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annotate rank_pathways_pct.py @ 32:03c22b722882

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remove BeautifulSoup dependency
author Richard Burhans <burhans@bx.psu.edu>
date Fri, 20 Sep 2013 13:54:23 -0400
parents 8997f2ca8c7a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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 # KEGGFisher.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 pathways 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_KEGG,NoSAPs_KEGG,SAPs_all,NoSAPs_all,CntKEGG_All,totalSAPs,pKEGG):
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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(CntKEGG_All,k):
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35 return factorial(CntKEGG_All) / Decimal(str(factorial(k)*factorial(CntKEGG_All-k)))
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36 probLow = 0
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37 for k in range(0, SAPs_KEGG+1):
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38 cp=Decimal(str(comb(CntKEGG_All,k)))
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39 bp=Decimal(str(pKEGG**k))
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40 dp=Decimal(str(1.0-pKEGG))**Decimal(str(CntKEGG_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_KEGG),CntKEGG_All+1):
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45 cp=Decimal(str(comb(CntKEGG_All,k)))
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46 bp=Decimal(str(pKEGG**k))
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47 dp=Decimal(str(1.0-pKEGG))**Decimal(str(CntKEGG_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, CntKEGG_All, SAPs_all, totalSAPs):
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52 CntKEGG_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 CntKEGG_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, CntKEGG_All-X)
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69 except ValueError:
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70 return 0
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71 r3 = logchoose(totalSAPs,CntKEGG_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_KEGG,NoSAPs_KEGG,SAPs_all,NoSAPs_all,CntKEGG_All,totalSAPs,pKEGG):
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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_KEGG,min(SAPs_all,CntKEGG_All)+1):
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81 s += max(gauss_hypergeom(i,CntKEGG_All,SAPs_all,totalSAPs), 0.0)
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82 for i in range(0, SAPs_KEGG+1):
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83 t += max(gauss_hypergeom(i,CntKEGG_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_KEGG,NoSAPs_KEGG,SAPs_all,NoSAPs_all,CntKEGG_All,totalSAPs,pKEGG):
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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_KEGG,NoSAPs_KEGG,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 rtrnKEGGcENSEMBLc(inBckgrndfile,columnENSEMBLTBckgrnd,columnKEGGBckgrnd):
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95 """
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96 """
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97 dKEGGTENSEMBLT={}
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98 for eachl in open(inBckgrndfile,'r'):
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99 if eachl.strip():
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100 ENSEMBLT=eachl.splitlines()[0].split('\t')[columnENSEMBLTBckgrnd]
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101 KEGGTs=set(eachl.splitlines()[0].split('\t')[columnKEGGBckgrnd].split('.'))
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102 KEGGTs=KEGGTs.difference(set(['','U','N']))
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103 for KEGGT in KEGGTs:
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104 try:
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105 dKEGGTENSEMBLT[KEGGT].add(ENSEMBLT)
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106 except:
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107 dKEGGTENSEMBLT[KEGGT]=set([ENSEMBLT])
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108 ENSEMBLTGinKEGG=set.union(*dKEGGTENSEMBLT.values())
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109 return dKEGGTENSEMBLT,ENSEMBLTGinKEGG
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110
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111 def rtrnENSEMBLcSAPs(inSAPsfile,columnENSEMBLT,ENSEMBLTGinKEGG):
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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 KEGG file
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115 """
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116 sENSEMBLTSAPsinKEGG=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 ENSEMBLTGinKEGG:
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120 sENSEMBLTSAPsinKEGG.add(ENSEMBLT)
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121 return sENSEMBLTSAPsinKEGG
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122
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123 def rtrnCounts(dKEGGTENSEMBLT,ENSEMBLTGinKEGG,sENSEMBLTSAPsinKEGG,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 KEGG file. The pathways in this list are: 'Go Term','# Genes in
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127 the KEGG Term','# Genes in the list and in the KEGG Term','Enrichement
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128 of the KEGG Term for genes in the input list','Genes in the input list
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129 present in the KEGG term'
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130 """
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131 totalSAPs=len(ENSEMBLTGinKEGG)
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132 SAPs_all=len(sENSEMBLTSAPsinKEGG)
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133 NoSAPs_all=totalSAPs-SAPs_all
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134 pKEGG=SAPs_all/float(totalSAPs)
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135 #~
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136 lp=len(dKEGGTENSEMBLT)
22
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137 cnt=0
27
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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 echKEGGT in dKEGGTENSEMBLT:
22
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148 cnt+=1
27
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149 CntKEGG_All=len(dKEGGTENSEMBLT[echKEGGT])
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150 SAPs_KEGG=len(dKEGGTENSEMBLT[echKEGGT].intersection(sENSEMBLTSAPsinKEGG))
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151 NoSAPs_KEGG=CntKEGG_All-SAPs_KEGG
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152 probLow,probHigh=ptest(SAPs_KEGG,NoSAPs_KEGG,SAPs_all,NoSAPs_all,CntKEGG_All,totalSAPs,pKEGG)
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153 ltfreqs.append([(SAPs_KEGG/Decimal(CntKEGG_All)),SAPs_KEGG,probLow,probHigh,echKEGGT])
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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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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
22
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parents:
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169
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170 def main():
27
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171 #~
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172 parser = argparse.ArgumentParser(description='Returns the count of genes in KEGG categories and their statistical overrrepresentation, from a list of genes and an background file (i.e. plane text with ENSEMBLT and KEGG pathways).')
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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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174 parser.add_argument('--inBckgrndfile',metavar='input TXT file',type=str,help='the input file with the background table in txt format.',required=True)
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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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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('--columnENSEMBLTBckgrnd',metavar='column number',type=int,help='column with the ENSEMBL transcript code in the background file.',required=True)
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178 parser.add_argument('--columnKEGGBckgrnd',metavar='column number',type=int,help='column with the KEGG pathways in the background file.',required=True)
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179 parser.add_argument('--statsTest',metavar='input TXT file',type=str,help='statistical test to compare KEGG pathways (i.e. fisher, hypergeometric, binomial).',required=True)
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180
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181 args = parser.parse_args()
22
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parents:
diff changeset
182
27
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183 inSAPsfile = args.input
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184 inBckgrndfile = args.inBckgrndfile
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185 saleKEGGPCount = args.output
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186 columnENSEMBLT = args.columnENSEMBLT
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187 columnENSEMBLTBckgrnd = args.columnENSEMBLTBckgrnd
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188 columnKEGGBckgrnd = args.columnKEGGBckgrnd
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189 statsTest = args.statsTest
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diff changeset
190 columnENSEMBLT-=1
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diff changeset
191 columnENSEMBLTBckgrnd-=1
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diff changeset
192 columnKEGGBckgrnd=-1
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diff changeset
193 #~
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194 dKEGGTENSEMBLT,ENSEMBLTGinKEGG=rtrnKEGGcENSEMBLc(inBckgrndfile,columnENSEMBLTBckgrnd,columnKEGGBckgrnd)
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195 sENSEMBLTSAPsinKEGG=rtrnENSEMBLcSAPs(inSAPsfile,columnENSEMBLT,ENSEMBLTGinKEGG)
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diff changeset
196 outl=rtrnCounts(dKEGGTENSEMBLT,ENSEMBLTGinKEGG,sENSEMBLTSAPsinKEGG,statsTest)
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diff changeset
197 #~
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diff changeset
198 saleKEGGPCount=open(saleKEGGPCount,'w')
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diff changeset
199 saleKEGGPCount.write('\n'.join(outl))
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diff changeset
200 saleKEGGPCount.close()
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parents: 22
diff changeset
201 #~
22
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parents:
diff changeset
202 return 0
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parents:
diff changeset
203
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parents:
diff changeset
204 if __name__ == '__main__':
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parents:
diff changeset
205 main()
27
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parents: 22
diff changeset
206