de.charite.compbio.jannovar.reference.TranscriptModel Maven / Gradle / Ivy
package de.charite.compbio.jannovar.reference;
import java.io.Serializable;
import java.util.Map;
import com.google.common.collect.ImmutableList;
import com.google.common.collect.ImmutableMap;
import com.google.common.collect.ImmutableSortedMap;
import de.charite.compbio.jannovar.Immutable;
/**
* The information representing a transcript model.
*
* @author Manuel Holtgrewe
*/
@Immutable
public final class TranscriptModel implements Serializable, Comparable {
/**
* Accession number of the transcript (e.g., the UCSC knownGene id - uc011nca.2). The version number may be
* included.
*/
private final String accession;
/**
* Gene symbol of the known Gene. Can be null for some genes. Note that in annovar, $name2 corresponds to the
* geneSymbol if available, otherwise the kgID is used.
*/
private final String geneSymbol;
/** Genomic interval with transcript begin/end. */
private final GenomeInterval txRegion;
/**
* Genomic interval with CDS begin/end.
*
* Note that in Jannovar, the CDS region includes the start and stop codon.
*/
private final GenomeInterval cdsRegion;
/** Genomic intervals with the exons, order is dictated by strand of transcript. */
private final ImmutableList exonRegions;
/** cDNA sequence of the spliced RNA of this known gene transcript. */
private final String sequence;
/**
* The gene ID, from Ensembl ("ENS[MUS]*G0+([0-9]+)"), Entrez ("ENTREZ([0-9]+)
* "), RefSeq ("gene([0-9]+)").
*
* null for no available gene ID.
*/
private final String geneID;
/**
* Alternative gene IDs, as parsed from RefSeq GFF3 file
*
* See {@link #getAltGeneIDs()} for more information
*/
private final ImmutableSortedMap altGeneIDs;
/**
* The transcript support level of the this transcript (the lower the better).
*
* @see TranscriptSupportLevels
* @see http://www.ensembl.org/Help/Glossary?id=492
*/
private final int transcriptSupportLevel;
/** Class version (for serialization). */
private static final long serialVersionUID = 3L;
/**
* Initialize the TranscriptInfo object from the given parameters.
*/
public TranscriptModel(String accession, String geneSymbol, GenomeInterval txRegion, GenomeInterval cdsRegion,
ImmutableList exonRegions, String sequence, String geneID, int transcriptSupportLevel) {
this(accession, geneSymbol, txRegion, cdsRegion, exonRegions, sequence, geneID, transcriptSupportLevel,
ImmutableMap. of());
}
/**
* Initialize the TranscriptInfo object from the given parameters.
*/
public TranscriptModel(String accession, String geneSymbol, GenomeInterval txRegion, GenomeInterval cdsRegion,
ImmutableList exonRegions, String sequence, String geneID, int transcriptSupportLevel,
Map altGeneIDs) {
this.accession = accession;
this.geneSymbol = geneSymbol;
this.txRegion = txRegion;
this.cdsRegion = cdsRegion;
this.exonRegions = exonRegions;
this.sequence = sequence;
this.geneID = geneID;
this.transcriptSupportLevel = transcriptSupportLevel;
this.altGeneIDs = ImmutableSortedMap.copyOf(altGeneIDs);
checkForConsistency();
}
/** @return accession number */
public String getAccession() {
return accession;
}
/** @return the gene symbol */
public String getGeneSymbol() {
return geneSymbol;
}
/** @return transcript's genomic region */
public GenomeInterval getTXRegion() {
return txRegion;
}
/** @return CDS genomic region */
public GenomeInterval getCDSRegion() {
return cdsRegion;
}
/** @return genomic intervals with the exons, order is dictated by strand of transcript. */
public ImmutableList getExonRegions() {
return exonRegions;
}
/** @return mDNA sequence of the spliced RNA of this known gene transcript. */
public String getSequence() {
return sequence;
}
/**
* @return The gene ID, from Ensembl ("ENS[MUS]*G0+([0-9]+)"), Entrez ("ENTREZ([0-9]+)
* "), RefSeq ("gene([0-9]+)"). null for no available gene ID.
*/
public String getGeneID() {
return geneID;
}
/**
* Return mapping containing alternative gene IDs, as parsed from RefSeq GFF3 file
*
* The alternative identifiers used are the values of {@link AltGeneIDType} converted to strings.
*/
public ImmutableSortedMap getAltGeneIDs() {
return altGeneIDs;
}
/**
* @return transcript support level of the this transcript (the lower the better).
*
* @see TranscriptSupportLevels
* @see http://www.ensembl.org/Help/Glossary?id=492
*/
public int getTranscriptSupportLevel() {
return transcriptSupportLevel;
}
/** @return the strand of the transcript */
public Strand getStrand() {
return txRegion.getStrand();
}
/** @return the chromosome of the transcript */
public int getChr() {
return txRegion.getChr();
}
/**
* @return true if this is a gene-coding transcript, marked by cdsRegion being empty.
*/
public boolean isCoding() {
return (this.cdsRegion.getBeginPos() < this.cdsRegion.getEndPos());
}
/**
* @return the length of the coding exon sequence
*/
public int cdsTranscriptLength() {
int result = 0;
for (GenomeInterval region : exonRegions)
result += region.intersection(cdsRegion).length();
return result;
}
/**
* @return the sum of the exon sequence lengths
*/
public int transcriptLength() {
int result = 0;
for (GenomeInterval region : exonRegions)
result += region.length();
return result;
}
/**
* @param i
* 0-based index of the intron's region to return
* @return {@link GenomeInterval} with the intron's region
*/
public GenomeInterval intronRegion(int i) {
// TODO(holtgrem): test me!
GenomeInterval exonRegionL = exonRegions.get(i);
GenomeInterval exonRegionR = exonRegions.get(i + 1);
return new GenomeInterval(exonRegionL.refDict, exonRegionL.getStrand(), exonRegionL.getChr(),
exonRegionL.getEndPos(), exonRegionR.getBeginPos(), PositionType.ZERO_BASED);
}
/**
* Ensures that the strands are consistent.
*/
private void checkForConsistency() {
Strand strand = txRegion.getStrand();
assert (txRegion.getStrand() == strand);
assert (cdsRegion.getStrand() == strand);
for (GenomeInterval region : exonRegions)
assert (region.getStrand() == strand);
}
@Override
public String toString() {
return accession + "(" + txRegion + ")";
}
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result + ((accession == null) ? 0 : accession.hashCode());
result = prime * result + ((cdsRegion == null) ? 0 : cdsRegion.hashCode());
result = prime * result + ((exonRegions == null) ? 0 : exonRegions.hashCode());
result = prime * result + ((geneID == null) ? 0 : geneID.hashCode());
result = prime * result + ((geneSymbol == null) ? 0 : geneSymbol.hashCode());
result = prime * result + ((sequence == null) ? 0 : sequence.hashCode());
result = prime * result + transcriptSupportLevel;
result = prime * result + ((txRegion == null) ? 0 : txRegion.hashCode());
return result;
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
TranscriptModel other = (TranscriptModel) obj;
if (accession == null) {
if (other.accession != null)
return false;
} else if (!accession.equals(other.accession))
return false;
if (cdsRegion == null) {
if (other.cdsRegion != null)
return false;
} else if (!cdsRegion.equals(other.cdsRegion))
return false;
if (exonRegions == null) {
if (other.exonRegions != null)
return false;
} else if (!exonRegions.equals(other.exonRegions))
return false;
if (geneID == null) {
if (other.geneID != null)
return false;
} else if (!geneID.equals(other.geneID))
return false;
if (geneSymbol == null) {
if (other.geneSymbol != null)
return false;
} else if (!geneSymbol.equals(other.geneSymbol))
return false;
if (sequence == null) {
if (other.sequence != null)
return false;
} else if (!sequence.equals(other.sequence))
return false;
if (transcriptSupportLevel != other.transcriptSupportLevel)
return false;
if (txRegion == null) {
if (other.txRegion != null)
return false;
} else if (!txRegion.equals(other.txRegion))
return false;
return true;
}
public int compareTo(TranscriptModel o) {
int result = -1;
if (geneID != null && o.geneID != null) {
result = geneID.compareTo(o.geneID);
if (result != 0)
return result;
}
result = geneSymbol.compareTo(o.geneSymbol);
if (result != 0)
return result;
return accession.compareTo(o.accession);
}
}
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