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* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
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* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
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* 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
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package org.broad.igv.feature.tribble;
import org.broad.igv.Globals;
import org.broad.igv.feature.PSLRecord;
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;
/**
* @author jrobinso
* @date Aug 5, 2010
* <p/>
* Columns:
* <p/>
* 1. matches - Number of bases that match that aren't repeats
* 2. misMatches - Number of bases that don't match
* 3. repMatches - Number of bases that match but are part of repeats
* 4. nCount - Number of 'N' bases
* 5. qNumInsert - Number of inserts in query
* 6. qBaseInsert - Number of bases inserted in query
* 7. tNumInsert - Number of inserts in target
* 8. tBaseInsert - Number of bases inserted in target
* 9. strand - '+' or '-' for query strand. For translated alignments, second '+'or '-' is for genomic strand
* 10. qName - Query sequence name
* 11. qSize - Query sequence size
* 12. qStart - Alignment start position in query
* 13. qEnd - Alignment end position in query
* 14. tName - Target sequence name
* 15. tSize - Target sequence size
* 16. tStart - Alignment start position in target
* 17. tEnd - Alignment end position in target
* 18. blockCount - Number of blocks in the alignment (a block contains no gaps)
* 19. blockSizes - Comma-separated list of sizes of each block
* 20. qStarts - Comma-separated list of starting positions of each block in query
* 21. tStarts - Comma-separated list of starting positions of each block in target
*/
public class PSLCodec extends UCSCCodec<BasicFeature> {
Genome genome;
boolean keepText;
public PSLCodec(){
this(null);
}
public PSLCodec(Genome genome) {
this(genome, false);
}
public PSLCodec(Genome genome, boolean keepText) {
super(BasicFeature.class);
this.genome = genome;
this.keepText = keepText;
}
public PSLRecord decode(String line) {
PSLRecord f = null;
try {
if (line.trim().length() == 0 ||
line.startsWith("#") ||
line.startsWith("track") ||
line.startsWith("browser") ||
line.startsWith("psLayout") ||
line.startsWith("match") ||
line.startsWith("---")) {
return null;
}
String[] tokens = Globals.singleTabMultiSpacePattern.split(line);
int nTokens = tokens.length;
if (nTokens < 21) {
// log.info("Skipping line ")
return null;
}
int tSize = Integer.parseInt(tokens[14]);
String chrToken = tokens[13];
String chr = genome == null ? chrToken : genome.getCanonicalChrName(chrToken);
int start = Integer.parseInt(tokens[15]); // IS PSL 1 or ZERO based, closed or open?
String strandString = tokens[8];
Strand strand = strandString.startsWith("+") ? Strand.POSITIVE : Strand.NEGATIVE;
boolean gNeg = false;
if (strandString.length() > 1) {
gNeg = strandString.charAt(1) == '-';
}
f = new PSLRecord();
f.setName(tokens[9]);
f.setChr(chr);
f.setStart(start);
f.setEnd(Integer.parseInt(tokens[16]));
f.setStrand(strand);
int exonCount = Integer.parseInt(tokens[17]);
String[] exonSizes = tokens[18].split(",");
String[] startsBuffer = tokens[20].split(",");
if (startsBuffer.length == exonSizes.length && exonCount == startsBuffer.length) {
for (int i = 0; i < startsBuffer.length; i++) {
int exonSize = Integer.parseInt(exonSizes[i]);
int exonStart = Integer.parseInt(startsBuffer[i]);
if (gNeg) {
exonStart = tSize - exonStart - exonSize;
}
int exonEnd = exonStart + exonSize;
Exon exon = new Exon(chr, exonStart, exonEnd, strand);
f.addExon(exon);
}
} else {
// TODO -- warn
}
//score = percentId = 100.0 * (match + repMatch) / (misMatch + match + repMatch + qGapCount + tGapCount)
int match = Integer.parseInt(tokens[0]);
int misMatch = Integer.parseInt(tokens[1]);
int repMatch = Integer.parseInt(tokens[2]);
int ns = Integer.parseInt(tokens[3]);
int qGapCount = Integer.parseInt(tokens[4]);
int qGapBases = Integer.parseInt(tokens[5]);
int tGapCount = Integer.parseInt(tokens[6]);
int tGapBases = Integer.parseInt(tokens[7]);
int qSize = Integer.parseInt(tokens[10]);
float score = (1000.0f * (match + repMatch - misMatch - qGapCount - tGapCount)) / qSize;
f.setMatch(match);
f.setMisMatch(misMatch);
f.setRepMatch(repMatch);
f.setNs(ns);
f.setQGapCount(qGapCount);
f.setQGapBases(qGapBases);
f.setTGapCount(tGapCount);
f.setTGapBases(tGapBases);
f.setQSize(qSize);
f.setScore(score);
// Build description
StringBuffer desc = new StringBuffer();
desc.append("matches = " + tokens[0]);
desc.append("<br>");
desc.append("mismatches = " + tokens[1]);
desc.append("<br>");
desc.append("repeat matches = " + tokens[2]);
desc.append("<br>");
desc.append("# inserts in query = " + tokens[4]);
desc.append("<br>");
desc.append("# inserts in target = " + tokens[6]);
f.setDescription(desc.toString());
if(keepText) {
f.setText(line);
}
} catch (NumberFormatException e) {
return null;
}
return f;
}
/**
* 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 path.toLowerCase().endsWith(".psl") || path.toLowerCase().endsWith(".psl.gz");
}
}