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update poisson test tool for R warnings.

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This commit is contained in:
Wen-Yu Chung
2008-11-14 13:21:02 -05:00
parent 14fc955efc
commit 87a68ea595
2 changed files with 4 additions and 3 deletions
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tools/taxonomy/poisson2test.py
+3 -2
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@@ -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])
tools/taxonomy/poisson2test.xml
+1 -1
View File
@@ -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"/>