1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
|
package driver;
import java.util.ArrayList;
import java.util.Locale;
import dna.AminoAcid;
import dna.Motif;
import dna.MotifProbsN;
public class SniffSplices {
public static void main(String[] args){
// MotifProbsN mAG=MotifProbsN.makeMotif("AG Exon Starts MP2", 11, 13, 11, 2);
// MotifProbsN mGT=MotifProbsN.makeMotif("GT Exon Stops MP2", 3, 10, 3, 2);
//
// MotifProbsN eStarts2=MotifProbsN.makeMotif("Exon Starts MP2", 9, 11, 9, 2);
// MotifProbsN eStops2=MotifProbsN.makeMotif("Exon Stops MP2", 3, 10, 3, 2);
//
// MotifProbsN gStarts2=MotifProbsN.makeMotif("Gene Starts MP2", 9, 11, 9, 2);
// MotifProbsN gStops2=MotifProbsN.makeMotif("Gene Stops MP2", 3, 10, 3, 2);
Motif m=eStops2;
// Motif m=eStarts2;
// Motif m=eStarts2_15;
ArrayList<String> list=new ArrayList<String>();
boolean rcomp=false;
if(args.length>0){
for(String s1 : args){
String s=s1.toLowerCase();
if(s.equalsIgnoreCase("rcomp")){rcomp=true;}
if(s.contains("estart_ac")){m=eStarts2_AC;}
else if(s.contains("estart_15")){m=eStarts2_15;}
else if(s.contains("estart")){m=eStarts2;}
else if(s.contains("estop_gc")){m=eStops2_GC;}
else if(s.contains("estop")){m=eStops2;}
else if(s.contains("gstart")){m=gStarts2;}
else if(s.contains("gstop")){m=gStops2;}
else{list.add(s.toUpperCase());}
}
}
System.out.println("Using motif "+m);
int initialLoc=0;
int increment=1; //1 for plus strand, -1 for minus strand
// String s="NNNNNNNNAGCGGGAATCGGGGGGTCCTTCTGCTCCCCTGAGCGTCCTTCCTGTGTTCCCAGGC"+
// "ACTATCGCCTACCTGTTTTTCACCAACCGCCACGAGGTGAGGAAGATGACCCTGGACCGAAGCGAATACACCAGCCTCAT"+
// "CCCAAACTTGAAGAACGTGGTCGCCCTGGACACCGAGGTGGCCAGCAACAGAATATACTGGTCCGACCTGTCCCAAAGGA"+
// "AGATCTACAGGTGAGCCTTGGAGCCACACCCAGCGCTCAACCCCCGGTGGCGCGGGGGCCCCTCTCACTGACGCTCTCCT"+
// "TCCCCTGCTCCTCCCCCTCAGCACCCAAATCGACAGAGCCCCCGGCTTCTCCTCCTATGACACCGTCGTCAGCGAGGACC"+
// "TCCAGGCCCCTGATGGGCTGGCGGTGGACTGGATCCACAGCAACATATACTGGACAGACTCCATCCTGGGCACCGTCTCC"+
// "GTGGCCGACACCAAGGGCGTGAAGAGAAAGACGCTCTTCAAGGAGAAAGGCTCTAAGCCACGTGCCATCGTGGTGGATCC"+
// "CGTTCACGGGTGGGTGCTGCTAAAGCCGAGGGCCACGGAAGGAANNNNNNNN";
// "AAGTACAGGAATTATATGCCCCCAGGTAA * AGTACAGGAATTATATGCCCCCAGGTAAC"
// String[] array={
// "GCCTACTTTGTATGATGACCCTGTCCT",
// "AGCCCTGGCCGCCTACTTTGTATGATGACCCTGTCCTCCCTCACCCA",
// };
// String[] array={
// "TGGCCGCCGCCGACCGTAAGTTTTGCGCGCAAACTCCC",
// "TGGCCGCCGCCGACCGTTAAGTTTTGCGCGCAAACTCCC",
// };
// String[] array={
// "CAACTGCCAAGGGAAGGGCACGGTTAGCGGCACCCTCATAGGTAAGTGATGGCCCCAGACGCTGGTCTCTCTCCATCTGGACCTGGCCTGGGAGGTGGCTTGG",
// "CAACTGCCAAGGGAAGGGCACGGTTAGCGGCACCCTCATAGGTGAGTGATGGCCCCAGACGCTGGTCTCTCTCCATCTGGACCTGGCCTGGGAGGTGGCTTGG",
// };
// String[] array={
// "GTCTTTCTCATGTGGTCCTTGTGTTCGTCGAGCAGGCCAGCAAGTGTGACAGTCATGGCACCCACCTGGCAGGGG",
// "GTCTTTCTCATGTGGTCCTTGTGTTCGTTGAGCAGGCCAGCAAGTGTGACAGTCATGGCACCCACCTGGCAGGGG",
// };
// String[] array={
// "GCAGGGTCATGGTCACCGACTTCGAGAATGTGCCCGAGGAGGACGGGACCCGCCTCCACAGACAGGTAAGCACAGCCGTCTGATGGGAGGGCTGCCTCTGCCCATATCCCCATCCTGGAG",
// "GCAGGGTCATGGTCACCGACTTCGAGAATGTGCCCGAGGAGGACGGGACCCGCTTCCACAGACAGGTAAGCACGGCCGTCTGATGGGAGGGCTGCCTCTGCCCATATCCCCATCCTGGAG",
// };
// String[] array={
// "RTGTTTTCACTCCAGCCACGGAGCTGGGTCTCTGGTCTCGGGGGCAGCTGTGTGACAGAGCGT" +
// "GCCTCTCCCTACAGTGCTCTTCGTCTTCCTTTGCCTGGGGGTCTTCCTTCTATGGAAGAACTG",
// "RTGTTTTCACTCCAGCCACGGAGCTGGGTCTCTGGTCTCGGGGGCAGCTGTGTGACAGAGCGT" +
// "GCCTCTCCTTACAGTGCTCTTCGTCTTCCTTTGCCTGGGGGTCTTCCTTCTATGGAAGAACTG",
// };
// String[] array={
//// "CAGCGAAGATGCGAAGGTGATTCCCGGGTGGG",
//// "CAGCGAAGATGCGAAGGTGATTTCCGGGTGGG",
// "GCGGCCGAAGCGGGCCATGGACGCGCTCAAGT",
// "GCGGCCGGAGCGGGCCATGGACGCGCTCAAGT",
// };
// String[] array={
// "AAGTATGTTTTTGCTTTTAGGAGGATTCTCT",
// "AAGTATGTTTTTGTTTTTAGGAGGATTCTCT",
// };
// String[] array={
// "TTAGGTTGCTGGTGTCTGTATAATGTGTGT"+
// "A"+
// "TCTTTGTTGCAGGTTTGTTTTTTATTCTGC",
//
// "TTAGGTTGCTGGTGTCTGTATAATGTGTGT"+
// "G"+
// "TCTTTGTTGCAGGTTTGTTTTTTATTCTGC"
// };
// ATGTATTCTACTTTT[TCTTTT]AAGTATGTTTTTGTTTTTAGGAGGATTCTCTATGG
// String[] array={
// "CAGGTCCTCGAGATCCTGGGATACAGGAAA",
// "CAGGTCCTCGAGATCCTGGGATATAGGAAA"
// };
// String[] array={
// "TGTTTTTGCTTTTAGGAGGATTCTCTATG",
// "TGTTTTTGTTTTTAGGAGGATTCTCTATG"
// };
for(String s : list){
if(rcomp){s=AminoAcid.reverseComplementBases(s);}
System.out.println("For string "+s+":");
if(!s.startsWith("N") || !s.endsWith("N")){
s="NNNN"+s+"NNNN";
}
byte[] code=s.getBytes();
for(int i=0; i<s.length(); i++){
float strength=m.matchStrength(code, i);
float norm=m.normalize(strength);
float percent=-1;
try {
percent=m.percentile(norm);
} catch (Exception e) {
// TODO Auto-generated catch block
// e.printStackTrace();
}
System.out.print((initialLoc+i*increment)+"\t");
System.out.print(s.charAt(i)+" Strength = "+String.format(Locale.ROOT, "%.4f ",norm));
if(percent!=-1){System.out.print(String.format(Locale.ROOT, "-> %.4f ",percent));}
float norm2=norm;
while(norm2>0.1f){
norm2-=.1f;
System.out.print("*");
}
// System.out.print("\t"+String.format(Locale.ROOT, "%.3f ",m.percentile(norm)));
System.out.println();
}
}
}
private static final int N_MOTIF=2;
// private static final MotifProbsN eStarts2=MotifProbsN.makeMotif("Exon Starts MP"+N_MOTIF, 12, 9, 2);
//// private static final MotifProbsN eStops2=MotifProbsN.makeMotif("Exon Stops MP"+N_MOTIF, 3, 11, 3, 2);
// private static final MotifProbsN eStops2=MotifProbsN.makeMotif("Exon Stops MP"+N_MOTIF, 12, 3, 2);
//
// private static final MotifProbsN gStarts2=MotifProbsN.makeMotif("Gene Starts MP"+N_MOTIF, 13, 9, 2);
// private static final MotifProbsN gStops2=MotifProbsN.makeMotif("Gene Stops MP"+N_MOTIF, 11, 3, 2);
//
// private static final MotifProbsN trStarts2=MotifProbsN.makeMotif("Tr Starts MP"+N_MOTIF, 12, 7, 2);
// private static final MotifProbsN trStops2=MotifProbsN.makeMotif("Tr Stops MP"+N_MOTIF, 11, 6, 2);
private static final MotifProbsN eStarts2=MotifProbsN.makeMotif("Exon Starts MP"+N_MOTIF, 13, 9, 2);
private static final MotifProbsN eStarts2_AC=MotifProbsN.makeMotif("AC Exon Starts MP"+N_MOTIF, 13, 9, 2);
private static final MotifProbsN eStarts2_15=MotifProbsN.makeMotif("Exon Starts MP"+N_MOTIF, 19, 15, 2);
private static final MotifProbsN eStops2=MotifProbsN.makeMotif("Exon Stops MP"+N_MOTIF, 13, 4, 2);
private static final MotifProbsN eStops2_GC=MotifProbsN.makeMotif("GC Exon Stops MP"+N_MOTIF, 13, 4, 2);
private static final MotifProbsN gStarts2=MotifProbsN.makeMotif("Gene Starts MP"+N_MOTIF, 13, 9, 2);
private static final MotifProbsN gStops2=MotifProbsN.makeMotif("Gene Stops MP"+N_MOTIF, 13, 4, 2);
private static final MotifProbsN trStarts2=MotifProbsN.makeMotif("Tr Starts MP"+N_MOTIF, 13, 7, 2);
private static final MotifProbsN trStops2=MotifProbsN.makeMotif("Tr Stops MP"+N_MOTIF, 13, 7, 2);
}
|
