annotate rank_pathways_pct.py @ 33:5064f618ec1c

remove munkres dependency
author Richard Burhans <burhans@bx.psu.edu>
date Fri, 20 Sep 2013 14:01:30 -0400
parents 8997f2ca8c7a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
22
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
1 #!/usr/bin/env python
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
2 # -*- coding: utf-8 -*-
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
3 #
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
4 # KEGGFisher.py
22
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
5 #
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
6 # Copyright 2013 Oscar Reina <oscar@niska.bx.psu.edu>
22
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
7 #
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
8 # This program is free software; you can redistribute it and/or modify
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
9 # it under the pathways of the GNU General Public License as published by
22
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
10 # the Free Software Foundation; either version 2 of the License, or
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
11 # (at your option) any later version.
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
12 #
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
13 # This program is distributed in the hope that it will be useful,
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
14 # but WITHOUT ANY WARRANTY; without even the implied warranty of
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
15 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
16 # GNU General Public License for more details.
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
17 #
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
18 # You should have received a copy of the GNU General Public License
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
19 # along with this program; if not, write to the Free Software
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
20 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
21 # MA 02110-1301, USA.
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
22
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
23 import argparse
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
24 import os
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
25 import sys
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
26 from fisher import pvalue as fisher
22
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
27 from decimal import Decimal,getcontext
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
28 from math import lgamma,exp,factorial
22
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
29
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
30 def binProb(SAPs_KEGG,NoSAPs_KEGG,SAPs_all,NoSAPs_all,CntKEGG_All,totalSAPs,pKEGG):
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
31 """
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
32 Returns binomial probability.
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
33 """
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
34 def comb(CntKEGG_All,k):
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
35 return factorial(CntKEGG_All) / Decimal(str(factorial(k)*factorial(CntKEGG_All-k)))
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
36 probLow = 0
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
37 for k in range(0, SAPs_KEGG+1):
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
38 cp=Decimal(str(comb(CntKEGG_All,k)))
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
39 bp=Decimal(str(pKEGG**k))
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
40 dp=Decimal(str(1.0-pKEGG))**Decimal(str(CntKEGG_All-k))
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
41 probLow+=cp*bp*dp
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
42 #~
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
43 probHigh = 0
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
44 for k in range(int(SAPs_KEGG),CntKEGG_All+1):
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
45 cp=Decimal(str(comb(CntKEGG_All,k)))
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
46 bp=Decimal(str(pKEGG**k))
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
47 dp=Decimal(str(1.0-pKEGG))**Decimal(str(CntKEGG_All-k))
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
48 probHigh+=cp*bp*dp
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
49 return probLow,probHigh
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
50
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
51 def gauss_hypergeom(X, CntKEGG_All, SAPs_all, totalSAPs):
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
52 CntKEGG_All,SAPs_all,totalSAPs
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
53 """
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
54 Returns the probability of drawing X successes of SAPs_all marked items
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
55 in CntKEGG_All draws from a bin of totalSAPs total items
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
56 """
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
57 def logchoose(ni, ki):
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
58 try:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
59 lgn1 = lgamma(ni+1)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
60 lgk1 = lgamma(ki+1)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
61 lgnk1 = lgamma(ni-ki+1)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
62 except ValueError:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
63 raise ValueError
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
64 return lgn1 - (lgnk1 + lgk1)
22
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
65 #~
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
66 r1 = logchoose(SAPs_all, X)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
67 try:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
68 r2 = logchoose(totalSAPs-SAPs_all, CntKEGG_All-X)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
69 except ValueError:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
70 return 0
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
71 r3 = logchoose(totalSAPs,CntKEGG_All)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
72 return exp(r1 + r2 - r3)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
73
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
74 def hypergeo_sf(SAPs_KEGG,NoSAPs_KEGG,SAPs_all,NoSAPs_all,CntKEGG_All,totalSAPs,pKEGG):
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
75 """
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
76 Runs Hypergeometric probability test
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
77 """
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
78 s = 0
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
79 t=0
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
80 for i in range(SAPs_KEGG,min(SAPs_all,CntKEGG_All)+1):
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
81 s += max(gauss_hypergeom(i,CntKEGG_All,SAPs_all,totalSAPs), 0.0)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
82 for i in range(0, SAPs_KEGG+1):
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
83 t += max(gauss_hypergeom(i,CntKEGG_All,SAPs_all,totalSAPs), 0.0)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
84 return min(max(t,0.0), 1),min(max(s,0.0), 1)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
85
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
86 def fisherexct(SAPs_KEGG,NoSAPs_KEGG,SAPs_all,NoSAPs_all,CntKEGG_All,totalSAPs,pKEGG):
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
87 """
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
88 Runs Fisher's exact test
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
89 """
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
90 ftest=fisher(SAPs_KEGG,NoSAPs_KEGG,SAPs_all,NoSAPs_all)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
91 probLow,probHigh=ftest.left_tail,ftest.right_tail
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
92 return probLow,probHigh
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
93
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
94 def rtrnKEGGcENSEMBLc(inBckgrndfile,columnENSEMBLTBckgrnd,columnKEGGBckgrnd):
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
95 """
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
96 """
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
97 dKEGGTENSEMBLT={}
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
98 for eachl in open(inBckgrndfile,'r'):
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
99 if eachl.strip():
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
100 ENSEMBLT=eachl.splitlines()[0].split('\t')[columnENSEMBLTBckgrnd]
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
101 KEGGTs=set(eachl.splitlines()[0].split('\t')[columnKEGGBckgrnd].split('.'))
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
102 KEGGTs=KEGGTs.difference(set(['','U','N']))
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
103 for KEGGT in KEGGTs:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
104 try:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
105 dKEGGTENSEMBLT[KEGGT].add(ENSEMBLT)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
106 except:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
107 dKEGGTENSEMBLT[KEGGT]=set([ENSEMBLT])
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
108 ENSEMBLTGinKEGG=set.union(*dKEGGTENSEMBLT.values())
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
109 return dKEGGTENSEMBLT,ENSEMBLTGinKEGG
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
110
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
111 def rtrnENSEMBLcSAPs(inSAPsfile,columnENSEMBLT,ENSEMBLTGinKEGG):
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
112 """
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
113 returns a set of the ENSEMBLT codes present in the input list and
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
114 in the KEGG file
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
115 """
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
116 sENSEMBLTSAPsinKEGG=set()
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
117 for eachl in open(inSAPsfile,'r'):
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
118 ENSEMBLT=eachl.splitlines()[0].split('\t')[columnENSEMBLT]
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
119 if ENSEMBLT in ENSEMBLTGinKEGG:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
120 sENSEMBLTSAPsinKEGG.add(ENSEMBLT)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
121 return sENSEMBLTSAPsinKEGG
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
122
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
123 def rtrnCounts(dKEGGTENSEMBLT,ENSEMBLTGinKEGG,sENSEMBLTSAPsinKEGG,statsTest):
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
124 """
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
125 returns a list of the ENSEMBLT codes present in the input list and
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
126 in the KEGG file. The pathways in this list are: 'Go Term','# Genes in
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
127 the KEGG Term','# Genes in the list and in the KEGG Term','Enrichement
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
128 of the KEGG Term for genes in the input list','Genes in the input list
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
129 present in the KEGG term'
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
130 """
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
131 totalSAPs=len(ENSEMBLTGinKEGG)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
132 SAPs_all=len(sENSEMBLTSAPsinKEGG)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
133 NoSAPs_all=totalSAPs-SAPs_all
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
134 pKEGG=SAPs_all/float(totalSAPs)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
135 #~
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
136 lp=len(dKEGGTENSEMBLT)
22
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
137 cnt=0
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
138 #~
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
139 if statsTest=='fisher':
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
140 ptest=fisherexct
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
141 elif statsTest=='hypergeometric':
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
142 ptest=hypergeo_sf
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
143 elif statsTest=='binomial':
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
144 ptest=binProb
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
145 #~
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
146 ltfreqs=[]
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
147 for echKEGGT in dKEGGTENSEMBLT:
22
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
148 cnt+=1
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
149 CntKEGG_All=len(dKEGGTENSEMBLT[echKEGGT])
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
150 SAPs_KEGG=len(dKEGGTENSEMBLT[echKEGGT].intersection(sENSEMBLTSAPsinKEGG))
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
151 NoSAPs_KEGG=CntKEGG_All-SAPs_KEGG
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
152 probLow,probHigh=ptest(SAPs_KEGG,NoSAPs_KEGG,SAPs_all,NoSAPs_all,CntKEGG_All,totalSAPs,pKEGG)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
153 ltfreqs.append([(SAPs_KEGG/Decimal(CntKEGG_All)),SAPs_KEGG,probLow,probHigh,echKEGGT])
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
154 #~
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
155 ltfreqs.sort()
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
156 ltfreqs.reverse()
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
157 outl=[]
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
158 cper,crank=Decimal('2'),0
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
159 #~
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
160 getcontext().prec=2#set 2 decimal places
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
161 for perc,cnt_go,pvalLow,pvalHigh,goTerm in ltfreqs:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
162 if perc<cper:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
163 crank+=1
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
164 cper=perc
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
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]))
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
166 #~
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
167 return outl
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
168
22
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
169
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
170 def main():
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
171 #~
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
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).')
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
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)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
174 parser.add_argument('--inBckgrndfile',metavar='input TXT file',type=str,help='the input file with the background table in txt format.',required=True)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
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)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
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)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
177 parser.add_argument('--columnENSEMBLTBckgrnd',metavar='column number',type=int,help='column with the ENSEMBL transcript code in the background file.',required=True)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
178 parser.add_argument('--columnKEGGBckgrnd',metavar='column number',type=int,help='column with the KEGG pathways in the background file.',required=True)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
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)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
180
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
181 args = parser.parse_args()
22
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
182
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
183 inSAPsfile = args.input
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
184 inBckgrndfile = args.inBckgrndfile
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
185 saleKEGGPCount = args.output
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
186 columnENSEMBLT = args.columnENSEMBLT
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
187 columnENSEMBLTBckgrnd = args.columnENSEMBLTBckgrnd
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
188 columnKEGGBckgrnd = args.columnKEGGBckgrnd
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
189 statsTest = args.statsTest
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
190 columnENSEMBLT-=1
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
191 columnENSEMBLTBckgrnd-=1
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
192 columnKEGGBckgrnd=-1
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
193 #~
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
194 dKEGGTENSEMBLT,ENSEMBLTGinKEGG=rtrnKEGGcENSEMBLc(inBckgrndfile,columnENSEMBLTBckgrnd,columnKEGGBckgrnd)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
195 sENSEMBLTSAPsinKEGG=rtrnENSEMBLcSAPs(inSAPsfile,columnENSEMBLT,ENSEMBLTGinKEGG)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
196 outl=rtrnCounts(dKEGGTENSEMBLT,ENSEMBLTGinKEGG,sENSEMBLTSAPsinKEGG,statsTest)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
197 #~
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
198 saleKEGGPCount=open(saleKEGGPCount,'w')
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
199 saleKEGGPCount.write('\n'.join(outl))
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
200 saleKEGGPCount.close()
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
201 #~
22
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
202 return 0
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
203
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
204 if __name__ == '__main__':
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
205 main()
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
206