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attachWelchpValue.py
executable file
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attachWelchpValue.py
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#!/usr/bin/env python
'''
attach welch t-test (two groups) p-value to new col
Albert W. Cheng
Annotated Mar 7 2009
Copyright 2010 Wu Albert Cheng <albertwcheng@gmail.com>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
'''
import warnings;
warnings.simplefilter("ignore",DeprecationWarning)
import welchttest;
import sys;
from getopt import getopt;
def attachWelchpValue(filename,cols1,cols2,startRow1,sortByFDR):
fin=open(filename);
lino=0;
pvaluesMap=dict()
orderedAsInFile=[]
#[pvalue][ [line,p-value,FDR] ]
for line in fin:
line=line.strip();
lino+=1;
if lino<startRow1:
print >> sys.stdout, line, "\tWelch p-value\tWelch FDR";
continue;
spliton=line.split("\t");
arr1=[];
arr2=[];
for i0 in cols1:
try:
arr1.append(float(spliton[i0]));
except:
pass
for i0 in cols2:
try:
arr2.append(float(spliton[i0]));
except:
pass
try:
welchRes=welchttest.welchs_approximate_ttest_arr(arr1,arr2);
pval=welchRes[3];
except:
pval=1.0
try:
copvalues=pvaluesMap[pval]
except KeyError:
copvalues=[]
pvaluesMap[pval]=copvalues
thisEntry=[line,pval,0]
copvalues.append(thisEntry)
orderedAsInFile.append(thisEntry)
#print >> sys.stdout, line, "\t", str(pval);
fin.close();
totalEntry=len(orderedAsInFile)
nAlready=0
#Now cal FDR and output
sortedpvalues=pvaluesMap.keys()
sortedpvalues.sort()
for pval in sortedpvalues:
copvalues=pvaluesMap[pval]
lcopvalues=len(copvalues)
nAlready+=lcopvalues
FDR=totalEntry*float(pval)/nAlready
for copvalue in copvalues:
copvalue[2]=FDR
if sortByFDR:
for pval in sortedpvalues:
copvalues=pvaluesMap[pval]
for copvalue in copvalues:
line,pval,FDR=copvalue
print >> sys.stdout, line+"\t"+str(pval)+"\t"+str(FDR)
else:
for line,pval,FDR in orderedAsInFile:
print >> sys.stdout, line+"\t"+str(pval)+"\t"+str(FDR)
programName=sys.argv[0]
if(len(sys.argv)<5):
print >>sys.stderr, "Usage: "+str(programName)+"-[s] filename [cols1,..] [cols2,...] startRow1";
print >>sys.stderr, "Options:"
print >> sys.stderr,"-s sort by p-value"
exit();
optlist, args=getopt(sys.argv[1:],'s')
sortByFDR=False
for k,v in optlist:
if k=='-s':
sortByFDR=True
cols1=[];
cols2=[];
colstr=args[1].split(",");
for s in colstr:
cols1.append(int(s)-1);
colstr=args[2].split(",");
for s in colstr:
cols2.append(int(s)-1);
attachWelchpValue(args[0],cols1,cols2,int(args[3]),sortByFDR);