Fixes to various tools: scatterplot, cor, grouping

tools/plotting/scatterplot_code.py

@@ -0,0 +1,39 @@
+
+def get_columns( input ):
+    columns = []
+    elems = []
+
+    for i, line in enumerate( file ( input.file_name ) ):
+        valid = True
+        if line and not line.startswith( '#' ): 
+            line = line.rstrip('\r\n')
+            elems = line.split( '\t' )
+    
+            """
+            Since this tool requires users to select only those columns
+            that contain numerical values, we'll restrict the column select
+            list appropriately.
+            """
+            if len(elems) > 0:
+                for col in range(1, input.metadata.columns+1):
+                    try:
+                        val = float(elems[col-1])
+                    except:
+                        val = elems[col-1]
+                        if val:
+                            if val.strip().lower() != "na":
+                                valid = False
+                        else:
+                            valid = False
+                    if valid:
+                        option = "c" + str(col)
+                        columns.append((option,str(col),False))
+            if len(columns) > 0:
+                """
+                We have our select list built, so we can break out of the outer most for loop
+                """
+                break 
+        if i == 30:
+            break # Hopefully we never get here...
+
+    return columns