umcg.genetica.ensembl.Features Maven / Gradle / Ivy
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.ensembl;
import umcg.genetica.containers.Transcript;
import umcg.genetica.containers.Exon;
import umcg.genetica.containers.Gene;
import umcg.genetica.containers.Chromosome;
import java.io.IOException;
import java.util.HashMap;
import umcg.genetica.io.text.TextFile;
/**
*
* @author harmjan
*/
public class Features {
private HashMap chromosomeHash = new HashMap();
private HashMap geneHash = new HashMap();
private HashMap transcriptHash = new HashMap();
private HashMap exonHash = new HashMap();
/**
* @return the chromosomeHash
*/
public HashMap getChromosomeHash() {
return chromosomeHash;
}
/**
* @param chromosomeHash the chromosomeHash to set
*/
public void setChromosomeHash(HashMap chromosomeHash) {
this.chromosomeHash = chromosomeHash;
}
/**
* @return the geneHash
*/
public HashMap getGeneHash() {
return geneHash;
}
/**
* @param geneHash the geneHash to set
*/
public void setGeneHash(HashMap geneHash) {
this.geneHash = geneHash;
}
/**
* @return the transcriptHash
*/
public HashMap getTranscriptHash() {
return transcriptHash;
}
/**
* @param transcriptHash the transcriptHash to set
*/
public void setTranscriptHash(HashMap transcriptHash) {
this.transcriptHash = transcriptHash;
}
/**
* @return the exonHash
*/
public HashMap getExonHash() {
return exonHash;
}
/**
* @param exonHash the exonHash to set
*/
public void setExonHash(HashMap exonHash) {
this.exonHash = exonHash;
}
/*
* 0 Ensembl Gene ID 1 Ensembl Transcript ID 2 Ensembl Protein ID
*
* 3 Chromosome Name 4 Gene Start (bp) 5 Gene End (bp) 6 Transcript Start (bp) 7 Transcript End (bp) 8 Strand 9 Associated Gene Name 10 Associated Gene DB
* 11 5' UTR Start 12 5' UTR End 13 3' UTR Start 14 3' UTR End 15 CDS Length 16 Transcript count 17 Description 18 Gene Biotype 19 Ensembl Exon ID 20 Exon
* Chr Start (bp) 21 Exon Chr End (bp) 22 Constitutive Exon 23 Exon Rank in Transcript 24 phase 25 cDNA coding start 26 Genomic coding start 27 cDNA coding
* end 28 Genomic coding end 29 CDS End 30 CDS Start
*/
public void loadAnnotation(String fileName) throws IOException {
System.out.println("Loading sequence feature annotation from: " + fileName);
TextFile in = new TextFile(fileName, TextFile.R);
String[] linesplit = in.readLineElems(TextFile.tab);
HashMap elementToColId = new HashMap();
for (int i = 0; i < linesplit.length; i++) {
System.out.println(linesplit[i] + "\t" + i);
elementToColId.put(linesplit[i], i);
}
int lnCounter = 0;
String[] elems = in.readLineElems(TextFile.tab);
while (elems != null) {
/*
* Ensembl Gene ID Ensembl Transcript ID Ensembl Protein ID Chromosome Name Gene Start (bp) Gene End (bp) Transcript Start (bp) Transcript End (bp)
* Strand Associated Gene Name Gene Biotype Description Transcript count CDS Length 3' UTR End 3' UTR Start 5' UTR End 5' UTR Start Ensembl Exon ID
* Exon Chr Start (bp) Exon Chr End (bp) Exon Rank in Transcript phase Associated Gene DB
*
*
*
*
*
*/
if (elems.length > 1) {
String gene = elems[elementToColId.get("Ensembl Gene ID")];
String transcript = elems[elementToColId.get("Ensembl Transcript ID")];
String protein = elems[elementToColId.get("Ensembl Protein ID")];
String chromosome = elems[elementToColId.get("Chromosome Name")];
Integer genestart = Integer.parseInt(elems[elementToColId.get("Gene Start (bp)")]);
Integer genestop = Integer.parseInt(elems[elementToColId.get("Gene End (bp)")]);
Integer transcriptstart = Integer.parseInt(elems[elementToColId.get("Transcript Start (bp)")]);
Integer transcriptstop = Integer.parseInt(elems[elementToColId.get("Transcript End (bp)")]);
Integer strand = Integer.parseInt(elems[elementToColId.get("Strand")]);
String hgnc = elems[elementToColId.get("Associated Gene Name")];
// String db = elems[10];
// Integer utr5start = Integer.parseInt(elems[11]);
// Integer utr5end = Integer.parseInt(elems[12]);
// Integer utr3start = Integer.parseInt(elems[13]);
// Integer utr3end = Integer.parseInt(elems[14]);
// Integer cdslen = Integer.parseInt(elems[15]);
// Integer numTranscripts = Integer.parseInt(elems[16]);
// String Desc = Integer.parseInt(elems[17]);
// String biotype = elems[18];
String exon = elems[elementToColId.get("Ensembl Exon ID")];
Integer exonstart = Integer.parseInt(elems[elementToColId.get("Exon Chr Start (bp)")]);
Integer exonend = Integer.parseInt(elems[elementToColId.get("Exon Chr End (bp)")]);
// String exonconstitutive = elems[23];
Integer exonrankintranscript = Integer.parseInt(elems[elementToColId.get("Exon Rank in Transcript")]);
// String phase = elems[24];
// Integer cDNACodingStart = Integer.parseInt(elems[25]);
// Integer genomicCodingStart = Integer.parseInt(elems[26]);
// Integer cDNACodingEnd = Integer.parseInt(elems[27]);
// Integer genomicCodingEnd = Integer.parseInt(elems[28]);
// Integer CDSStart = Integer.parseInt(elems[29]);
// Integer CDSEnd = Integer.parseInt(elems[30]);
Chromosome currChr = null;
Gene currGen = null;
Transcript currTra = null;
Exon currExo = null;
if (chromosome.trim().length() > 0) {
if (chromosomeHash.get(chromosome) == null) {
Chromosome tmpChr = new Chromosome(chromosome);
tmpChr.setName(chromosome);
chromosomeHash.put(chromosome, tmpChr);
System.out.println("Adding chromosome: " + chromosome);
}
currChr = chromosomeHash.get(chromosome);
}
if (gene.trim().length() > 0) {
if (geneHash.get(gene) == null) {
Gene tmpGen = new Gene();
tmpGen.setName(gene);
tmpGen.setStart(genestart);
tmpGen.setEnd(genestop);
tmpGen.setStrand(strand);
tmpGen.setAnnotation(hgnc);
geneHash.put(gene, tmpGen);
}
currGen = geneHash.get(gene);
}
if (transcript.trim().length() > 0) {
if (transcriptHash.get(transcript) == null) {
Transcript tmpTra = new Transcript();
tmpTra.setName(transcript);
tmpTra.setStart(transcriptstart);
tmpTra.setEnd(transcriptstop);
tmpTra.setStrand(strand);
tmpTra.setProtein(protein);
transcriptHash.put(transcript, tmpTra);
}
currTra = transcriptHash.get(transcript);
}
if (exon.trim().length() > 0) {
if (exonHash.get(exon) == null) {
Exon tmpExo = new Exon();
tmpExo.setName(exon);
tmpExo.setStart(exonstart);
tmpExo.setEnd(exonend);
tmpExo.setStrand(strand);
exonHash.put(exon, tmpExo);
}
currExo = exonHash.get(exon);
}
if (currGen != null) {
currChr.addGene(currGen);
currGen.setParentChromosome(currChr);
}
if (currGen != null && currTra != null) {
currGen.addTranscript(currTra);
currTra.setParentGene(currGen);
currTra.setParentChromosome(currChr);
}
if (currTra != null && currExo != null) {
currTra.addExon(currExo);
currExo.setParentTranscript(currTra);
currExo.setParentChromosome(currChr);
currTra.setExonRank(currExo, exonrankintranscript);
}
}
if (lnCounter % 100000 == 0) {
System.out.print(".");
}
elems = in.readLineElems(TextFile.tab);
lnCounter++;
}
System.out.println("\tDone.");
in.close();
System.out.println("Loaded " + chromosomeHash.size() + " chromosomes, " + geneHash.size() + " genes, " + transcriptHash.size() + " transcripts, " + exonHash.size() + " exons.");
}
public Exon getExon(String match) {
return exonHash.get(match);
}
public Transcript getTranscript(String match) {
return transcriptHash.get(match);
}
}
© 2015 - 2025 Weber Informatics LLC | Privacy Policy