Now also encodes amino acids, includes documentation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2361 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
sjia
parent
9b0bdbbf29
commit
4148991d81
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@ -1,5 +1,6 @@
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/*
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* Creates a ped file given reads (for SNP analysis, imputation, etc)
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/**
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* Creates a ped file of SNPs and amino acids coded as SNPs given an input ped file with 4-digit HLA alleles. Usage: java -jar GenomeAnalysisTK.jar -T CreatePedFile --allelesFile INPUT.ped -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-sc\
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r1/GSA/sjia/454_HLA/HLA/HLA.combined.4digitUnique.bam > OUTPUT.log
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*/
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package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
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@ -9,6 +10,7 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
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import java.util.ArrayList;
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import java.util.Hashtable;
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import java.util.Enumeration;
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/**
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*
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* @author shermanjia
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@ -21,11 +23,17 @@ public class CreatePedFileWalker extends ReadWalker<Integer, Integer> {
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@Argument(fullName = "pedIntervals", shortName = "pedIntervals", doc = "Create genotypes in these intervals", required = false)
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public String pedIntervalsFile = "";
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@Argument(fullName = "HLAexonIntervals", shortName = "HLAexonIntervals", doc = "HLA exonic intervals", required = false)
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public String exonIntervalsFile = "/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA_EXON_POSITIONS.txt";
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@Argument(fullName = "DNAcode", shortName = "DNAcode", doc = "Amino acid codes", required = false)
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public String dnaCodesFile = "/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/DNA_CODE.txt";
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String[] HLAnames, HLAreads, inputFileContents;
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Integer[] HLAstartpos, HLAstoppos;
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ArrayList<String> HLAnamesAL, HLAreadsAL;
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ArrayList<Integer> HLAstartposAL, HLAstopposAL;
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int[][] intervals;
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int[][] intervals; String[][] exonIntervals;
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int numIntervals;
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ReadCigarFormatter formatter = new ReadCigarFormatter();
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@ -48,6 +56,7 @@ public class CreatePedFileWalker extends ReadWalker<Integer, Integer> {
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Integer I;
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Hashtable indexer = new Hashtable();
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Hashtable DNAcode = new Hashtable();
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public Integer reduceInit() {
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if (!FilesLoaded){
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@ -79,10 +88,70 @@ public class CreatePedFileWalker extends ReadWalker<Integer, Integer> {
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out.printf("INFO Interval %s: %s-%s\n",i+1,intervals[i][0],intervals[i][1]);
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}
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}
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//load HLA exonic intervals
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if (!exonIntervalsFile.equals("")){
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fileReader = new TextFileReader();
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fileReader.ReadFile(exonIntervalsFile);
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String[] lines = fileReader.GetLines();
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exonIntervals = new String[lines.length][5];
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for (int i = 0; i < lines.length; i++) {
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String[] s = lines[i].split("\t");
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String[] intervalPieces = s[1].split("-");
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exonIntervals[i][1] = intervalPieces[0];
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exonIntervals[i][2] = intervalPieces[1];
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exonIntervals[i][0] = s[0]; // Locus
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exonIntervals[i][3] = s[2]; // Exon number
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exonIntervals[i][4] = s[3]; // +/- strand
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}
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numIntervals = exonIntervals.length;
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for (int i = 0; i < numIntervals; i++){
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out.printf("INFO HLA-%s %s (%s): %s-%s\n",exonIntervals[i][0],exonIntervals[i][3],exonIntervals[i][4],exonIntervals[i][1],exonIntervals[i][2]);
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}
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}
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//load amino-acid coding DNA triplets
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if (!dnaCodesFile.equals("")){
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fileReader = new TextFileReader();
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fileReader.ReadFile(dnaCodesFile);
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String[] lines = fileReader.GetLines();
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for (int i = 0; i < lines.length; i++) {
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String[] s = lines[i].split("\t");
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DNAcode.put(s[0],s[1]);
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}
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Enumeration e = DNAcode.keys();
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while( e.hasMoreElements() ){
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String key = e.nextElement().toString();
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out.printf("INFO %s encodes %s\n",key,DNAcode.get(key));
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}
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}
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}
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return 0;
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}
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private String[][] GetExonIntervals(String locus, boolean isForwardStrand){
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int numExons = 0; int exonNum;
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for (int i = 0; i < exonIntervals.length; i++){
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if (exonIntervals[i][0].equals(locus)){
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numExons++;
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}
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}
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String[][] ExonIntervals = new String[numExons][5];
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if (isForwardStrand){exonNum = 1;}else{exonNum = ExonIntervals.length;}
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for (int i = 0; i < exonIntervals.length; i++){
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if (exonIntervals[i][0].equals(locus)){
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ExonIntervals[exonNum-1]=exonIntervals[i];
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if (isForwardStrand){
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exonNum++;
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}else{
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exonNum--;
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}
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}
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}
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return ExonIntervals;
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}
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private int BaseCharToInt(char c){
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switch(c){
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case 'A': return 1;
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@ -93,6 +162,23 @@ public class CreatePedFileWalker extends ReadWalker<Integer, Integer> {
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}
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}
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private char Complement(char c){
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switch(c){
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case 'A': return 'T';
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case 'C': return 'G';
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case 'G': return 'C';
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case 'T': return 'A';
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default: return '0';
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}
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}
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private char GetAminoAcid(String codon){
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if (DNAcode.containsKey(codon)){
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return DNAcode.get(codon).toString().charAt(0);
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}else{
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return '0';
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}
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}
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public Integer map(char[] ref, SAMRecord read) {
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HLAnamesAL.add(read.getReadName());
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@ -135,29 +221,107 @@ public class CreatePedFileWalker extends ReadWalker<Integer, Integer> {
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}
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for (int pos = startpos; pos <= stoppos; pos++){
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if (pos >= start1 && pos <= stop1){
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c1 = s1.charAt(pos-start1);
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if (c1 == 'D'){c1 = '0';}
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}else{
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c1 = '0';
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}
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if (pos >= start2 && pos <= stop2){
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c2 = s2.charAt(pos-start2);
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if (c2 == 'D'){c2 = '0';}
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}else{
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c2 = '0';
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}
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c1 = GetBase(pos,s1,start1,stop1);
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c2 = GetBase(pos,s2,start2,stop2);
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out.printf("\t%s %s",c1,c2);
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}
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return error;
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}
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private String PrintAminoAcids(String ID, String alleleName1, String alleleName2, String[][] ExonIntervals){
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String error = "";
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//prints genotypes for allele1 and allele2 at given interval
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int i1 = GetAlleleIndex(alleleName1);
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int i2 = GetAlleleIndex(alleleName2);
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String s1, s2;
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int start1, start2, stop1, stop2;
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char c1, c2;
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boolean isForwardStrand = false;
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if (ExonIntervals[0][4].equals("+")){isForwardStrand=true;}
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int AAcount=0;
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int baseCount=0;
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String codon1 = ""; String codon2 = "";
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if (i1 > -1){
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s1 = HLAreads[i1];
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start1 = HLAstartpos[i1];
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stop1 = HLAstoppos[i1];
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}else{
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s1 = "";
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start1 = -1;
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stop1 = -1;
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error = error + "INFO " + alleleName1 + " for " + ID + " not found in HLA dictionary\n";
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}
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if (i2 > -1){
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s2 = HLAreads[i2];
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start2 = HLAstartpos[i2];
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stop2 = HLAstoppos[i2];
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}else{
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s2 = "";
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start2 = -1;
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stop2 = -1;
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error = error + "INFO " + alleleName2 + " for " + ID + " not found in HLA dictionary\n";
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}
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int i;
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for (int exonNum = 1; exonNum <= ExonIntervals.length; exonNum++){
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if (isForwardStrand){i=exonNum-1;}else{i=ExonIntervals.length-exonNum;}
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int exonStart = Integer.parseInt(ExonIntervals[i][1]);
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int exonStop = Integer.parseInt(ExonIntervals[i][2]);
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for (int pos = exonStart; pos <= exonStop; pos++){
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c1 = GetBase(pos,s1,start1,stop1);
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c2 = GetBase(pos,s2,start2,stop2);
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if (!isForwardStrand){
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c1 = Complement(c1);
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c2 = Complement(c2);
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}
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if (baseCount < 3){
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if (isForwardStrand){
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codon1 = codon1 + c1;
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codon2 = codon2 + c2;
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}else{
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codon1 = c1 + codon1;
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codon2 = c2 + codon2;
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}
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baseCount++;
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}
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if (baseCount == 3){
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out.printf("\t%s %s",GetAminoAcid(codon1),GetAminoAcid(codon2));
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baseCount = 0;
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AAcount++;
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codon1 = "";
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codon2 = "";
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}
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}
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}
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if (baseCount > 0){
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//Print stop or start codon depending on strandedness
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if (isForwardStrand){out.printf("\tO O");}else{out.printf("\tM M");}
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}
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return error;
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}
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private char GetBase(int pos, String str, int start, int stop){
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char base;
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if (pos >= start && pos <= stop){
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base = str.charAt(pos-start);
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if (base == 'D'){base = '0';}
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}else{
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base = '0';
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}
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return base;
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}
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private int GetAlleleIndex(String alleleName){
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//Find first allele that matches name, or matches part of name for 2-digit allele
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int i;
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for (i = 0; i < HLAnames.length; i++){
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if (HLAnames[i].equals(alleleName)){
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if (HLAnames[i].indexOf(alleleName) > -1){
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return i;
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}
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}
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@ -169,6 +333,14 @@ public class CreatePedFileWalker extends ReadWalker<Integer, Integer> {
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return value + sum;
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}
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private String GetAlleleName(String locus, String sep, String allele){
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if (allele.length() > 1){
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return locus + sep + allele;
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}else{
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return locus + sep + "0000";
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}
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}
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public void onTraversalDone(Integer numreads) {
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HLAnames = HLAnamesAL.toArray(new String[numreads]);
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HLAreads = HLAreadsAL.toArray(new String[numreads]);
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@ -177,6 +349,15 @@ public class CreatePedFileWalker extends ReadWalker<Integer, Integer> {
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String star = "*";
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String error = "";
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//out.printf("INFO %s alleles in dictionary\n",HLAnames.length);
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String[][] A_exons = GetExonIntervals("A",true);
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String[][] B_exons = GetExonIntervals("B",false);
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String[][] C_exons = GetExonIntervals("C",false);
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String[][] DRB1_exons = GetExonIntervals("DRB1",false);
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String[][] DQB1_exons = GetExonIntervals("DQB1",false);
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String[][] DQA1_exons = GetExonIntervals("DQA1",true);
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String[][] DPB1_exons = GetExonIntervals("DPB1",true);
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String[][] DPA1_exons = GetExonIntervals("DPA1",false);
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//Print individual info and genotypes
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for (int i = 0; i < inputFileContents.length; i++){
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String[] s = inputFileContents[i].split(" ");
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@ -184,46 +365,70 @@ public class CreatePedFileWalker extends ReadWalker<Integer, Integer> {
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if (s.length > 10){
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error = "";
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out.printf("%s\t%s\t%s\t%s\t%s\t%s",s[0],s[1],s[2],s[3],s[4],s[5]);
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String HLA_A_1 = "HLA_A" + star + s[6];
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String HLA_A_2 = "HLA_A" + star + s[7];
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String HLA_B_1 = "HLA_B" + star + s[8];
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String HLA_B_2 = "HLA_B" + star + s[9];
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String HLA_C_1 = "HLA_C" + star + s[10];
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String HLA_C_2 = "HLA_C" + star + s[11];
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String HLA_DPA1_1 = "HLA_DPA1" + star + s[12];
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String HLA_DPA1_2 = "HLA_DPA1" + star + s[13];
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String HLA_DPB1_1 = "HLA_DPB1" + star + s[14];
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String HLA_DPB1_2 = "HLA_DPB1" + star + s[15];
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String HLA_DQA1_1 = "HLA_DQA1" + star + s[16];
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String HLA_DQA1_2 = "HLA_DQA1" + star + s[17];
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String HLA_DQB1_1 = "HLA_DQB1" + star + s[18];
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String HLA_DQB1_2 = "HLA_DQB1" + star + s[19];
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String HLA_DRB1_1 = "HLA_DRB1" + star + s[20];
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String HLA_DRB1_2 = "HLA_DRB1" + star + s[21];
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String HLA_A_1 = GetAlleleName("HLA_A",star,s[6]);
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String HLA_A_2 = GetAlleleName("HLA_A",star,s[7]);
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String HLA_B_1 = GetAlleleName("HLA_B",star,s[8]);
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String HLA_B_2 = GetAlleleName("HLA_B",star,s[9]);
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String HLA_C_1 = GetAlleleName("HLA_C",star,s[10]);
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String HLA_C_2 = GetAlleleName("HLA_C",star,s[11]);
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String HLA_DPA1_1 = GetAlleleName("HLA_DPA1",star,s[12]);
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String HLA_DPA1_2 = GetAlleleName("HLA_DPA1",star,s[13]);
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String HLA_DPB1_1 = GetAlleleName("HLA_DPB1",star,s[14]);
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String HLA_DPB1_2 = GetAlleleName("HLA_DPB1",star,s[15]);
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String HLA_DQA1_1 = GetAlleleName("HLA_DQA1",star,s[16]);
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String HLA_DQA1_2 = GetAlleleName("HLA_DQA1",star,s[17]);
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String HLA_DQB1_1 = GetAlleleName("HLA_DQB1",star,s[18]);
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String HLA_DQB1_2 = GetAlleleName("HLA_DQB1",star,s[19]);
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String HLA_DRB1_1 = GetAlleleName("HLA_DRB1",star,s[20]);
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String HLA_DRB1_2 = GetAlleleName("HLA_DRB1",star,s[21]);
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error = error + PrintGenotypes(s[1], HLA_A_1,HLA_A_2, HLA_A_start,HLA_A_end);
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error = error + PrintGenotypes(s[1], HLA_C_1,HLA_C_2, HLA_C_start,HLA_C_end);
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error = error + PrintGenotypes(s[1], HLA_B_1,HLA_B_2, HLA_B_start,HLA_B_end);
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error = error + PrintGenotypes(s[1], HLA_DRB1_1,HLA_DRB1_2, HLA_DRB1_start,HLA_DRB1_end);
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error = error + PrintGenotypes(s[1], HLA_DQA1_1,HLA_DQA1_2, HLA_DQA1_start,HLA_DQA1_end);
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error = error + PrintGenotypes(s[1], HLA_DQB1_1,HLA_DQB1_2, HLA_DQB1_start,HLA_DQB1_end);
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error = error + PrintGenotypes(s[1], HLA_DPA1_1,HLA_DPA1_2, HLA_DPA1_start,HLA_DPA1_end);
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error = error + PrintGenotypes(s[1], HLA_DPB1_1,HLA_DPB1_2, HLA_DPB1_start,HLA_DPB1_end);
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out.printf("\n");
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out.printf("%s",error);
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if (true) {
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error = error + PrintGenotypes(s[1], HLA_A_1,HLA_A_2, HLA_A_start,HLA_A_end);
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error = error + PrintGenotypes(s[1], HLA_C_1,HLA_C_2, HLA_C_start,HLA_C_end);
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error = error + PrintGenotypes(s[1], HLA_B_1,HLA_B_2, HLA_B_start,HLA_B_end);
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error = error + PrintGenotypes(s[1], HLA_DRB1_1,HLA_DRB1_2, HLA_DRB1_start,HLA_DRB1_end);
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error = error + PrintGenotypes(s[1], HLA_DQA1_1,HLA_DQA1_2, HLA_DQA1_start,HLA_DQA1_end);
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error = error + PrintGenotypes(s[1], HLA_DQB1_1,HLA_DQB1_2, HLA_DQB1_start,HLA_DQB1_end);
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error = error + PrintGenotypes(s[1], HLA_DPA1_1,HLA_DPA1_2, HLA_DPA1_start,HLA_DPA1_end);
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error = error + PrintGenotypes(s[1], HLA_DPB1_1,HLA_DPB1_2, HLA_DPB1_start,HLA_DPB1_end);
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error = error + PrintAminoAcids(s[1], HLA_A_1,HLA_A_2, A_exons);
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error = error + PrintAminoAcids(s[1], HLA_C_1,HLA_C_2, C_exons);
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error = error + PrintAminoAcids(s[1], HLA_B_1,HLA_B_2, B_exons);
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error = error + PrintAminoAcids(s[1], HLA_DRB1_1,HLA_DRB1_2, DRB1_exons);
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error = error + PrintAminoAcids(s[1], HLA_DQA1_1,HLA_DQA1_2, DQA1_exons);
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error = error + PrintAminoAcids(s[1], HLA_DQB1_1,HLA_DQB1_2, DQB1_exons);
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error = error + PrintAminoAcids(s[1], HLA_DPA1_1,HLA_DPA1_2, DPA1_exons);
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error = error + PrintAminoAcids(s[1], HLA_DPB1_1,HLA_DPB1_2, DPB1_exons);
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out.printf("\n");
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out.printf("%s",error);
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}
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}
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}
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//Prints SNP names for each site
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PrintSNPS(HLA_A_start,HLA_A_end);
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PrintSNPS(HLA_C_start,HLA_C_end);
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||||
PrintSNPS(HLA_B_start,HLA_B_end);
|
||||
PrintSNPS(HLA_DRB1_start,HLA_DRB1_end);
|
||||
PrintSNPS(HLA_DQA1_start,HLA_DQA1_end);
|
||||
PrintSNPS(HLA_DQB1_start,HLA_DQB1_end);
|
||||
PrintSNPS(HLA_DPA1_start,HLA_DPA1_end);
|
||||
PrintSNPS(HLA_DPB1_start,HLA_DPB1_end);
|
||||
if (true){
|
||||
PrintSNPS(HLA_A_start,HLA_A_end);
|
||||
PrintSNPS(HLA_C_start,HLA_C_end);
|
||||
PrintSNPS(HLA_B_start,HLA_B_end);
|
||||
PrintSNPS(HLA_DRB1_start,HLA_DRB1_end);
|
||||
PrintSNPS(HLA_DQA1_start,HLA_DQA1_end);
|
||||
PrintSNPS(HLA_DQB1_start,HLA_DQB1_end);
|
||||
PrintSNPS(HLA_DPA1_start,HLA_DPA1_end);
|
||||
PrintSNPS(HLA_DPB1_start,HLA_DPB1_end);
|
||||
|
||||
PrintAminoAcidSites(A_exons,"A",true);
|
||||
PrintAminoAcidSites(C_exons,"C",false);
|
||||
PrintAminoAcidSites(B_exons,"B",false);
|
||||
PrintAminoAcidSites(DRB1_exons,"DRB1",false);
|
||||
PrintAminoAcidSites(DQA1_exons,"DQA1",true);
|
||||
PrintAminoAcidSites(DQB1_exons,"DQB1",false);
|
||||
PrintAminoAcidSites(DPA1_exons,"DPA1",false);
|
||||
PrintAminoAcidSites(DPB1_exons,"DPB1",true);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private void PrintSNPS(int startpos, int stoppos){
|
||||
|
|
@ -232,4 +437,41 @@ public class CreatePedFileWalker extends ReadWalker<Integer, Integer> {
|
|||
out.printf("6\t%s\t0\t%s\n",SNPname,pos);
|
||||
}
|
||||
}
|
||||
|
||||
private void PrintAminoAcidSites(String[][] ExonIntervals, String locus, boolean isForwardStrand){
|
||||
int AAcount=1; int baseCount = 1; int exonNum;
|
||||
|
||||
if (!isForwardStrand){
|
||||
for (int i = 1; i <= ExonIntervals.length; i++){
|
||||
int exonStart = Integer.parseInt(ExonIntervals[i-1][1]);
|
||||
int exonStop = Integer.parseInt(ExonIntervals[i-1][2]);
|
||||
for (int pos = exonStart; pos <= exonStop; pos++){
|
||||
if (baseCount == 3){
|
||||
AAcount++;
|
||||
baseCount = 1;
|
||||
}else{
|
||||
baseCount++;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
for (int i = 1; i <= ExonIntervals.length; i++){
|
||||
if (isForwardStrand){exonNum = i;}else{exonNum = ExonIntervals.length - i + 1;}
|
||||
int exonStart = Integer.parseInt(ExonIntervals[exonNum-1][1]);
|
||||
int exonStop = Integer.parseInt(ExonIntervals[exonNum-1][2]);
|
||||
for (int pos = exonStart; pos <= exonStop; pos++){
|
||||
if (baseCount == 2){
|
||||
SNPname = locus + "_AA" + String.valueOf(AAcount) + "_E" + exonNum + "_" + String.valueOf(pos);
|
||||
out.printf("6\t%s\t0\t%s\n",SNPname,pos);
|
||||
}
|
||||
if (baseCount == 3){
|
||||
if (isForwardStrand){AAcount++;}else{AAcount--;}
|
||||
baseCount = 1;
|
||||
}else{
|
||||
baseCount++;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue