Moved AnnotatorInputTableFeature and Codec to org.broadinstitute.sting.gatk.refdata.features.annotator
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3424 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
weisburd
parent
42fa12d9e4
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64ed770250
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/*
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* Copyright (c) 2010 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
|
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
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* copies of the Software, and to permit persons to whom the
|
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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||||
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.refdata.features.annotator;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.IOException;
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import java.util.ArrayList;
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import org.apache.log4j.Logger;
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import org.broad.tribble.FeatureCodec;
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import org.broad.tribble.util.AsciiLineReader;
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import org.broad.tribble.util.LineReader;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.Utils;
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public class AnnotatorInputTableCodec implements FeatureCodec<AnnotatorInputTableFeature> {
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private static Logger logger = Logger.getLogger(AnnotatorInputTableCodec.class);
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public static final String DELIMITER = "\t";
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private ArrayList<String> header;
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/**
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* Parses the header.
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*
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* @param reader
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*
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* @return The # of header lines for this file.
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*/
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public int readHeader(LineReader reader)
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{
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int[] lineCounter = new int[1];
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try {
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header = readHeader(reader, lineCounter);
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} catch(IOException e) {
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throw new IllegalArgumentException("Unable to read from file.", e);
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}
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return lineCounter[0];
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}
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/**
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* Parses the line into an AnnotatorInputTableFeature object.
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*
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* @param line
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*/
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public AnnotatorInputTableFeature decode(String line) {
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final ArrayList<String> header = this.header; //optimization
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final ArrayList<String> values = Utils.split(line, DELIMITER, header.size());
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//if ( values.size() > header.size()) {
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// throw new CodecLineParsingException(String.format("Encountered a line within " + file + " that has %d columns which is > the number of columns in the header which has %d columns.\nHeader: " + header + "\nLine: " + values, values.size(), header.size()));
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//}
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final AnnotatorInputTableFeature feature = new AnnotatorInputTableFeature(header);
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for ( int i = 0; i < header.size(); i++ ) {
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feature.putColumnValue(header.get(i), values.get(i));
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}
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final GenomeLoc loc = GenomeLocParser.parseGenomeLoc(values.get(0)); //GenomeLocParser.parseGenomeInterval(values.get(0)); - TODO switch to this
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//parse the location
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feature.setChr(loc.getContig());
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feature.setStart((int) loc.getStart());
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feature.setEnd((int) loc.getStop());
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return feature;
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}
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/**
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* Returns the header.
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* @param source
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* @return
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* @throws IOException
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*/
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public static ArrayList<String> readHeader(final File source) throws IOException {
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FileInputStream is = new FileInputStream(source);
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try {
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return readHeader(new AsciiLineReader(is), null);
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} finally {
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is.close();
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}
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}
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/**
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* Returns the header, and also sets the 2nd arg to the number of lines in the header.
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* @param source
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* @param lineCounter An array of length 1 or null. If not null, array[0] will be set to the number of lines in the header.
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* @return The header fields.
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* @throws IOException
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*/
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private static ArrayList<String> readHeader(final LineReader source, int[] lineCounter) throws IOException {
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ArrayList<String> header = null;
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int numLines = 0;
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//find the 1st line that's non-empty and not a comment
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String line = null;
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while( (line = source.readLine()) != null ) {
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numLines++;
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line = line.trim();
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if ( line.isEmpty() || line.startsWith("#") ) {
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continue;
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}
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//parse the header
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header = Utils.split(line, DELIMITER);
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break;
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}
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// check that we found the header
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if ( header == null ) {
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throw new IllegalArgumentException("No header in " + source + ". All lines are either comments or empty.");
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}
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if(lineCounter != null) {
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lineCounter[0] = numLines;
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}
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logger.info(String.format("Found header line containing %d columns:\n[%s]", header.size(), Utils.join("\t", header)));
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return header;
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}
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}
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@ -0,0 +1,260 @@
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/*
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* Copyright (c) 2010 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.refdata.features.annotator;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.HashMap;
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import java.util.Map;
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import java.util.Set;
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import java.util.Map.Entry;
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import org.broad.tribble.Feature;
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/**
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* This class represents a single record in an AnnotatorInputTable.
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*/
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public class AnnotatorInputTableFeature implements Feature {
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private ArrayList<String> columnNames;
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private HashMap<String, String> columnValues;
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private String chr;
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private int start;
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private int end;
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// Temporary attributes were added to make it easier to implement certain
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// optimizations for RODs that span an interval. For example, if a Walker
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// needs to do a time-consuming computation on data from a ROD, it would normally
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// have to repeat this computation every time its map(..) method is called.
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// If a ROD spans an interval, the Walker's map(..) method will be called for every position in ROD.
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// However, many computations (including validation and parsing) are done per ROD rather than
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// per position. Therefore, substantial optimizations are possible if the result
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// of the first computation is cached and reused on subsequent map(..) calls.
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// Temporary attributes provide a convenient place to store these results,
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// freeing the Walkers from having to maintain their own ROD -> result hashmaps.
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private Map<Object, Object> temporaryAttributes;
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/**
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* Constructor.
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* @param columnNames The column names as parsed out of the file header.
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*/
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public AnnotatorInputTableFeature(ArrayList<String> columnNames) {
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this.columnNames = columnNames;
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this.columnValues = new HashMap<String, String>();
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}
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/**
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* Returns the list of column names from the file header.
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* @return
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*/
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public ArrayList<String> getHeader() {
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return columnNames;
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}
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/**
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* Returns the value of the given column.
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*
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* @param columnName The column name as it appears in the file header.
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* @return The value
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*/
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public String getColumnValue(final Object columnName) {
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return columnValues.get(columnName);
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}
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public boolean containsColumnName(final Object columnName) {
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return columnValues.containsKey(columnName);
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}
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/**
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* Sets the value for the given column.
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*
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* @param columnName The column name as it appears in the file header.
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* @param value The value
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* @return The existing value associated with the columnName, if there is one.
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*/
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protected String putColumnValue(final String columnName, final String value) {
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return columnValues.put(columnName, value);
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}
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/**
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* Returns all values in this line, hashed by their column names.
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*
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* @return
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*/
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public Map<String,String> getColumnValues() {
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return Collections.unmodifiableMap(columnValues);
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}
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/**
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* Returns the entry set of all column name-value pairs.
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*
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* @return
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*/
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public Set<Entry<String, String>> getEntrySet() {
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return columnValues.entrySet();
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}
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public String getChr() {
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return chr;
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}
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public int getStart() {
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return start;
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}
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public int getEnd() {
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return end;
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}
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protected void setChr(String chr) {
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this.chr = chr;
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}
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protected void setStart(int start) {
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this.start = start;
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}
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protected void setEnd(int end) {
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this.end = end;
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}
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/**
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* Checks whether an attribute has been set for the given key.
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*
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* Temporary attributes make it easier to implement certain
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* optimizations for RODs that span an interval. For example, if a Walker
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* needs to do a time-consuming computation on data from a ROD, it would normally
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* have to repeat this computation every time its map(..) method is called.
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* If a ROD spans an interval, the Walker's map(..) method will be called for every position in ROD.
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* However, many computations (including validation and parsing) are done per ROD rather than
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* per position. Therefore, substantial optimizations are possible if the result
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* of the first computation is cached and reused on subsequent map(..) calls.
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* Temporary attributes provide a convenient place to store these results,
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* freeing the Walkers from having to maintain their own ROD -> result hashmaps.
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*
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* @param key key
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* @return True if an attribute has been set for this key.
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*/
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public boolean containsTemporaryAttribute(Object key) {
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if(temporaryAttributes != null) {
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return temporaryAttributes.containsKey(key);
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}
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return false;
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}
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/**
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* Sets the key to the given value, replacing any previous value. The previous
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* value is returned.
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*
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* Temporary attributes make it easier to implement certain
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* optimizations for RODs that span an interval. For example, if a Walker
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* needs to do a time-consuming computation on data from a ROD, it would normally
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* have to repeat this computation every time its map(..) method is called.
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* If a ROD spans an interval, the Walker's map(..) method will be called for every position in ROD.
|
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* However, many computations (including validation and parsing) are done per ROD rather than
|
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* per position. Therefore, substantial optimizations are possible if the result
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* of the first computation is cached and reused on subsequent map(..) calls.
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* Temporary attributes provide a convenient place to store these results,
|
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* freeing the Walkers from having to maintain their own ROD -> result hashmaps.
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*
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* @param key key
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* @param value value
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* @return attribute
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*/
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public Object setTemporaryAttribute(Object key, Object value) {
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if(temporaryAttributes == null) {
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temporaryAttributes = new HashMap<Object, Object>();
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}
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return temporaryAttributes.put(key, value);
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}
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/**
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* Looks up the value associated with the given key.
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*
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* Temporary attributes make it easier to implement certain
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* optimizations for RODs that span an interval. For example, if a Walker
|
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* needs to do a time-consuming computation on data from a ROD, it would normally
|
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* have to repeat this computation every time its map(..) method is called.
|
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* If a ROD spans an interval, the Walker's map(..) method will be called for every position in ROD.
|
||||
* However, many computations (including validation and parsing) are done per ROD rather than
|
||||
* per position. Therefore, substantial optimizations are possible if the result
|
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* of the first computation is cached and reused on subsequent map(..) calls.
|
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* Temporary attributes provide a convenient place to store these results,
|
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* freeing the Walkers from having to maintain their own ROD -> result hashmaps.
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*
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* @param key key
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* @return The value, or null.
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*/
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public Object getTemporaryAttribute(Object key) {
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if(temporaryAttributes != null) {
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return temporaryAttributes.get(key);
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}
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return null;
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}
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/**
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* Removes the attribute that has the given key.
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*
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* Temporary attributes make it easier to implement certain
|
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* optimizations for RODs that span an interval. For example, if a Walker
|
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* needs to do a time-consuming computation on data from a ROD, it would normally
|
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* have to repeat this computation every time its map(..) method is called.
|
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* If a ROD spans an interval, the Walker's map(..) method will be called for every position in ROD.
|
||||
* However, many computations (including validation and parsing) are done per ROD rather than
|
||||
* per position. Therefore, substantial optimizations are possible if the result
|
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* of the first computation is cached and reused on subsequent map(..) calls.
|
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* Temporary attributes provide a convenient place to store these results,
|
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* freeing the Walkers from having to maintain their own ROD -> result hashmaps.
|
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*
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* @param key key
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* @return The value that was associated with this key, or null.
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*/
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public Object removeTemporaryAttribute(Object key) {
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if(temporaryAttributes != null) {
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return temporaryAttributes.remove(key);
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}
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return null;
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}
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}
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@ -1,3 +1,28 @@
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/*
|
||||
* Copyright (c) 2010 The 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.broadinstitute.sting.playground.gatk.walkers.annotator;
|
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|
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/**
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|
|
|
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|
|
@ -1,3 +1,28 @@
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/*
|
||||
* Copyright (c) 2010 The 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.broadinstitute.sting.playground.gatk.walkers.annotator;
|
||||
|
||||
import java.util.HashMap;
|
||||
|
|
@ -14,7 +39,7 @@ import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
|
|||
import org.broadinstitute.sting.gatk.contexts.variantcontext.Allele;
|
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
|
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
||||
import org.broadinstitute.sting.gatk.refdata.features.sampileup.AnnotatorInputTableFeature;
|
||||
import org.broadinstitute.sting.gatk.refdata.features.annotator.AnnotatorInputTableFeature;
|
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import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
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import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
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import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
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Reference in New Issue