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package driver;
import java.util.ArrayList;
import java.util.HashSet;
import dna.AminoAcid;
import dna.ChromosomeArray;
import dna.Data;
import dna.Exon;
import dna.Gene;
import dna.MotifMulti;
import dna.MotifProbsN;
import shared.Shared;
import shared.Tools;
public class MeasureGene {
public static void main(String[] args){
byte minChrom=19;
byte maxChrom=22;
double sum=0;
long count=0;
for(byte chrom=minChrom; chrom<=maxChrom; chrom++){
Data.getChromosome(chrom);
Gene[] genes=Data.getGenes(chrom, Shared.PLUS);
genes=toNormalGenes(genes);
for(Gene g : genes){
// ArrayList<Exon> exons=getExons(g);
analyzeGene(g);
// System.out.println("\nchr"+g.chromosome+"\t"+g.name+"\t"+g.nameTranscript);
//
// for(int i=0; i<g.exons.length; i++){
// Exon e=g.exons[i];
//
// float f2=measureExonFrequency(e.a, e.b, e.chromosome, e.strand);
// float f1, f3;
//
// if(i==0 && g.exons.length==1){
// f1=mGStart.matchStrength(ca.array, e.a);
// f3=mGStop.matchStrength(ca.array, e.b);
// }else if(i==0){
// f1=mGStart.matchStrength(ca.array, e.a);
// f3=mEStop.matchStrength(ca.array, e.b);
// }else if(i==g.exons.length-1){
// f1=mEStart.matchStrength(ca.array, e.a);
// f3=mGStop.matchStrength(ca.array, e.b);
// }else{
// f1=mEStart.matchStrength(ca.array, e.a);
// f3=mEStop.matchStrength(ca.array, e.b);
// }
//
// if(f2!=0){
// sum+=f2;
// count++;
// System.out.println(Tools.format("%.3f, %.3f, %.5f", f1, f3, f2));
// }
// }
}
}
System.out.println("Sum: "+sum);
System.out.println("Count: "+count);
System.out.println("Average: "+sum/count);
}
public static float analyzeGene(Gene g){
assert(g.strand==Shared.PLUS) : "TODO";
ChromosomeArray ca=Data.getChromosome(g.chromosome);
System.out.println("\nchr"+g.chromosome+"\t"+g.symbol+"\t"+g.mrnaAcc);
double sum=0;
for(int i=0; i<g.exons.length; i++){
Exon e=g.exons[i];
float f2=measureExonFrequency(e.a, e.b, e.chromosome, e.strand);
float f1, f3;
if(i==0 && g.exons.length==1){
f1=mGStart.matchStrength(ca.array, e.a);
f3=mGStop.matchStrength(ca.array, e.b);
}else if(i==0){
f1=mGStart.matchStrength(ca.array, e.a);
f3=mEStop.matchStrength(ca.array, e.b);
}else if(i==g.exons.length-1){
f1=mEStart.matchStrength(ca.array, e.a);
f3=mGStop.matchStrength(ca.array, e.b);
}else{
f1=mEStart.matchStrength(ca.array, e.a);
f3=mEStop.matchStrength(ca.array, e.b);
}
sum=sum+f1+f3;
// if(f2!=0){System.out.println(Tools.format("%.3f, %.3f, %.5f", f1, f3, f2));}
}
float avg=(float)(sum/(2*g.exons.length));
System.out.println(Tools.format("Average: %.3f", avg));
return avg;
}
public static Gene[] toNormalGenes(Gene[] genes){
ArrayList<Gene> normal=new ArrayList<Gene>(genes.length);
for(Gene g : genes){
if(g.isNormalGene()){normal.add(g);}
}
return normal.toArray(new Gene[normal.size()]);
}
public static ArrayList<Exon> getExons(Gene...genes){
HashSet<Exon> exonTable=new HashSet<Exon>();
for(Gene g : genes){
for(int i=0; i<g.exons.length; i++){
Exon e=g.exons[i];
exonTable.add(e);
}
}
ArrayList<Exon> exons=new ArrayList<Exon>(exonTable.size());
exons.addAll(exonTable);
exonTable=null;
Shared.sort(exons);
return exons;
}
public static float measureExonFrequency(int a, int b, byte chrom, byte strand){
// assert e.strand==Gene.PLUS;
int start=a;
int stop=b-1;
double sum=0;
int count=0;
assert(strand==Shared.PLUS) : "TODO";
ChromosomeArray ca=Data.getChromosome(chrom);
for(int i=start; i<stop; i++){
int number=0;
boolean invalid=false;
for(int j=0; j<length; j++){
int code=AminoAcid.baseToNumberACGTN[ca.get(i+j)];
invalid=invalid || (code<0 || code>3);
number=((number<<2)|code);
}
if(!invalid){
count++;
sum+=freqDif[number];
}else{
return 0;
}
}
return count>0 ? (float)(sum/count) : 0;
}
private static final MotifProbsN mAG=MotifProbsN.makeMotif("AG Exon Starts MP2", 13, 11, 2);
private static final MotifProbsN mAC=MotifProbsN.makeMotif("AC Exon Starts MP2", 13, 11, 2);
private static final MotifProbsN mATG=MotifProbsN.makeMotif("ATG Exon Starts MP2", 13, 11, 2);
private static final MotifProbsN mGT=MotifProbsN.makeMotif("GT Exon Stops MP2", 10, 3, 2);
private static final MotifProbsN mGC=MotifProbsN.makeMotif("GC Exon Stops MP2", 10, 3, 2);
private static final MotifProbsN mGStartATG=MotifProbsN.makeMotif("Gene Starts MP2", 13, 11, 2);
private static final MotifProbsN mGStopTAA=MotifProbsN.makeMotif("TAA Gene Stops MP2", 13, 11, 2);
private static final MotifProbsN mGStopTAG=MotifProbsN.makeMotif("TAG Gene Stops MP2", 13, 11, 2);
private static final MotifProbsN mGStopTGA=MotifProbsN.makeMotif("TGA Gene Stops MP2", 13, 11, 2);
private static final MotifMulti mGStart=new MotifMulti("Gene Starts MP2", mGStartATG);
private static final MotifMulti mEStart=new MotifMulti("Exon Starts MP2", mAG, mAC);
private static final MotifMulti mEStop=new MotifMulti("Exon Stops MP2", mGT, mGC);
private static final MotifMulti mGStop=new MotifMulti("Gene Stops MP2", mGStopTAA, mGStopTAG, mGStopTGA);
private static final int length=2;
//Overall Frequency Exonic
public static final float[] exonicFreq1={0.259195f, 0.260530f, 0.260441f, 0.219835f};
//Overall Frequency Non-Exonic
public static final float[] nonExonicFreq1={0.277111f, 0.204189f, 0.213443f, 0.305257f};
//Overall Frequency Exonic
public static final float[] exonicFreq2={0.071395f, 0.055355f, 0.077256f, 0.052618f,
0.079593f, 0.077505f, 0.032685f, 0.071248f, 0.075189f, 0.070017f, 0.070666f,
0.045554f, 0.032210f, 0.057977f, 0.079080f, 0.051651f};
//Overall Frequency Non-Exonic
public static final float[] nonExonicFreq2={0.086472f, 0.047310f, 0.070451f, 0.072291f,
0.069003f, 0.055260f, 0.011722f, 0.071913f, 0.058469f, 0.045772f, 0.056984f,
0.054175f, 0.062555f, 0.059560f, 0.076273f, 0.101790f};
public static final float[] freqDif=(
length==2 ? makeDif(exonicFreq2, nonExonicFreq2) :
length==1 ? makeDif(exonicFreq1, nonExonicFreq1) :
null);
public static final float[] makeDif(float[] a, float[] b){
float[] dif=new float[a.length];
for(int i=0; i<a.length; i++){
dif[i]=a[i]-b[i];
}
return dif;
}
}
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