x <- x + 1
+        }
+      }
+      q <- list(q)
+      q <- as.data.frame(q[[1]])
+      colnames(q)[1] <- "col1"
+      q <- subset(q, col1 != "")
+      q[,1] <- sapply(q[,1], as.character)
+      q[,1] <- sapply(q[,1], as.numeric)
+      i <- 1
+      while (i <= nrow(q)) {
+        if (i == 1) { 
+          if (as.numeric(q[i,1]-1) >=1) {
+            non3[m,g[m]] <- paste(as.character(l[m,1:(as.numeric(q[i,1]-1))]), collapse = " ")
+            g[m] <- g[m] + 1
+          }else {
+            g[m] <- 2
+          }
+        }
+        if ((i %% 2 == 0) & (i != nrow(q)) & ((as.numeric(q[i+1,1]-1)) >= (as.numeric(q[i,1]+1)))) {
+          non3[m,g[m]] <- paste(as.character(l[m,(as.numeric(q[i,1]+1)):(as.numeric(q[i+1,1]-1))]), collapse = " ")
+          g[m] <- g[m] + 1
+        }
+        if ((i %% 2 == 0) & (i != nrow(q)) & ((as.numeric(q[i+1,1]-1)) < (as.numeric(q[i,1]+1)))) {
+          g[m] <- g[m] + 1
+        }
+        if ((i %% 2 == 0) & (i == nrow(q)) & (as.numeric(q[i,1]+1) <= as.numeric(ncol(l)))) {
+          non3[m,g[m]] <- paste(as.character(l[m,(as.numeric(q[i,1]+1)):(as.numeric(ncol(l)))]), collapse = " ")
+          g[m] <- g[m] + 1
+        }
+        if (i < nrow(q)) {
+          i <- i + 1
+        }else {
+          break
+        }
+      }
+    }
+    
+    
+    for (i in 1:ncol(seq)) {
+      if (seq[1,i] == "IGNORE") {
+        seq[1,i] <- "BLANK" 
+      }
+    }
+    
+    non3 <- as.data.frame(t(non3))
+    non3 <- cbind(non3, rep("f", times = nrow(non3)))
+    colnames(non3)[ncol(non3)] <- "tf"
+    non3[] <- lapply(non3, as.character)
+    
+    for (i in 1:nrow(non3)) {
+      if (paste(as.character(print(non3[i,1:(ncol(non3)-1)])), collapse = " ") == paste(as.character(rep("IGNORE", times = ncol(non3)-1)), collapse = " ")) {
+        non3[i,ncol(non3)] <- "t" 
+      }
+    }
+    
+    non3 <- subset(non3, tf == "f")  
+    non3 <- non3[,-(ncol(non3))]
+    non3 <- as.data.frame(t(non3))
+    
+    seq <- as.data.frame(t(seq))
+    seq <- cbind(seq, rep("f", times = nrow(seq)))
+    colnames(seq)[ncol(seq)] <- "tf"
+    seq[] <- lapply(seq, as.character)
+    
+    for (i in 2:nrow(seq)) {
+      if (seq[i,1] == "BLANK") {
+        if (seq[i,1] == seq[(i-1),1]) {
+          seq[i,2] <- "t"
+        }
+      }
+    }
+    
+    if (seq[nrow(seq),1] == "BLANK") {
+      if (igcheck == 1) {
+        seq[nrow(seq),2] <- "t" 
+      }
+    }
+    
+    seq <- subset(seq, tf == "f")  
+    seq <- as.data.frame(seq[,-(ncol(seq))])
+    
+    
+    
+    
+    colnames(seq)[1] <- "Template"
+    seq <- as.data.frame(t(seq))
+    
+    
+    template <- seq
+    
+    
+    
+    fillins <- non3
+    
+    if (ncol(non3) > 0) {
+      
+      for (j in 1:ncol(fillins)) {
+        fillinstest <- as.character(fillins[,j])
+        for (i in 1:length(fillinstest)) {
+          fillinstest[i] <- gsub("IGNORE", "", fillinstest[i])
+        }
+        fillins[,j] <- fillinstest
+      }
+      
+      
+      
+      i <- 1
+      while (i <=  ncol(fillins)) {
+        fillins <- as.data.frame(cbind (fillins[,c(1:i)], rep(1, times = nrow(fillins)), fillins[,-c(1:i)]))
+        i <- i+ 2
+      }
+      
+      for (i in 1:ncol(fillins)) {
+        if (i %% 2 == 0) {
+          colnames(fillins)[i] <- "Frequency"
+          fillins[,i] <- sapply(fillins[,i], as.character)
+          fillins[,i] <- sapply(fillins[,i], as.numeric)
+        }
+      }
+      for (i in 1:ncol(fillins)) {
+        if (i %% 2 == 1) {
+          colnames(fillins)[i] <- paste("Blank", (i+1)/2, collapse ="")
+          fillins[,i] <- sapply(fillins[,i], as.character)
+        }
+      }
+      for (j in 1:ncol(fillins)) {
+        for (i in 1:nrow(fillins)) {
+          if (j %% 2 == 1) {
+            for (k in 1:i) {
+              if (k < i) {
+                if (trimws(fillins[i, j], which = "both") == trimws(fillins[k,j], which = "both")) {
+                  fillins[k, j+1] <- fillins[k, j+1] + 1
+                  fillins[i, j] <- paste("IGNORE", i, collapse ="")
+                  fillins[i, j + 1] <- 0 
+                }
+              }
+            }
+          }
+        }
+      }
+      
+    }
+    
+  } else {
+    template <- fillins <- as.data.frame(matrix("", ncol = 1, nrow = 1))
+  }
+  
+  
+  template <- cbindPad(template, b)
+  fillins <- cbindPad(fillins, b)
+  names(template)[ncol(template)] <- "Cluster Text"
+  names(fillins)[ncol(fillins)] <- "Cluster Text"
+  setwd("/media/hdd0/unraiddisk1/student/neilm/primestmp/clusters") 
+  numbochar <- as.character(numbo)
+  numbotempstr <- paste("template", numbochar, ".csv", sep = "")
+  numbofillinsstr <- paste("fillins", numbochar, ".csv", sep = "")
+  write.csv(template, file = numbotempstr, row.names = F)
+  write.csv(fillins, file = numbofillinsstr, col.names = F)
+  
+}
+numbo <- numbo + 1
+
+
+
+
+
+while (numbo <= (750)) {
+  
+  if (numbo <= 750) {
+    str2 <- paste("clust_", numbo, ".txt", sep = "")
+  }
+  setwd("/media/hdd0/unraiddisk1/student/neilm/primestmp/clusters")
+  
+  res <- try(read.table(str2),silent = TRUE)
+  
+  if (!inherits(res, 'try-error')) {
+    b <- read.table(str2)
+    b <- b[,2, drop = F] 
+    b[] <- lapply(b, as.character)
+    b[] <- lapply(b, tolower)
+    
+    l <- as.data.frame(matrix(0, ncol = 1, nrow = (nrow(b))))
+    
+    
+    for (i in 1:nrow(b)) {
+      if (length( unlist(strsplit(unlist(strsplit (b[i,1], "[^[:alnum:]<>=./]")), "(?=[<>=./])", perl = TRUE))) > ncol(l)) {
+        l <- as.data.frame(matrix(0, ncol = length( unlist(strsplit(unlist(strsplit (b[i,1], "[^[:alnum:]<>=./]")), "(?=[<>=./])", perl = TRUE))), nrow = (nrow(b))))
+      }
+      
+    }
+    n <- 1
+    for (i in 1:nrow(b)) {
+      
+      n <- as.numeric(as.numeric(ncol(l)) - as.numeric(length( unlist(strsplit(unlist(strsplit (b[i,1], "[^[:alnum:]<>=./]")), "(?=[<>=./])", perl = TRUE)))))
+      l[i,] <- c( unlist(strsplit(unlist(strsplit (b[i,1], "[^[:alnum:]<>=./]")), "(?=[<>=./])", perl = TRUE)), rep("IGNORE", times = as.numeric(n)))
+    }
+    
+    l <- cbind(l, rep(0, times = nrow(l)))
+    names(l)[ncol(l)] <- "wc"
+    for (i in 1:nrow(l)) {
+      l[i,ncol(l)] <- length(grep("IGNORE", l[i,]))
+    }
+    
+    
+    row1 <- unlist(strsplit(unlist(strsplit(b[which.max(l$wc),1], "[^[:alnum:]<>=./]")), "(?=[<>=./])", perl = TRUE))
+    
+    l <- l[1:(ncol(l)-1)]
+    d <- as.data.frame(matrix(.Machine$double.xmax, ncol = ncol(l), nrow = nrow(l)), stringsAsFactors = F)
+    listo <- rep(.Machine$double.xmax, times = nrow(l))
+    
+    results <- rep('IGNORE', times = ncol(l))
+    n <- 1
+    k <- 1
+    g <- 1
+    p <- 0
+    s <- 1
+    check <- 0
+    ignorecheck <- 0
+    switch01 <- 0
+    while (n <= length(row1)) {
+      while (k <= length(row1)) {
+        p <- 0 
+        if (n > 0) {
+          if (k > 0) {
+            for (i in 1:nrow(l)) {
+              if (i > 0) {
+                for (v in 1:ncol(l)) {
+                  for (w in 1:ncol(l)) {  
+                    if (s == 1) {  
+                      if ( ((paste(l[i, v:w], collapse = ' ')) == (paste(row1[n:k], collapse = ' '))) ){
+                        if (w < listo[i]) {  
+                          p <- p + 1
+                          listo[i] <- w
+                          if (n == 1 & v > 1) {
+                            check <- check + 1
+                          }
+                        }
+                      }
+                    }else {
+                      if ( ((paste(l[i, v:w], collapse = ' ')) == (paste(row1[n:k], collapse = ' '))) ){
+                        if (v > d[i,s-1]) {
+                          if (w < listo[i]) {
+                            p <- p + 1
+                            listo[i] <- w
+                          }
+                        }
+                      }
+                    } 
+                  } 
+                }
+              }    
+            }
+          }
+        }
+        if (p >= nrow(b)) {
+          results[g] <- paste(row1[n:k], collapse = ' ')
+          if (k == length(row1)) {
+            n <- k
+          }
+          if (k < length(row1)) {
+            k <- k + 1
+          }
+          d[,s] <- listo
+          listo <- rep(.Machine$double.xmax, times = nrow(l))
+          ignorecheck <- ignorecheck + 1
+          switch01 <- 1
+        }
+        if ((p < nrow(b))) {
+          if (n < length(row1)) {
+            if (switch01 == 0) {
+              n <- k + 1
+              k <- n
+            }
+            if (switch01 == 1) {
+              n <- k
+            }
+            g <- g + 2
+            if (d[1,s] != .Machine$double.xmax) {
+              s <- s + 1
+            }
+            listo <- rep(.Machine$double.xmax, times = nrow(l))
+            switch01 <- 0 
+          }
+        }
+        if (n == length(row1)) {
+          n <- n + 1
+          k <- k + 1
+        }
+      }
+    }
+    if (ignorecheck > 0) {
+      results <- unlist(strsplit(results, " "))
+      
+      results <- as.data.frame((results))
+      results <- cbind(results, rep("f", times = nrow(results)))
+      colnames(results)[ncol(results)] <- "tf"
+      results[] <- lapply(results, as.character)
+      results <- results[complete.cases(results),]
+      
+      for (i in 2:nrow(results)) {
+        if (results[i,1] == "IGNORE") {
+          if (results[i,1] == results[(i-1),1]) {
+            results[i,2] <- "t"
+          }
+        }
+      }
+      
+      igcheck <- 0
+      results <- subset(results, tf == "f")  
+      results <- as.data.frame(results[,-(ncol(results))])
+      colnames(results)[1] <- "Template"
+      results <- as.character(results[,1])
+      if (length(results) < ncol(l)) {
+        for (i in (length(results)+1):(ncol(l))) {
+          results[i] <- "IGNORE"
+          igcheck <- 1
+        }
+      }
+      
+      if (check > 0) {
+        results <- c("IGNORE", results)
+      }
+      
+      seq <- as.data.frame(t(as.data.frame(results)))
+      seq <- seq[,(1:(ncol(l)))]
+      seq [] <- lapply(seq, as.character)
+      l[] <- lapply(l, as.character)
+      
+      p <- list(as.character(print(seq[1,])))
+      p <- as.data.frame(p)
+      colnames(p)[1] <- "col1"
+      p <- cbind(p, rep("f", times =nrow(p)))
+      colnames(p)[2] <- "tf"
+      p[,2] <- sapply(p[,2], as.character)
+      for (i in 2:nrow(p)) {
+        if ((trimws(p[i,1], which = "both")) == "IGNORE") {
+          if (p[i,1] == p[(i-1),1])
+            p[i,2] <- "t"
+        }
+      }
+      
+      
+      p <- subset(p, tf == "f")
+      p <- as.character(print(p[,1]))
+      p <- paste(p,collapse=" ")
+      w <- strsplit(p, "IGNORE")
+      w <- as.data.frame(w[[1]])
+      colnames(w)[1] <- "col1"
+      w <- subset(w, col1 != " ")
+      w <- subset(w, col1 != "")
+      w <- as.character(w[,1])
+      w <- gsub(" ","", w)
+      
+      
+      non2 <- as.data.frame(matrix(0, ncol = ncol(l), nrow = nrow(l)), stringsAsFactors = F)
+      d2 <- as.data.frame(matrix("f", ncol = length(w), nrow = nrow(l)), stringsAsFactors = F)
+      
+      non2[] <- lapply(non2, as.numeric)
+      
+      g <- 1 
+      
+      for (j in 1:nrow(l)) {
+        if (j > 0) {
+          for (i in 1:length(w)) {
+            if (i > 0) {
+              for (k in 1:ncol(l)) {
+                for (m in 1:ncol(l)) {
+                  if ( (gsub(" ","",paste(l[j,k:m],collapse=" ")) == w[i]) & (d2[j,i] == "f") ){
+                    d2[j,i] <- "t"
+                    if (g == 1) {
+                      non2[j, g] <- k
+                      non2[j, g+1] <- m
+                      g <- g + 2
+                    }else if ((k > as.numeric(non2[j, (g-1)])) & (m > as.numeric(non2[j, (g-1)]))) {
+                      non2[j, g] <- k
+                      non2[j, g+1] <- m
+                      g <- g + 2
+                    }
+                  }
+                }
+              }
+            }
+          }
+        }
+        g <- 1
+      }
+      
+      non3 <- as.data.frame(matrix("IGNORE", ncol = ncol(l), nrow = nrow(l)), stringsAsFactors = F)
+      
+      g <- rep(1, times = nrow(non2))
+      f <- 1
+      
+      
+      for (m in 1:nrow(non2)) {
+        q <- as.character(print(non2[m,]))
+        q <- paste(q,collapse=" ")
+        q <- unlist(strsplit(q, " "))
+        x <- 1
+        while (x <= length(q)) {
+          if (q[x] == "0") {
+            q <- q[-x]
+          }else {
+            x <- x + 1
+          }
+        }
+        q <- list(q)
+        q <- as.data.frame(q[[1]])
+        colnames(q)[1] <- "col1"
+        q <- subset(q, col1 != "")
+        q[,1] <- sapply(q[,1], as.character)
+        q[,1] <- sapply(q[,1], as.numeric)
+        i <- 1
+        while (i <= nrow(q)) {
+          if (i == 1) { 
+            if (as.numeric(q[i,1]-1) >=1) {
+              non3[m,g[m]] <- paste(as.character(l[m,1:(as.numeric(q[i,1]-1))]), collapse = " ")
+              g[m] <- g[m] + 1
+            }else {
+              g[m] <- 2
+            }
+          }
+          if ((i %% 2 == 0) & (i != nrow(q)) & ((as.numeric(q[i+1,1]-1)) >= (as.numeric(q[i,1]+1)))) {
+            non3[m,g[m]] <- paste(as.character(l[m,(as.numeric(q[i,1]+1)):(as.numeric(q[i+1,1]-1))]), collapse = " ")
+            g[m] <- g[m] + 1
+          }
+          if ((i %% 2 == 0) & (i != nrow(q)) & ((as.numeric(q[i+1,1]-1)) < (as.numeric(q[i,1]+1)))) {
+            g[m] <- g[m] + 1
+          }
+          if ((i %% 2 == 0) & (i == nrow(q)) & (as.numeric(q[i,1]+1) <= as.numeric(ncol(l)))) {
+            non3[m,g[m]] <- paste(as.character(l[m,(as.numeric(q[i,1]+1)):(as.numeric(ncol(l)))]), collapse = " ")
+            g[m] <- g[m] + 1
+          }
+          if (i < nrow(q)) {
+            i <- i + 1
+          }else {
+            break
+          }
+        }
+      }
+      
+      
+      for (i in 1:ncol(seq)) {
+        if (seq[1,i] == "IGNORE") {
+          seq[1,i] <- "BLANK" 
+        }
+      }
+      
+      non3 <- as.data.frame(t(non3))
+      non3 <- cbind(non3, rep("f", times = nrow(non3)))
+      colnames(non3)[ncol(non3)] <- "tf"
+      non3[] <- lapply(non3, as.character)
+      
+      for (i in 1:nrow(non3)) {
+        if (paste(as.character(print(non3[i,1:(ncol(non3)-1)])), collapse = " ") == paste(as.character(rep("IGNORE", times = ncol(non3)-1)), collapse = " ")) {
+          non3[i,ncol(non3)] <- "t" 
+        }
+      }
+      
+      non3 <- subset(non3, tf == "f")  
+      non3 <- non3[,-(ncol(non3))]
+      non3 <- as.data.frame(t(non3))
+      
+      seq <- as.data.frame(t(seq))
+      seq <- cbind(seq, rep("f", times = nrow(seq)))
+      colnames(seq)[ncol(seq)] <- "tf"
+      seq[] <- lapply(seq, as.character)
+      
+      for (i in 2:nrow(seq)) {
+        if (seq[i,1] == "BLANK") {
+          if (seq[i,1] == seq[(i-1),1]) {
+            seq[i,2] <- "t"
+          }
+        }
+      }
+      
+      if (seq[nrow(seq),1] == "BLANK") {
+        if (igcheck == 1) {
+          seq[nrow(seq),2] <- "t" 
+        }
+      }
+      
+      seq <- subset(seq, tf == "f")  
+      seq <- as.data.frame(seq[,-(ncol(seq))])
+      
+      
+      
+      
+      colnames(seq)[1] <- "Template"
+      seq <- as.data.frame(t(seq))
+      
+      
+      template <- seq
+      
+      
+      
+      fillins <- non3
+      
+      if (ncol(non3) > 0) {
+        
+        for (j in 1:ncol(fillins)) {
+          fillinstest <- as.character(fillins[,j])
+          for (i in 1:length(fillinstest)) {
+            fillinstest[i] <- gsub("IGNORE", "", fillinstest[i])
+          }
+          fillins[,j] <- fillinstest
+        }
+        
+        
+        
+        i <- 1
+        while (i <=  ncol(fillins)) {
+          fillins <- as.data.frame(cbind (fillins[,c(1:i)], rep(1, times = nrow(fillins)), fillins[,-c(1:i)]))
+          i <- i+ 2
+        }
+        
+        for (i in 1:ncol(fillins)) {
+          if (i %% 2 == 0) {
+            colnames(fillins)[i] <- "Frequency"
+            fillins[,i] <- sapply(fillins[,i], as.character)
+            fillins[,i] <- sapply(fillins[,i], as.numeric)
+          }
+        }
+        for (i in 1:ncol(fillins)) {
+          if (i %% 2 == 1) {
+            colnames(fillins)[i] <- paste("Blank", (i+1)/2, collapse ="")
+            fillins[,i] <- sapply(fillins[,i], as.character)
+          }
+        }
+        for (j in 1:ncol(fillins)) {
+          for (i in 1:nrow(fillins)) {
+            if (j %% 2 == 1) {
+              for (k in 1:i) {
+                if (k < i) {
+                  if (trimws(fillins[i, j], which = "both") == trimws(fillins[k,j], which = "both")) {
+                    fillins[k, j+1] <- fillins[k, j+1] + 1
+                    fillins[i, j] <- paste("IGNORE", i, collapse ="")
+                    fillins[i, j + 1] <- 0 
+                  }
+                }
+              }
+            }
+          }
+        }
+        
+      }
+      
+    } else {
+      template <- fillins <- as.data.frame(matrix("", ncol = 1, nrow = 1))
+    }
+    
+    
+    template <- cbindPad(template, b)
+    fillins <- cbindPad(fillins, b)
+    names(template)[ncol(template)] <- "Cluster Text"
+    names(fillins)[ncol(fillins)] <- "Cluster Text"
+    setwd("C:/Users/AI/Downloads/PipelineTestRun4PLAY") 
+    numbochar <- as.character(numbo)
+    numbotempstr <- paste("template", numbochar, ".csv", sep = "")
+    numbofillinsstr <- paste("fillins", numbochar, ".csv", sep = "")
+    write.csv(template, file = numbotempstr, row.names = F)
+    write.csv(fillins, file = numbofillinsstr, col.names = F)
+    
+  }
+  numbo <- numbo + 1
+  
+}