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* 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
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* furnished to do so, subject to the following conditions:
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* The above copyright notice and this permission notice shall be included in
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*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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package org.broad.igv.feature.tribble;
import org.broad.igv.Globals;
import org.broad.igv.cli_plugin.Argument;
import org.broad.igv.cli_plugin.LineFeatureDecoder;
import org.broad.igv.cli_plugin.LineFeatureEncoder;
import org.broad.igv.feature.*;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.ui.color.ColorUtilities;
import org.broad.igv.util.StringUtils;
import htsjdk.tribble.Feature;
import java.util.List;
import java.util.Map;
import java.util.regex.Pattern;
/**
* Codec for UCSC DGV Table
*
* @author jrobinso
* Date: 10/30/13
* Time: 8:23 AM
*
field example SQL type info description
1 bin 73 smallint(6) range Indexing field to speed chromosome range queries.
2 chrom chr1 varchar(255) values Reference sequence chromosome or scaffold
3 chromStart 10000 int(10) unsigned range Start position in chromosome
4 chromEnd 846808 int(10) unsigned range End position in chromosome
5 name dgv2n71 varchar(255) values ID of merged variant or supporting variant
6 score 0 int(10) unsigned range Score from 0-1000 (placeholder for BED 9+ format)
7 strand + char(1) values + or - (placeholder for BED 9+ format)
8 thickStart 10000 int(10) unsigned range Same as chromStart (placeholder for BED 9+ format)
9 thickEnd 10000 int(10) unsigned range Same as chromStart (placeholder for BED 9+ format)
10 itemRgb 200 int(10) unsigned range Item R,G,B color.
11 varType Gain varchar(255) values Type of variation
12 reference Xu et al 2011 varchar(255) values Literature reference for the study that included this variant
13 pubMedId 21882294 int(10) unsigned range For linking to pubMed abstract of reference
14 method SNP array longblob Brief description of method
15 platform longblob Sequencing platform (if specified)
16 mergedVariants varchar(255) values If this is a supporting variant, ID of merged variant
17 supportingVariants nsv871664,nsv871113 longblob If this is a merged variant, IDs of supporting variants
18 sampleSize 6533 int(10) unsigned range Number of samples in study
19 observedGains 3 int(10) unsigned range Number of samples with copy number gains
20 observedLosses 0 int(10) unsigned range Number of samples with copy number losses
21 cohortDescription longblob Description of sample population for the study
22 genes FAM138A, FAM138F, FAM41C, L... longblob Genes overlapping this variant
23 samples IS30771,IS39243,IS41043 longblob Sample IDs if available
*/
/**
*
*/
public class DGVCodec extends UCSCCodec<BasicFeature> implements LineFeatureEncoder<Feature>, LineFeatureDecoder<BasicFeature> {
static final Pattern BR_PATTERN = Pattern.compile("<br>");
static final Pattern EQ_PATTERN = Pattern.compile("=");
Genome genome;
public DGVCodec() {
this(null);
}
public DGVCodec(Genome genome) {
super(BasicFeature.class);
this.genome = genome;
}
static String[] attributeLabels = {"Type", "Reference", "PubMed ID", "Method", "Platform", "Merged variants",
"Supporting variants", "Sample size", "Observed gains", "Observed losses", "Cohort description",
"Genes", "Samples"};
public BasicFeature decode(String[] tokens) {
int tokenCount = tokens.length;
String c = tokens[0];
String chr = genome == null ? c : genome.getCanonicalChrName(c);
//BED format, and IGV, use starting element as 0.
int start = Integer.parseInt(tokens[1]);
int end = Integer.parseInt(tokens[2]);
BasicFeature feature = new BasicFeature(chr, start, end);
String name = tokens[3].replaceAll("\"", "");
feature.setName(name);
feature.setIdentifier(name);
String colorString = tokens[4];
if (colorString.trim().length() > 0 && !colorString.equals(".")) {
feature.setColor(ColorUtilities.stringToColor(colorString));
}
for (int i = 5; i < tokens.length; i++) {
if (tokens[i].length() > 0)
feature.setAttribute(attributeLabels[i - 5], tokens[i]);
}
/*
varType Gain varchar(255) values Type of variation
reference Xu et al 2011 varchar(255) values Literature reference for the study that included this variant
pubMedId 21882294 int(10) unsigned range For linking to pubMed abstract of reference
method SNP array longblob Brief description of method
platform longblob Sequencing platform (if specified)
mergedVariants varchar(255) values If this is a supporting variant, ID of merged variant
supportingVariants nsv871664,nsv871113 longblob If this is a merged variant, IDs of supporting variants
sampleSize 6533 int(10) unsigned range Number of samples in study
observedGains 3 int(10) unsigned range Number of samples with copy number gains
observedLosses 0 int(10) unsigned range Number of samples with copy number losses
cohortDescription longblob Description of sample population for the study
genes FAM138A, FAM138F, FAM41C, L... longblob Genes overlapping this variant
samples IS30771,IS39243,IS41043 longblob Sample IDs if available
*/
return feature;
}
@Override
public BasicFeature decode(String nextLine) {
if (nextLine.trim().length() == 0) {
return null;
}
if (nextLine.startsWith("#") || nextLine.startsWith("track") || nextLine.startsWith("browser")) {
this.readHeaderLine(nextLine);
return null;
}
String[] tokens = Globals.tabPattern.split(nextLine);
return decode(tokens);
}
/**
* 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
*/
@Override
public boolean canDecode(String path) {
return path.toLowerCase().endsWith(".bed");
}
/**
* Encode a feature as a BED string.
*
* @param feature - feature to encode
* @return the encoded string
*/
public String encode(Feature feature) {
StringBuffer buffer = new StringBuffer();
buffer.append(feature.getChr());
buffer.append("\t");
final int featureStart = feature.getStart();
buffer.append(String.valueOf(featureStart));
buffer.append("\t");
buffer.append(String.valueOf(feature.getEnd()));
BasicFeature basicFeature = null;
if (!(feature instanceof BasicFeature)) {
return buffer.toString();
} else {
basicFeature = (BasicFeature) feature;
}
if (basicFeature.getName() != null || (isGffTags() && basicFeature.getDescription() != null)) {
buffer.append("\t");
if (isGffTags() && basicFeature.getDescription() != null) {
// mRNA<br>ID = LOC_Os01g01010.2<br>Name = LOC_Os01g01010.2<br>Parent = LOC_Os01g01010<br>
//ID=LOC_Os01g01010.1:exon_1;Parent=LOC_Os01g01010.1
String[] attrs = BR_PATTERN.split(basicFeature.getDescription());
buffer.append("\"");
for (String att : attrs) {
String[] kv = EQ_PATTERN.split(att, 2);
if (kv.length > 1) {
buffer.append(kv[0].trim());
buffer.append("=");
String value = kv[1].trim();
buffer.append(StringUtils.encodeURL(value));
buffer.append(";");
}
}
buffer.append("\"");
} else {
buffer.append(basicFeature.getName());
}
boolean more = !Float.isNaN(basicFeature.getScore()) || basicFeature.getStrand() != Strand.NONE ||
basicFeature.getColor() != null || basicFeature.getExonCount() > 0;
if (more) {
buffer.append("\t");
// UCSC scores are integers between 0 and 1000, but
float score = basicFeature.getScore();
if (Float.isNaN(score)) {
buffer.append("1000");
} else {
boolean isInt = (Math.floor(score) == score);
buffer.append(String.valueOf(isInt ? (int) score : score));
}
more = basicFeature.getStrand() != Strand.NONE || basicFeature.getColor() != null || basicFeature.getExonCount() > 0;
if (more) {
buffer.append("\t");
Strand strand = basicFeature.getStrand();
if (strand == Strand.NONE) buffer.append(" ");
else if (strand == Strand.POSITIVE) buffer.append("+");
else if (strand == Strand.NEGATIVE) buffer.append("-");
more = basicFeature.getColor() != null || basicFeature.getExonCount() > 0;
if (more) {
// Must continue if basicFeature has color or exons
java.util.List<Exon> exons = basicFeature.getExons();
if (basicFeature.getColor() != null || exons != null) {
buffer.append("\t");
buffer.append(String.valueOf(basicFeature.getThickStart()));
buffer.append("\t");
buffer.append(String.valueOf(basicFeature.getThickEnd()));
buffer.append("\t");
java.awt.Color c = basicFeature.getColor();
buffer.append(c == null ? "." : ColorUtilities.colorToString(c));
buffer.append("\t");
if (exons != null && exons.size() > 0) {
buffer.append(String.valueOf(exons.size()));
buffer.append("\t");
for (Exon exon : exons) {
buffer.append(String.valueOf(exon.getLength()));
buffer.append(",");
}
buffer.append("\t");
for (Exon exon : exons) {
int exonStart = exon.getStart() - featureStart;
buffer.append(String.valueOf(exonStart));
buffer.append(",");
}
}
}
}
}
}
}
return buffer.toString();
}
@Override
public int getNumCols(String line) {
return line.split("\t").length;
}
@Override
public String getHeader() {
return null;
}
@Override
public void setInputs(List<String> commands, Map<Argument, Object> argumentMap, Argument argument) {
//To change body of implemented methods use File | Settings | File Templates.
}
}