+ resolved some index bugs concerning the intron boundaries resp. splicesite
[qpalma.git] / qpalma / computeSpliceWeights.py
1 #!/usr/bin/env python
2 # -*- coding: utf-8 -*-
3
4 from numpy import inf
5 from numpy.matlib import zeros
6 import pdb
7
8 # 3 * 30 supporting points: x_1 ... x_30 => 3 * 30 parameters (1 .. 90): y_1 ... y_30
9 # piecewise linear function:
10 # take score from SVM vektor (don_supp: case 1, acc_supp: case 2) and compute length of intron: case 3
11 # these are our values x
12 #
13 # | y_1 if x <= x_1
14 # |
15 # | x_i+1 - x x - x_i
16 # f(x) = | y_i * ----------- + y_i+1 * ----------- if x_i <= x <= x_i+1
17 # | x_i+1 - x_i x_i+1 - x_i
18 # |
19 # | y_30 if x_n <= x
20 #
21 # y_i and y_i+1 parameters, so the fractions are saved in the weight vectors!
22
23 def calculateWeights(plf, scores):
24 currentWeight = zeros((30,1))
25
26 for k in range(len(scores)):
27 value = scores[k]
28 Lower = len([elem for elem in plf.limits if elem <= value])
29
30 if Lower == 0:
31 currentWeight[0] += 1
32 elif Lower == len(plf.limits):
33 currentWeight[-1] += 1
34 else:
35 # because we count from 0 in python
36 Lower -= 1
37 Upper = Lower+1 ; # x-werte bleiben fest
38 #print value,Lower,Upper
39 weightup = 1.0*(value - plf.limits[Lower]) / (plf.limits[Upper] - plf.limits[Lower])
40 weightlow = 1.0*(plf.limits[Upper] - value) / (plf.limits[Upper] - plf.limits[Lower])
41 currentWeight[Upper] = currentWeight[Upper] + weightup
42 currentWeight[Lower] = currentWeight[Lower] + weightlow
43
44 #print plf.limits[Lower],plf.limits[Upper]
45 #print weightup,weightlow,currentWeight[Upper],currentWeight[Lower]
46
47 return currentWeight
48
49 def computeSpliceWeights(d, a, h, SpliceAlign, don_supp, acc_supp,dec=False):
50 ####################################################################################
51 # 1. Donor: In don_supp stehen Werte der SVM., in SpliceAlign die Einsen
52 ####################################################################################
53
54 # Picke die Positionen raus, an denen eine Donorstelle ist
55 try:
56 #if dec:
57 DonorScores = [elem for pos,elem in enumerate(don_supp) if SpliceAlign[pos] == 1]
58 #else:
59 # DonorScores = [elem for pos,elem in enumerate(don_supp) if pos > 0 and SpliceAlign[pos-1] == 1]
60 assert not ( -inf in DonorScores )
61 except:
62 print 'Error'
63 pdb.set_trace()
64
65 #print 'donor'
66 weightDon = calculateWeights(d,DonorScores)
67
68 ####################################################################################
69 # 2. Acceptor: In acc_supp stehen Werte der SVM., in SpliceAlign die Einsen
70 ####################################################################################
71
72 #Den Vektor Acceptorstellen durchgehen und die Gewichtsvektoren belasten:
73 try:
74 #if dec:
75 #AcceptorScores = [elem for pos,elem in enumerate(acc_supp) if pos > 0 and SpliceAlign[pos-1] == 2]
76 AcceptorScores = [elem for pos,elem in enumerate(acc_supp) if pos > 0 and SpliceAlign[pos-1] == 2]
77 #else:
78 # AcceptorScores = [elem for pos,elem in enumerate(acc_supp) if pos > 0 and SpliceAlign[pos] == 2]
79 assert not ( -inf in AcceptorScores )
80 except:
81 print 'Error'
82 pdb.set_trace()
83
84 #print 'acceptor'
85 weightAcc = calculateWeights(a,AcceptorScores)
86
87 ####################################################################################
88 # 3. Intron length: SpliceAlign: Gaps zaehlen und auf Gapgewichte addieren
89 ####################################################################################
90
91 intron_starts = []
92 intron_ends = []
93 for pos,elem in enumerate(SpliceAlign):
94 if elem == 1:
95 intron_starts.append(pos)
96
97 if elem == 2:
98 intron_ends.append(pos)
99
100 assert len(intron_starts) == len(intron_ends)
101
102 for i in range(len(intron_starts)):
103 assert intron_starts[i] < intron_ends[i]
104
105 values = [0.0]*len(intron_starts)
106 for pos in range(len(intron_starts)):
107 values[pos] = intron_ends[pos] - intron_starts[pos] + 1
108
109 weightIntron = calculateWeights(h,values)
110
111 return weightDon, weightAcc, weightIntron