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annotate rank_terms.py @ 29:fb944979bf35

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Update to Miller Lab devshed revision 5f0be4d1db30
author Richard Burhans <burhans@bx.psu.edu>
date Thu, 25 Jul 2013 12:01:47 -0400
parents 8997f2ca8c7a
children
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27
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1 #!/usr/bin/env python
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2 # -*- coding: utf-8 -*-
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3 #
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4 # GOFisher.py
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5 #
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6 # Copyright 2013 Oscar Reina <oscar@niska.bx.psu.edu>
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7 #
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8 # This program is free software; you can redistribute it and/or modify
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9 # it under the terms of the GNU General Public License as published by
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10 # the Free Software Foundation; either version 2 of the License, or
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11 # (at your option) any later version.
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12 #
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13 # This program is distributed in the hope that it will be useful,
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14 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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15 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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16 # GNU General Public License for more details.
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17 #
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18 # You should have received a copy of the GNU General Public License
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19 # along with this program; if not, write to the Free Software
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20 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
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21 # MA 02110-1301, USA.
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22
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23 import argparse
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24 import os
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25 import sys
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26 from fisher import pvalue as fisher
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27 from decimal import Decimal,getcontext
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28 from math import lgamma,exp,factorial
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29
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30 def binProb(SAPs_GO,NoSAPs_GO,SAPs_all,NoSAPs_all,CntGO_All,totalSAPs,pGO):
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31 """
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32 Returns binomial probability.
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33 """
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34 def comb(CntGO_All,k):
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35 return factorial(CntGO_All) / Decimal(str(factorial(k)*factorial(CntGO_All-k)))
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36 probLow = 0
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37 for k in range(0, SAPs_GO+1):
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38 cp=Decimal(str(comb(CntGO_All,k)))
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39 bp=Decimal(str(pGO**k))
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40 dp=Decimal(str(1.0-pGO))**Decimal(str(CntGO_All-k))
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41 probLow+=cp*bp*dp
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42 #~
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43 probHigh = 0
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44 for k in range(int(SAPs_GO),CntGO_All+1):
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45 cp=Decimal(str(comb(CntGO_All,k)))
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46 bp=Decimal(str(pGO**k))
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47 dp=Decimal(str(1.0-pGO))**Decimal(str(CntGO_All-k))
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48 probHigh+=cp*bp*dp
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49 return probLow,probHigh
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50
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51 def gauss_hypergeom(X, CntGO_All, SAPs_all, totalSAPs):
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52 CntGO_All,SAPs_all,totalSAPs
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53 """
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54 Returns the probability of drawing X successes of SAPs_all marked items
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55 in CntGO_All draws from a bin of totalSAPs total items
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56 """
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57 def logchoose(ni, ki):
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58 try:
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59 lgn1 = lgamma(ni+1)
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60 lgk1 = lgamma(ki+1)
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61 lgnk1 = lgamma(ni-ki+1)
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62 except ValueError:
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63 raise ValueError
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64 return lgn1 - (lgnk1 + lgk1)
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65 #~
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66 r1 = logchoose(SAPs_all, X)
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67 try:
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68 r2 = logchoose(totalSAPs-SAPs_all, CntGO_All-X)
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69 except ValueError:
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70 return 0
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71 r3 = logchoose(totalSAPs,CntGO_All)
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72 return exp(r1 + r2 - r3)
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73
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74 def hypergeo_sf(SAPs_GO,NoSAPs_GO,SAPs_all,NoSAPs_all,CntGO_All,totalSAPs,pGO):
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75 """
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76 Runs Hypergeometric probability test
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77 """
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78 s = 0
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79 t=0
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80 for i in range(SAPs_GO,min(SAPs_all,CntGO_All)+1):
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81 s += max(gauss_hypergeom(i,CntGO_All,SAPs_all,totalSAPs), 0.0)
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82 for i in range(0, SAPs_GO+1):
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83 t += max(gauss_hypergeom(i,CntGO_All,SAPs_all,totalSAPs), 0.0)
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84 return min(max(t,0.0), 1),min(max(s,0.0), 1)
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85
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86 def fisherexct(SAPs_GO,NoSAPs_GO,SAPs_all,NoSAPs_all,CntGO_All,totalSAPs,pGO):
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87 """
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88 Runs Fisher's exact test
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89 """
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90 ftest=fisher(SAPs_GO,NoSAPs_GO,SAPs_all,NoSAPs_all)
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91 probLow,probHigh=ftest.left_tail,ftest.right_tail
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92 return probLow,probHigh
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93
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94 def rtrnGOcENSEMBLc(inExtnddfile,columnENSEMBLTExtndd,columnGOExtndd):
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95 """
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96 """
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97 dGOTENSEMBLT={}
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98 for eachl in open(inExtnddfile,'r'):
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99 if eachl.strip():
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100 ENSEMBLT=eachl.splitlines()[0].split('\t')[columnENSEMBLTExtndd]
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101 GOTs=set(eachl.splitlines()[0].split('\t')[columnGOExtndd].split('.'))
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102 GOTs=GOTs.difference(set(['','U','N']))
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103 for GOT in GOTs:
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104 try:
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105 dGOTENSEMBLT[GOT].add(ENSEMBLT)
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106 except:
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107 dGOTENSEMBLT[GOT]=set([ENSEMBLT])
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108 ENSEMBLTGinGO=set.union(*dGOTENSEMBLT.values())
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109 return dGOTENSEMBLT,ENSEMBLTGinGO
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110
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111 def rtrnENSEMBLcSAPs(inSAPsfile,columnENSEMBLT,ENSEMBLTGinGO):
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112 """
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113 returns a set of the ENSEMBLT codes present in the input list and
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114 in the GO file
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115 """
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116 sENSEMBLTSAPsinGO=set()
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117 for eachl in open(inSAPsfile,'r'):
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118 ENSEMBLT=eachl.splitlines()[0].split('\t')[columnENSEMBLT]
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119 if ENSEMBLT in ENSEMBLTGinGO:
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120 sENSEMBLTSAPsinGO.add(ENSEMBLT)
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121 return sENSEMBLTSAPsinGO
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122
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123 def rtrnCounts(dGOTENSEMBLT,ENSEMBLTGinGO,sENSEMBLTSAPsinGO,statsTest):
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124 """
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125 returns a list of the ENSEMBLT codes present in the input list and
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126 in the GO file. The terms in this list are: 'Go Term','# Genes in
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127 the GO Term','# Genes in the list and in the GO Term','Enrichement
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128 of the GO Term for genes in the input list','Genes in the input list
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diff changeset
129 present in the GO term'
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130 """
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131 totalSAPs=len(ENSEMBLTGinGO)
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132 SAPs_all=len(sENSEMBLTSAPsinGO)
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133 NoSAPs_all=totalSAPs-SAPs_all
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134 pGO=SAPs_all/float(totalSAPs)
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135 #~
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136 lp=len(dGOTENSEMBLT)
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137 cnt=0
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138 #~
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139 if statsTest=='fisher':
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140 ptest=fisherexct
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141 elif statsTest=='hypergeometric':
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142 ptest=hypergeo_sf
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143 elif statsTest=='binomial':
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144 ptest=binProb
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145 #~
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146 ltfreqs=[]
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147 for echGOT in dGOTENSEMBLT:
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148 cnt+=1
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149 CntGO_All=len(dGOTENSEMBLT[echGOT])
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150 SAPs_GO=len(dGOTENSEMBLT[echGOT].intersection(sENSEMBLTSAPsinGO))
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151 NoSAPs_GO=CntGO_All-SAPs_GO
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152 probLow,probHigh=ptest(SAPs_GO,NoSAPs_GO,SAPs_all,NoSAPs_all,CntGO_All,totalSAPs,pGO)
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153 ltfreqs.append([(SAPs_GO/Decimal(CntGO_All)),SAPs_GO,probLow,probHigh,echGOT])
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154 #~
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155 ltfreqs.sort()
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156 ltfreqs.reverse()
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157 outl=[]
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158 cper,crank=Decimal('2'),0
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159 #~
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160 getcontext().prec=2#set 2 decimal places
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161 for perc,cnt_go,pvalLow,pvalHigh,goTerm in ltfreqs:
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diff changeset
162 if perc<cper:
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163 crank+=1
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164 cper=perc
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165 outl.append('\t'.join([str(cnt_go),str(Decimal(perc)*Decimal('1.0')),str(crank),str(Decimal(pvalLow)*Decimal('1.0')),str(Decimal(pvalHigh)*Decimal('1.0')),goTerm]))
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166 #~
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167 return outl
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168
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169
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170 def main():
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171 #~
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172 parser = argparse.ArgumentParser(description='Returns the count of genes in GO categories and their statistical overrrepresentation, from a list of genes and an extended file (i.e. plane text with ENSEMBLT and GO terms).')
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diff changeset
173 parser.add_argument('--input',metavar='input TXT file',type=str,help='the input file with the table in txt format.',required=True)
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diff changeset
174 parser.add_argument('--inExtnddfile',metavar='input TXT file',type=str,help='the input file with the extended table in txt format.',required=True)
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diff changeset
175 parser.add_argument('--output',metavar='output TXT file',type=str,help='the output file with the table in txt format.',required=True)
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diff changeset
176 parser.add_argument('--columnENSEMBLT',metavar='column number',type=int,help='column with the ENSEMBL transcript code in the input file.',required=True)
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177 parser.add_argument('--columnENSEMBLTExtndd',metavar='column number',type=int,help='column with the ENSEMBL transcript code in the extended file.',required=True)
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diff changeset
178 parser.add_argument('--columnGOExtndd',metavar='column number',type=int,help='column with the GO terms in the extended file.',required=True)
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diff changeset
179 parser.add_argument('--statsTest',metavar='input TXT file',type=str,help='statistical test to compare GO terms (i.e. fisher, hypergeometric, binomial).',required=True)
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diff changeset
180
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diff changeset
181 args = parser.parse_args()
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diff changeset
182
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diff changeset
183 inSAPsfile = args.input
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diff changeset
184 inExtnddfile = args.inExtnddfile
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185 saleGOPCount = args.output
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diff changeset
186 columnENSEMBLT = args.columnENSEMBLT
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diff changeset
187 columnENSEMBLTExtndd = args.columnENSEMBLTExtndd
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diff changeset
188 columnGOExtndd = args.columnGOExtndd
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diff changeset
189 statsTest = args.statsTest
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diff changeset
190
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diff changeset
191 #~
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diff changeset
192 dGOTENSEMBLT,ENSEMBLTGinGO=rtrnGOcENSEMBLc(inExtnddfile,columnENSEMBLTExtndd,columnGOExtndd)
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diff changeset
193 sENSEMBLTSAPsinGO=rtrnENSEMBLcSAPs(inSAPsfile,columnENSEMBLT,ENSEMBLTGinGO)
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diff changeset
194 outl=rtrnCounts(dGOTENSEMBLT,ENSEMBLTGinGO,sENSEMBLTSAPsinGO,statsTest)
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diff changeset
195 #~
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diff changeset
196 saleGOPCount=open(saleGOPCount,'w')
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diff changeset
197 saleGOPCount.write('\n'.join(outl))
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diff changeset
198 saleGOPCount.close()
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diff changeset
199 #~
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diff changeset
200 return 0
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parents: 24
diff changeset
201
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diff changeset
202 if __name__ == '__main__':
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diff changeset
203 main()
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parents: 24
diff changeset
204