Fix grouping tool broken in 7347d75a4a / fd85979a86, and enhance performance when removing lines.

tools/stats/grouping.py

@@ -38,19 +38,20 @@ def main():
     round_val = []
 
     if sys.argv[5] != "None":
-        oldfile = open(inputfile, 'r')
-        oldfilelines = oldfile.readlines()
-        newinputfile = "input_cleaned.tsv"
-        newfile = open(newinputfile, 'w')
-        asciitodelete = sys.argv[5].split(',')
-        for i in range(len(asciitodelete)):
-            asciitodelete[i] = chr(int(asciitodelete[i]))
-        for line in oldfilelines:
-            if line[0] not in asciitodelete:
-                newfile.write(line)
-        oldfile.close()
-        newfile.close()
-        inputfile = newinputfile
+        asciitodelete = sys.argv[5]
+        if asciitodelete:
+            oldfile = open(inputfile, 'r')
+            newinputfile = "input_cleaned.tsv"
+            newfile = open(newinputfile, 'w')
+            asciitodelete = asciitodelete.split(',')
+            for i in range(len(asciitodelete)):
+                asciitodelete[i] = chr(int(asciitodelete[i]))
+            for line in oldfile:
+                if line[0] not in asciitodelete:
+                    newfile.write(line)
+            oldfile.close()
+            newfile.close()
+            inputfile = newinputfile
 
     for var in sys.argv[6:]:
         op, col, do_round = var.split()

tools/stats/grouping.xml

@@ -1,12 +1,12 @@
-<tool id="Grouping1" name="Group" version="2.1.0">
+<tool id="Grouping1" name="Group" version="2.1.1">
   <description>data by a column and perform aggregate operation on other columns.</description>
   <command interpreter="python">
     grouping.py 
-      $out_file1
-      $input1
-      $groupcol
-      $ignorecase
-      $ignorelines
+      "${out_file1}"
+      "${input1}"
+      "${groupcol}"
+      "${ignorecase}"
+      "${ignorelines}"
       #for $op in $operations
        '${op.optype}
         ${op.opcol}