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The IO bundle for Geneweaver.
/*-
*
* Copyright 2018, 2020 The Jackson Laboratory Inc.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
* @author Matthew Gerring
*/
package org.geneweaver.io.reader;
import java.io.IOException;
import java.io.InputStream;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.Map;
import java.util.function.Function;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.stream.Stream;
import org.apache.commons.beanutils.BeanMap;
import org.geneweaver.domain.Entity;
import org.geneweaver.domain.NamedEntity;
import org.geneweaver.domain.Peak;
import org.geneweaver.domain.Peak.Strand;
import org.geneweaver.domain.Track;
import org.geneweaver.io.connector.BedConnector;
import org.geneweaver.io.connector.ChromosomeService;
/**
* Bed file format @see https://m.ensembl.org/info/website/upload/bed.html
* @see https://en.wikipedia.org/wiki/BED_(file_format)#:~:text=is%20widely%20used.-,Description,coordinates%20of%20the%20sequences%20considered.
* @author gerrim
*
* @param
*/
public class BedReader extends LineIteratorReader {
private ChromosomeService cservice = ChromosomeService.getInstance();
/**
* Create the reader by setting its data
*
* @param request
* @throws ReaderException
*/
@SuppressWarnings("unchecked")
@Override
public BedReader init(ReaderRequest request) throws ReaderException {
super.setup(request);
setDelimiter("\\s+");
return this;
}
@SuppressWarnings("unchecked")
@Override
protected N create(String line) throws ReaderException {
N ret;
if (line.startsWith("track ")) {
String ln = line.substring(5); // Remove track
Map attr = parseQuotedAttributes(ln);
Track track = new Track();
BeanMap d = new BeanMap(track);
d.put("name", attr.get("name"));
d.put("type", attr.get("type"));
d.put("graphType", attr.get("graphType"));
d.put("description", attr.get("description"));
if (attr.containsKey("priority")) d.put("priority", attr.get("priority"));
if (attr.containsKey("color")) {
track.setColor(getIntArray(attr.get("color"), 3));
}
if (attr.containsKey("useScore")) d.put("useScore", attr.get("useScore"));
if (attr.containsKey("itemRgb")) {
String val = attr.get("itemRgb");
track.setItemRgb("on".equals(val));
}
ret = (N)track;
} else {
String[] rec = line.split(getDelimiter());
Peak peak = new Peak();
BeanMap d = new BeanMap(peak);
// At one time we allowed the bad chromosomes to
// come in through the peaks but now we do not.
String chrom = cservice.getChromosome(rec[0]);
if (chrom==null) return null;
d.put("chr", chrom);
d.put("start", rec[1]);
d.put("end", rec[2]);
if (rec.length>3) d.put("name", rec[3]);
if (rec.length>4) d.put("score", rec[4]);
if (rec.length>5) d.put("strand", Strand.from(rec[5]));
if (rec.length>6) d.put("thickStart", rec[6]);
if (rec.length>7) d.put("thickEnd", rec[7]);
if (rec.length>8) {
peak.setItemRgb(getIntArray(rec[8], 3));
}
if (rec.length>9) d.put("blockCount", rec[9]);
if (rec.length>10) d.put("blockSizes", getIntArray(rec[10], 1));
if (rec.length>11) d.put("blockStarts", getIntArray(rec[11], 1));
parseName(d);
String epi = peak.getEpigenome();
String feat = peak.getFeatureType();
if (epi==null && feat!=null) return null;
createPeakId(peak);
ret = (N)peak;
}
ret.setSpecies(getSpecies());
return ret;
}
public Stream stream() {
return super.stream();
}
private Peak createPeakId(Peak peak) {
int start = peak.getStart();
int end = peak.getEnd();
String peakId = createPeakId(peak.getEpigenome(), peak.getChr(), start, end, peak.getTissueDescription());
peak.setPeakId(peakId);
return peak;
}
/**
* Try to make a repeatable unique peakId from the properties
* of the peak.
*
* @param featureName
* @param chr
* @param path
* @param start
* @param end
* @param removeSpecialChars
* @return the peak id as a string.
*/
public static String createPeakId(String epiGen, String chr, int start, int end, String tissue) {
StringBuilder buf = new StringBuilder();
buf.append(epiGen);
buf.append("@");
buf.append(chr);
buf.append("#");
buf.append(start);
buf.append(":");
buf.append(end);
// Using this can find out from id if tissue
// was identified.
String tc = tissue!=null && !tissue.isBlank() ? "+t" : "-t";
buf.append(tc);
return buf.toString();
}
// Parse name in Ensembl format e.g.
// BCL3_A549__Enriched_Site
// H3K4me1_embryonic_facial_prominence_embryonic_10_5_days__Enriched_Site
private static final Pattern pattern = Pattern.compile("([a-zA-Z0-9]+)_([a-zA-Z0-9_]+)__Enriched_Site");
/**
* The name encodes the featureType and o
* @param d
* @throws ReaderException
*/
private void parseName(BeanMap d) throws ReaderException {
Object name = d.get("name");
if (name==null) return;
Matcher matcher = pattern.matcher(name.toString());
if (!matcher.matches()) return;
d.put("featureType", matcher.group(1));
String egen = matcher.group(2);
d.put("epigenome", egen);
Map des = getEpigenomeDescriptions(getSpecies());
if (des!=null) {
String ekey = getKey(egen);
String descr = des.get(ekey);
if (descr!=null) {
d.put("tissueDescription", descr);
}
}
}
Peak testParseName(String name) throws ReaderException {
Peak peak = new Peak(name);
parseName(new BeanMap(peak));
return peak;
}
private int[] getIntArray(String string, int min) {
String[] col = string.split(",");
Collection ret = new LinkedList<>();
for (String c : col) {
ret.add(Integer.parseInt(c));
}
if (ret.size() ret) {
int[] ia = new int[ret.size()];
Iterator it = ret.iterator();
for (int i = 0; i < ia.length; i++) {
ia[i] = it.next();
}
return ia;
}
@Override
protected String getAssignmentChar() {
return "=";
}
@Override
public Function> getDefaultConnector() {
Function> func = new BedConnector();
return func;
}
/**
* This is static data residing in classpath data. We keep it in memory
* once loaded to reduce parsing if there are a lot of BedReaders created.
* This can be the case (1000's at least) when parsing all the files to build
* the graph.
*/
private static final Map> descriptions = new HashMap<>();
Map getEpigenomeDescriptions(String species) throws ReaderException {
if (species==null) return Collections.emptyMap();
if (descriptions.get(species)!=null) return descriptions.get(species);
String path ="/epigenome_description/"+species.replace(" ", "_")+".tsv";
InputStream in = getClass().getResourceAsStream(path);
if (in == null) {
try {
String local = "src/main/resources"+path;
in = Files.newInputStream(Paths.get(local));
} catch (IOException ignored) {
// Of the local path cannot be determined,
// we ignore that we cannot do tissue lookups.
return null;
}
}
ReaderRequest req = new ReaderRequest(species, in, path);
req.setReaderHint("MapCSVReader");
req.setDelimiter("\t");
StreamReader> lines = ReaderFactory.getReader(req);
final Map fdescr = new HashMap<>();
lines.stream().forEach(m->{
String ekey = getKey(m.get("Epigenome"));
String des = m.get("Description");
fdescr.put(ekey, des);
});
descriptions.put(species, fdescr);
return fdescr;
}
private static Pattern postPattern = Pattern.compile("([a-z0-9]+?)(postnatal(\\d+)days)");
private static Pattern embPattern = Pattern.compile("([a-z0-9]+?)(embryonic(\\d+)days)");
private static Pattern daysPattern = Pattern.compile("([a-z0-9]+?)\\d+days");
private static Pattern weeksPattern = Pattern.compile("([a-z0-9]+?)\\d+weeks");
public static String getKey(final String origName) {
String keyName = origName.toLowerCase();
keyName = keyName.replaceAll("[^a-z0-9]+", "");
// P0 in one key is postnatal_0_days in the other.
Matcher post = postPattern.matcher(keyName);
if (post.matches()) {
keyName = post.group(1)+"p"+post.group(3);
}
// E10.5 in one key is embryonic_10_5_days in the other.
Matcher emb = embPattern.matcher(keyName);
if (emb.matches()) {
keyName = emb.group(1)+"e"+emb.group(3);
}
// Remove (8weeks) from end.
Matcher days = daysPattern.matcher(keyName);
if (days.matches()) {
keyName = days.group(1);
}
// Remove (8weeks) from end.
Matcher weeks = weeksPattern.matcher(keyName);
if (weeks.matches()) {
keyName = weeks.group(1);
}
return keyName;
}
}