From 87a68ea595bd0e5f76de4496dab29d8ad84cd7c3 Mon Sep 17 00:00:00 2001
From: Wen-Yu Chung <wychung@bx.psu.edu>
Date: Fri, 14 Nov 2008 13:21:02 -0500
Subject: [PATCH] update poisson test tool for R warnings.

---
 tools/taxonomy/poisson2test.py  | 5 +++--
 tools/taxonomy/poisson2test.xml | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/tools/taxonomy/poisson2test.py b/tools/taxonomy/poisson2test.py
index f3e64e9d0c1..0b31367605d 100644
--- a/tools/taxonomy/poisson2test.py
+++ b/tools/taxonomy/poisson2test.py
@@ -5,7 +5,7 @@ from math import *
 from rpy import *
 
 
-if ((len(sys.argv)-1) != 5):
+if ((len(sys.argv)-1) != 6):
     print 'too few parameters' 
     print 'usage: inputfile, col1, col2, d-value(not 0), p-val correction method(0 or 1)'
     sys.exit()
@@ -21,6 +21,7 @@ try:
     j = int(sys.argv[3]) #second colum to compare
     d = float(sys.argv[4]) #correction factor
     k = int(sys.argv[5]) #p-val correction method
+    outfile = open(sys.argv[6],'w') # output data
     
     if (i>j):
         print 'column order not correct col1 < col2'
@@ -114,7 +115,7 @@ else:
 
 #printing all columns
 for n in range(fsize):
-    print "%s\t%4.3f\t%4.3f\t%8.6f\t%8.6f\t%8.6f\t%8.6f" %(lines_arr[n].strip(),z1[n],z2[n],pz1[n],pz2[n],corrz1[n],corrz2[n])
+    print >> outfile, "%s\t%4.3f\t%4.3f\t%8.6f\t%8.6f\t%8.6f\t%8.6f" %(lines_arr[n].strip(),z1[n],z2[n],pz1[n],pz2[n],corrz1[n],corrz2[n])
 
 
       
diff --git a/tools/taxonomy/poisson2test.xml b/tools/taxonomy/poisson2test.xml
index d7af0cb1ad5..57d2b0791a1 100644
--- a/tools/taxonomy/poisson2test.xml
+++ b/tools/taxonomy/poisson2test.xml
@@ -1,6 +1,6 @@
 <tool id="poisson2test" name="Poisson two-sample test" version="1.0.0">
   <description></description>
-  <command interpreter="python">poisson2test.py $input1 $input2 $input3 $input4 $input5 > $output1 </command>
+  <command interpreter="python">poisson2test.py $input1 $input2 $input3 $input4 $input5 $output1 2>/dev/null </command>
   <inputs>
     <param name="input1" format="tabular" type="data" label="Input File"/>
     <param name="input2" type="integer" size="5" value="2" label="First Column"/>