/*
* 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
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package org.broad.igv.feature;
//~--- non-JDK imports --------------------------------------------------------
import org.apache.log4j.Logger;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.renderer.GeneTrackRenderer;
import org.broad.igv.track.FeatureCollectionSource;
import org.broad.igv.track.FeatureTrack;
import org.broad.igv.track.TrackProperties;
import org.broad.igv.util.ParsingUtils;
import org.broad.igv.util.ResourceLocator;
import java.io.*;
import java.util.*;
/**
* Parses exon information from the feature table section of an embl file.
* <p/>
* Note -- this is no a general parser, it is built specifically to handle the S Pombe annotation
* from Sanger. Example entry follows
* <p/>
* FT CDS join(180423..180528,180586..180721,180890..180911)
* FT /product="TIM22 inner membrane protein import complex
* FT subunit Tim8 (predicted)"
* FT /gene="tim8"
* FT /gene="SPAC13G6.04"
*/
public class EmblFeatureTableParser implements FeatureParser {
/**
* Method description
*
* @param gene
*/
public static void computeReadingShifts(IGVFeature gene) {
List<org.broad.igv.feature.Exon> exons = gene.getExons();
if (exons.size() == 0) {
return;
}
int startIndex = (gene.getStrand() == Strand.POSITIVE) ? 0 : exons.size() - 1;
int endIndex = (gene.getStrand() == Strand.POSITIVE) ? exons.size() : -1;
int increment = (gene.getStrand() == Strand.POSITIVE) ? 1 : -1;
int cds = 0;
int exonNumber = 1;
for (int i = startIndex; i != endIndex; i += increment) {
Exon exon = exons.get(i);
exon.setNumber(exonNumber++);
if (exon.getCodingLength() > 0 || cds > 0) { // Skip until we find the coding start
int modCds = cds % 3;
int phase = (modCds == 0) ? 0 : 3 - modCds;
exon.setPhase(phase);
cds += exon.getCodingLength();
}
}
}
public TrackProperties getTrackProperties() {
return null; //To change body of implemented methods use File | Settings | File Templates.
}
/**
* Method description
*
* @param locator
* @return
*/
public List<FeatureTrack> loadTracks(ResourceLocator locator, Genome genome) {
BufferedReader reader = null;
try {
reader = ParsingUtils.openBufferedReader(locator);
List<htsjdk.tribble.Feature> features = loadFeatures(reader, genome);
if (features.isEmpty()) {
return null;
} else {
FeatureTrack track = new FeatureTrack(locator, new FeatureCollectionSource(features, genome));
track.setName(locator.getTrackName());
track.setMinimumHeight(35);
track.setHeight(45);
track.setRendererClass(GeneTrackRenderer.class);
List<FeatureTrack> newTracks = new ArrayList();
newTracks.add(track);
FeatureDB.addFeatures(features, genome);
return newTracks;
}
} catch (IOException ex) {
ex.printStackTrace();
return null;
} finally {
if (reader != null) {
try {
reader.close();
} catch (IOException e) {
}
}
}
}
/**
* Method description
*
* @param reader
* @return
*/
public List<htsjdk.tribble.Feature> loadFeatures(BufferedReader reader, Genome genome) {
List<BasicFeature> features = new ArrayList();
String nextLine = null;
String chromosome = null;
EmblRecord currentRecord = null;
try {
while ((nextLine = reader.readLine()) != null) {
if (nextLine.startsWith("ID")) // Chromosome change
{
String chr = getFirstWord(nextLine.substring(2));
chromosome = chr.replace("chromosome", "chr").replace("_", "");
} else if (nextLine.startsWith("FT")) {
String featureKey = nextLine.substring(5, 19).trim();
if (featureKey.length() == 0) {
if (currentRecord != null) {
currentRecord.append(nextLine);
}
} else {
// New feature started.
if ((currentRecord != null)) {
features.add(createFeature(currentRecord));
}
String temp = nextLine.substring(21);
boolean isNegative = temp.contains("complement");
String lociString = parseJoinString(temp, reader).replace("<",
"").replace(">", "").trim();
currentRecord = new EmblRecord(featureKey.trim(), chromosome, lociString,
isNegative);
}
}
}
// features.addAll(convertEmblToGenes(emblGenes));
return combineGeneParts(features);
} catch (IOException ex) {
ex.printStackTrace();
return null;
}
}
static BasicFeature createFeature(EmblRecord emblRecord) {
BasicFeature feature = new BasicFeature(emblRecord.getChromosome(), emblRecord.getStart(),
emblRecord.getEnd());
feature.setType(emblRecord.getType());
feature.setIdentifier(emblRecord.getIdentifier());
feature.setName(emblRecord.getIdentifier());
feature.setStrand(emblRecord.getStrand());
feature.setDescription(emblRecord.getDescription());
if (emblRecord.getAlias() != null) {
feature.setName(emblRecord.getAlias());
}
// If this is a "gene part" add the exons
for (Exon exon : emblRecord.getExons()) {
feature.addExon(exon);
}
return feature;
}
static HashSet<String> geneParts = new HashSet();
static {
geneParts.add("CDS");
geneParts.add("5'UTR");
geneParts.add("3'UTR");
geneParts.add("intron");
}
// Combine the constituitve gene parts into a single feature (3', 5', and cds). This is
// necccessary with the current IGV gene model, which is heavily influence by ucsc conventions
static List<htsjdk.tribble.Feature> combineGeneParts(List<BasicFeature> features) {
List<htsjdk.tribble.Feature> newFeatureList = new ArrayList(features.size());
Map<String, BasicFeature> genes = new HashMap();
// Step 1 -- find the coding regions
for (BasicFeature feature : features) {
if (feature.getType().equals("CDS")) {
String geneId = feature.getIdentifier();
BasicFeature gene = genes.get(geneId);
if (gene == null) {
gene = new BasicFeature(feature);
gene.setType("transcript");
newFeatureList.add(gene);
genes.put(geneId, gene);
}
Exon exon = new Exon(feature.getChr(), feature.getStart(), feature.getEnd(),
feature.getStrand());
gene.addExon(exon);
}
}
// Step 2 -- add the UTRs and non-gene features
for (BasicFeature feature : features) {
String type = feature.getType();
if (type.equals("CDS")) {
// already accounted for
} else if (type.equals("3'UTR") || type.equals("5'UTR")) {
BasicFeature gene = genes.get(feature.getIdentifier());
if (gene != null) {
Exon exon = new Exon(feature.getChr(), feature.getStart(),
feature.getEnd(), feature.getStrand());
exon.setNonCoding(true);
boolean plus = (type.equals("5'UTR") && feature.getStrand() == Strand.POSITIVE) ||
(type.equals("3'UTR") && feature.getStrand() == Strand.NEGATIVE);
if (plus) {
exon.setCodingStart(feature.getEnd());
exon.setCodingEnd(feature.getEnd());
} else {
exon.setCodingStart(feature.getStart());
exon.setCodingEnd(feature.getStart());
}
gene.addExon(exon);
}
} else {
newFeatureList.add(feature);
}
}
// Compute the phases (reading shifts) for the genes
// TODO -- should we be doing this? It generally works but could there be reading shifts
// between exons that would throw this off?
for (IGVFeature gene : genes.values()) {
computeReadingShifts(gene);
}
return newFeatureList;
}
/**
* FT CDS join(complement(5000933..5001976),
* FT complement(5000325..5000891),complement(5000024..5000272))
* FT /product="GTPase activating protein (predicted)"
* FT /gene="SPAC1952.17c"
* FT /gene="SPAC890.01c"
*
* @param joinString
* @param reader
* @return
* @throws IOException
*/
public static String parseJoinString(String joinString, BufferedReader reader)
throws IOException {
if (joinString.startsWith("join") || joinString.startsWith("complement")) {
int leftParenCount = countChar(joinString, '(');
int rightParenCount = countChar(joinString, ')');
while (leftParenCount != rightParenCount) {
joinString += reader.readLine().replace("FT", "").trim();
leftParenCount = countChar(joinString, '(');
rightParenCount = countChar(joinString, ')');
}
// join and complement functions irrelevant
joinString = joinString.replace("join", "");
joinString = joinString.replace("complement", "");
joinString = joinString.replace("(", "");
joinString = joinString.replace(")", "");
joinString = joinString.replace('<', ' ');
return joinString;
} else {
return joinString;
}
}
/**
* This must exist in the jdk ?
*
* @param string
* @return
*/
static int countChar(String string, char c) {
int cnt = 0;
for (int i = 0; i < string.length(); i++) {
if (c == string.charAt(i)) {
cnt++;
}
}
return cnt;
}
static class EmblRecord {
private static Logger log = Logger.getLogger(EmblRecord.class);
boolean isNegative;
private String type;
private String chromosome;
private String identifier;
private String alias;
private String description;
private int start = Integer.MAX_VALUE;
private int end;
List<Exon> exons;
EmblRecord(String type, String chromosome, String lociString, boolean isNegative) {
this.isNegative = isNegative;
this.type = type;
this.chromosome = chromosome;
createExons(lociString, isNegative);
}
/**
* Method description
*
* @return
*/
public int getStart() {
return start;
}
/**
* Method description
*
* @return
*/
public int getEnd() {
return end;
}
/**
* Method description
*
* @return
*/
public boolean isGenePart() {
return type.equals("CDS") || type.equals("3'UTR") || type.equals("5'UTR");
}
/**
* Method description
*
* @return
*/
public Strand getStrand() {
return isNegative ? Strand.NEGATIVE : Strand.POSITIVE;
}
/**
* Method description
*
* @return
*/
public String getType() {
return type;
}
/**
* Method description
*
* @return
*/
public String getIdentifier() {
return identifier;
}
/**
* Method description
*
* @param identifier
*/
public void setIdentifier(String identifier) {
this.identifier = identifier;
}
/**
* Method description
*
* @return
*/
public String getAlias() {
return alias;
}
/**
* Method description
*
* @param alias
*/
public void setAlias(String alias) {
this.alias = alias;
}
/**
* Method description
*
* @return
*/
public List<Exon> getExons() {
return exons;
}
/**
* Method description
*
* @param nextLine
*/
public void append(String nextLine) {
String attrString = nextLine.substring(21);
if (attrString.startsWith("/gene=")) {
String[] kv = attrString.split("=");
String geneName = kv[1].replace("\"", "");
if (geneName.startsWith("SP")) {
// Some genes have multiple identifiers. Only use the first one
if (getIdentifier() == null) {
setIdentifier(geneName);
}
} else {
setAlias(geneName);
}
} else if (attrString.startsWith("/systematic_id=")) {
String[] kv = attrString.split("=");
String id = kv[1].replace("\"", "");
setIdentifier(id);
setAlias(id);
} else {
appendToDescription(nextLine.substring(22).trim());
}
}
/**
* Method description
*
* @param note
*/
public void appendToDescription(String note) {
if (description == null) {
description = note;
} else {
description += "<br>" + note;
}
}
/**
* Method description
*
* @return
*/
public String getDescription() {
return description;
}
/**
* Create a list of Exon objects from the Embl join string. Apparently exons in embl
* format are represented by a single CDS record.
*
* @param joinString
* @param isNegative
*/
void createExons(String joinString, boolean isNegative) {
String[] lociArray = joinString.split(",");
exons = new ArrayList(lociArray.length);
for (String loci : lociArray) {
try {
String[] tmp = loci.split("\\.\\.");
int exonStart = Integer.parseInt(tmp[0]) - 1; // - (isNegative ? 0 : 1);
int exonEnd = exonStart + 1;
if (tmp.length > 1) {
exonEnd = Integer.parseInt(tmp[1]);
}
Strand strand = isNegative ? Strand.NEGATIVE : Strand.POSITIVE;
Exon r = new Exon(chromosome, exonStart, exonEnd, strand);
start = Math.min(start, exonStart);
end = Math.max(end, exonEnd);
exons.add(r);
} catch (NumberFormatException e) {
log.error("Error parsing exon number; " + joinString, e);
}
}
}
/**
* Method description
*
* @return
*/
public String getChromosome() {
return chromosome;
}
}
static void combineFeatureTables(File[] emblFiles, String outputFile) throws IOException {
PrintWriter pw = new PrintWriter(new FileWriter(outputFile));
for (File ifile : emblFiles) {
BufferedReader br = new BufferedReader(new FileReader(ifile));
String nextLine = null;
while ((nextLine = br.readLine()) != null) {
if (nextLine.startsWith("ID") || nextLine.startsWith("FT")) {
pw.println(nextLine);
}
}
br.close();
}
pw.close();
}
static void splitByType(String emblFile, String outputDirectory) throws IOException {
BufferedReader br = new BufferedReader(new FileReader(emblFile));
String nextLine;
Set<String> codes = new HashSet();
while ((nextLine = br.readLine()) != null) {
if (nextLine.startsWith("FT") && (nextLine.length() > 19)) {
String code = nextLine.substring(5, 19).trim();
if (code.length() > 0) {
codes.add(code);
}
}
}
br.close();
Map<String, PrintWriter> writers = new HashMap();
for (String code : codes) {
writers.put(code,
new PrintWriter(new FileWriter(new File(outputDirectory, code + ".embl"))));
}
br = new BufferedReader(new FileReader(emblFile));
PrintWriter currentWriter = null;
while ((nextLine = br.readLine()) != null) {
if (nextLine.startsWith("ID")) {
for (PrintWriter pw : writers.values()) {
pw.println(nextLine);
}
} else if (nextLine.startsWith("FT")) {
String code = nextLine.substring(5, 19).trim();
if (code.length() > 0) {
currentWriter = writers.get(code);
}
if (currentWriter != null) {
currentWriter.println(nextLine);
}
} else {
currentWriter = null;
}
}
br.close();
for (PrintWriter pw : writers.values()) {
pw.close();
}
}
/**
* Utility method to extract the gene records from an embl file
*
* @param emblFile
* @param outputFile
* @throws java.io.IOException
*/
static void extractGenes(String emblFile, String outputFile) throws IOException {
BufferedReader br = new BufferedReader(new FileReader(emblFile));
String nextLine;
br = new BufferedReader(new FileReader(emblFile));
PrintWriter geneWriter = new PrintWriter(new FileWriter(outputFile));
PrintWriter currentWriter = null;
while ((nextLine = br.readLine()) != null) {
if (nextLine.startsWith("ID")) {
geneWriter.println(nextLine);
} else if (nextLine.startsWith("FT")) {
String code = nextLine.substring(5, 19).trim();
if (code.equals("CDS") || code.equals("3'UTR") || code.equals("5'UTR")) {
currentWriter = geneWriter;
} else if (code.length() > 0) {
currentWriter = null;
}
if (currentWriter != null) {
currentWriter.println(nextLine);
}
} else {
currentWriter = null;
}
}
br.close();
geneWriter.close();
}
// TODO -- put this in a utility class
private static String getFirstWord(String string) {
String trimmedString = string.trim();
char[] chars = trimmedString.toCharArray();
int whitespaceIndex = 0;
for (whitespaceIndex = 0; whitespaceIndex < chars.length; whitespaceIndex++) {
if (Character.isSpaceChar(chars[whitespaceIndex])) {
break;
}
}
return trimmedString.substring(0, whitespaceIndex).trim();
}
/**
* Method description
*
* @param args
* @throws IOException
*/
public static void main(String[] args) throws IOException {
// String[] ifiles = { "/Users/jrobinso/IGVTestData/SPombe/chromosome1.contig.embl",
// "/Users/jrobinso/IGVTestData/SPombe/chromosome2.contig.embl",
// "/Users/jrobinso/IGVTestData/SPombe/chromosome3.contig.embl" };
// splitByType("/Users/jrobinso/IGVTestData/SPombe/spombe.ft.embl",
// "/Users/jrobinso/IGVTestData/SPombe/");
// combineFeatureTables((new File("/Users/jrobinso/plasmodium/v2.1/Embl/")).listFiles(), "/Users/jrobinso/plasmodium/v2.1/Embl/MAL.embl");
// extractGenes("/Users/jrobinso/plasmodium/v2.1/Embl/MAL.embl",
// "/Users/jrobinso/plasmodium/v2.1/Embl/MAL.genes.embl");
splitByType("/Users/jrobinso/plasmodium/v2.1/Embl/MAL.embl",
"/Users/jrobinso/plasmodium/v2.1/Embl");
/*
*
* String fnTemp =
* "/Users/jrobinso/IGVTestData/SPombe/chromosome$.contig.embl";
*
* List<IGVFeature> allFeatures = new ArrayList();
*
* for (int i = 1; i <= 3; i++)
* {
* String chromosome = "chr" + i;
* String fn = fnTemp.replace("$", "" + i);
*
* List<IGVFeature> features = (new EmblFeatureTableParser()).loadTracks(fn);
* for (IGVFeature f : features)
* {
* ((BasicFeature) f).setChromosome(chromosome);
* ((BasicFeature) f).sortExons();
* if (f.getIdentifier().equals("SPAC212.04c"))
* {
* f.getAminoAcidSequence(1);
* }
* allFeatures.add(f);
* }
* }
*
* // SPAC212.04c
*
*
* AbstractFeatureFileParser.dumpFeatures(allFeatures,
* "/Users/jrobinso/spombe_160708.refflat");
*
*
* String test1 = "<5000933..5001976";
*
* System.out.println(test1.replace("<", ""));
*
* BufferedReader br = new BufferedReader(new StringReader(test1));
* System.out.println(parseJoinString(test1, br));
*
* String test2 =
* "join(5000933..5001976,5000325..5000891,5000024..5000272)";
*
* br = new BufferedReader(new StringReader(test2));
* System.out.println(parseJoinString(test2, br));
*/
}
}