From e75d08841366b1eb36d92347ced348beb1be8241 Mon Sep 17 00:00:00 2001
From: Guruprasad Anada <gua110@bx.psu.edu>
Date: Thu, 5 Jul 2007 16:51:53 +0000
Subject: [PATCH] Forgot to add tool_conf.xml.sample. Also adding a small
 change to the tool code file.

---
 tool_conf.xml.sample    |   1 +
 tools/stats/grouping.py | 101 +++++++++++++++++++++++-----------------
 2 files changed, 58 insertions(+), 44 deletions(-)

diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index fc8ff6038a1..0abda398e91 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -45,6 +45,7 @@
     <tool file="filters/tailWrapper.xml" />
   </section>
   <section name="Filter, Sort, Join, Compare, Subtract" id="filter">
+  	<tool file="stats/grouping.xml" />
     <tool file="stats/filtering.xml" />
     <tool file="filters/sorter.xml" />
     <tool file="filters/grep.xml" />
diff --git a/tools/stats/grouping.py b/tools/stats/grouping.py
index 302b1bfff5b..5b6c28bc6af 100644
--- a/tools/stats/grouping.py
+++ b/tools/stats/grouping.py
@@ -15,22 +15,31 @@ for var in sys.argv[4:]:
     ops.append(var.split()[0])
     cols.append(var.split()[1])
 
+if os.path.exists( inputfile ):
+    for line in open( inputfile ):
+        line = line.strip()
+        if line and not line.startswith( '#' ):
+            elems = line.split( '\t' )
+            break
+else:
+    print 'The data file you selected for filtering does not exist.'
+    sys.exit()
+    
 groupcol = string.atoi(sys.argv[3])
-if groupcol > len( open(inputfile).readline().split('\t') ):
+if groupcol > len( elems ):
     print >> sys.stderr, "Column %d does not exist." %(groupcol)
     sys.exit()
 groupcol = groupcol-1
 
 for k,col in enumerate(cols):
     col = int(col)
-    flds = open(inputfile).readline().split('\t')
-    if col > len( flds ):
+    if col > len( elems ):
         print >> sys.stderr, "Column %d does not exist." %(col)
         sys.exit()
     else:
         if ops[k] != "c":
             try:
-                assert float(flds[col-1])
+                assert float(elems[col-1])
             except:
                 print >> sys.stderr, "Operation '%s' cannot be performed on non-numeric column %d." %(ops[k],col)
                 sys.exit()
@@ -50,46 +59,50 @@ first_invalid_line = 0
 invalid_line = None
 
 for line in open(tmpfile.name):
-    fields = line.split("\t")
-    item = fields[groupcol]
-    if previtem != "":
-        if item == previtem:    #Keep iterating and storing values till a new item is encountered.
-            previtem = item
-            for i,col in enumerate(cols):
-                col = string.atoi(col)
-                col = col-1
-                prevvals[i].append(fields[col].strip())
-        else:   #When a new item is encountered, write the previous item and the corresponding aggregate values into the output file.
-            outstr = previtem
-            try:
-                for i,op in enumerate(ops):
-                    rfunc = "r." + op 
-                    if op != 'c':
-                        for j,elem in enumerate(prevvals[i]):
-                            prevvals[i][j] = float(elem)
-                        rout = "%.2f" %(eval(rfunc)(prevvals[i]))
-                    else:
-                        rout = eval(rfunc)(prevvals[i])
-                    outstr += "\t" + str(rout)
-                print >>fout, outstr
-            except:
-                skipped_lines += 1
-            previtem = item   
-            prevvals = [] 
-            for col in cols:
-                col = string.atoi(col)
-                col = col-1
-                vallist = []
-                vallist.append(fields[col].strip())
-                prevvals.append(vallist)
-    else:           #visited only once right at the start of the iteration.
-        previtem = item
-        for col in cols:
-            col = string.atoi(col)
-            col = col-1
-            vallist = []
-            vallist.append(fields[col].strip())
-            prevvals.append(vallist)
+    if line and (not line.startswith( '#' )) and line != '':
+        try:
+            fields = line.split("\t")
+            item = fields[groupcol]
+            if previtem != "":
+                if item == previtem:    #Keep iterating and storing values till a new item is encountered.
+                    previtem = item
+                    for i,col in enumerate(cols):
+                        col = string.atoi(col)
+                        col = col-1
+                        prevvals[i].append(fields[col].strip())
+                else:   #When a new item is encountered, write the previous item and the corresponding aggregate values into the output file.
+                    outstr = previtem
+                    try:
+                        for i,op in enumerate(ops):
+                            rfunc = "r." + op 
+                            if op != 'c':
+                                for j,elem in enumerate(prevvals[i]):
+                                    prevvals[i][j] = float(elem)
+                                rout = "%.2f" %(eval(rfunc)(prevvals[i]))
+                            else:
+                                rout = eval(rfunc)(prevvals[i])
+                            outstr += "\t" + str(rout)
+                        print >>fout, outstr
+                    except:
+                        skipped_lines += 1
+                    previtem = item   
+                    prevvals = [] 
+                    for col in cols:
+                        col = string.atoi(col)
+                        col = col-1
+                        vallist = []
+                        vallist.append(fields[col].strip())
+                        prevvals.append(vallist)
+            else:           #visited only once right at the start of the iteration.
+                previtem = item
+                for col in cols:
+                    col = string.atoi(col)
+                    col = col-1
+                    vallist = []
+                    vallist.append(fields[col].strip())
+                    prevvals.append(vallist)
+        except:
+            pass
 
 outstr = previtem
 for i,op in enumerate(ops):