/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* THE SOFTWARE.
*/
package org.broad.igv.feature.tribble;
import org.broad.igv.Globals;
import org.broad.igv.feature.BasicFeature;
import org.broad.igv.feature.Exon;
import org.broad.igv.feature.Strand;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.util.StringUtils;
import java.util.List;
/**
* @author Jim Robinson
* @date 11/19/11
*/
public class UCSCGeneTableCodec extends UCSCCodec<BasicFeature> {
private int nameColumn = 0;
private int idColumn = 1;
private int chrColumn = 2;
private int strandColumn = 3;
private int startColumn = 4;
private int endColumn = 5;
private int cdStartColumn = 6;
private int cdEndColumn = 7;
private int exonCountColumn = 8;
private int startsBufferColumn = 9;
private int endsBufferColumn = 10;
private int frameBufferColumn = 15;
public enum Type {
REFFLAT, GENEPRED, UCSCGENE
}
private Genome genome;
private Type type;
public UCSCGeneTableCodec(Type type, Genome genome) {
super(BasicFeature.class);
this.genome = genome;
this.type = type;
switch (type) {
case REFFLAT:
break;
case UCSCGENE:
idColumn = 0;
chrColumn = 1;
strandColumn = 2;
startColumn = 3;
endColumn = 4;
cdStartColumn = 5;
cdEndColumn = 6;
exonCountColumn = 7;
startsBufferColumn = 8;
endsBufferColumn = 9;
nameColumn = 10;
break;
case GENEPRED:
nameColumn = 12;
}
}
/**
* Decode a line as a Feature.
*
* @param line the input line to decode
* @return Return the Feature encoded by the line, or null if the line does not represent a feature (e.g. is
* a comment)
*/
public BasicFeature decode(String line) {
if (line.startsWith("#")) {
//Header line
readHeaderLine(line);
return null;
}
line = line.replaceAll("\"", "");
String[] tokens = Globals.singleTabMultiSpacePattern.split(line);
int tokenCount = tokens.length;
if (tokenCount <= strandColumn) {
return null;
}
String identifier = tokens[idColumn].trim();
String name = null;
if (tokenCount > nameColumn && tokens[nameColumn] != null) {
name = tokens[nameColumn];
}
if (name == null || name.length() == nameColumn) {
name = identifier;
}
String chrToken = tokens[chrColumn].trim();
String chr = genome == null ? StringUtils.intern(chrToken) : genome.getCanonicalChrName(chrToken);
int start = Integer.parseInt(tokens[startColumn]);
int end = Integer.parseInt(tokens[endColumn]);
String strandString = tokens[strandColumn];
Strand strand = Strand.NONE;
if (strandString != null) {
if (strandString.trim().equals("+")) {
strand = Strand.POSITIVE;
} else if (strandString.trim().equals("-")) {
strand = Strand.NEGATIVE;
}
}
BasicFeature gene = new BasicFeature(chr, start, end, strand);
gene.setRepresentation(line);
gene.setName(name);
gene.setIdentifier(identifier);
if (tokenCount > 7) {
gene.setThickStart(Integer.parseInt(tokens[6]));
gene.setThickEnd(Integer.parseInt(tokens[7]));
}
// Coding information is optional
if (tokenCount > 8) {
createExons(tokens, tokenCount, gene, chr, strand);
}
// Optional standard name column
if (tokenCount > 16) {
gene.setAttribute("Standard Name", tokens[16]);
}
return gene;
}
/**
* This function returns true iff the File potentialInput can be parsed by this
* codec.
* <p/>
* There is an assumption that there's never a situation where two different Codecs
* return true for the same file. If this occurs, the recommendation would be to error out.
* <p/>
* Note this function must never throw an error. All errors should be trapped
* and false returned.
*
* @param path the file to test for parsability with this codec
* @return true if potentialInput can be parsed, false otherwise
*/
public boolean canDecode(String path) {
return true;
}
private void createExons(String[] tokens, int tokenCount, BasicFeature gene, String chr,
Strand strand)
throws NumberFormatException {
int cdStart = Integer.parseInt(tokens[cdStartColumn]);
int cdEnd = Integer.parseInt(tokens[cdEndColumn]);
int exonCount = Integer.parseInt(tokens[exonCountColumn]);
String[] startsBuffer = Globals.commaPattern.split(tokens[startsBufferColumn]);
String[] endsBuffer = Globals.commaPattern.split(tokens[endsBufferColumn]);
if (startsBuffer.length == endsBuffer.length) {
int exonNumber = (strand == Strand.NEGATIVE ? exonCount : 1);
for (int i = 0; i < startsBuffer.length; i++) {
int exonStart = Integer.parseInt(startsBuffer[i]);
int exonEnd = Integer.parseInt(endsBuffer[i]);
Exon exon = new Exon(chr, exonStart, exonEnd, strand);
exon.setCodingStart(cdStart);
exon.setCodingEnd(cdEnd);
gene.addExon(exon);
exon.setNumber(exonNumber);
if (strand == Strand.NEGATIVE) {
exonNumber--;
} else {
exonNumber++;
}
}
}
List<Exon> exons = gene.getExons();
// Walk through exons setting mRNA start position
int start = strand == Strand.POSITIVE ? 0 : exonCount - 1;
int end = strand == Strand.POSITIVE ? exonCount : -1;
int increment = strand == Strand.POSITIVE ? 1 : -1;
int mRNABase = 0;
for (int i = start; i != end; i += increment) {
Exon exon = exons.get(i);
exon.setMrnaBase(mRNABase);
mRNABase += exon.getCodingLength();
}
if (type == Type.GENEPRED && tokenCount > 15) {
try {
String[] frameBuffer = Globals.commaPattern.split(tokens[frameBufferColumn]);
for (int i = 0; i < frameBuffer.length; i++) {
int exonFrame = Integer.parseInt(frameBuffer[i].trim());
if (exonFrame == -1) {
exons.get(i).setNonCoding(true);
} else {
int phase = (exonFrame == 0) ? 0 : 3 - exonFrame;
exons.get(i).setPhase(phase);
}
}
} catch (Exception e) {
// Ignore -- not getting the reading frame is not the end of the world.
//log.info("Could not parse frame buffer: ", e);
}
}
}
}