vcf2svg

src/main/java/com/github/lindenb/jvarkit/tools/vcf2html/VcfToHtml.java

@@ -0,0 +1,214 @@
+/*
+
+Copyright (c) 2021 Pierre Lindenbaum
+
+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
+The MIT License (MIT)
+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 com.github.lindenb.jvarkit.tools.vcf2html;
+
+import java.io.OutputStream;
+import java.io.PrintWriter;
+import java.io.StringWriter;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import javax.xml.stream.XMLOutputFactory;
+import javax.xml.stream.XMLStreamWriter;
+
+import com.beust.jcommander.Parameter;
+import com.github.lindenb.jvarkit.io.ArchiveFactory;
+import com.github.lindenb.jvarkit.lang.StringUtils;
+import com.github.lindenb.jvarkit.samtools.util.IntervalListProvider;
+import com.github.lindenb.jvarkit.samtools.util.SimpleInterval;
+import com.github.lindenb.jvarkit.util.bio.SequenceDictionaryUtils;
+import com.github.lindenb.jvarkit.util.jcommander.Launcher;
+import com.github.lindenb.jvarkit.util.jcommander.Program;
+import com.github.lindenb.jvarkit.util.log.Logger;
+import com.github.lindenb.jvarkit.util.samtools.ContigDictComparator;
+import com.github.lindenb.jvarkit.variant.vcf.VCFReaderFactory;
+import com.google.gson.stream.JsonWriter;
+
+import htsjdk.samtools.SAMSequenceDictionary;
+import htsjdk.samtools.reference.IndexedFastaSequenceFile;
+import htsjdk.samtools.reference.ReferenceSequenceFile;
+import htsjdk.samtools.reference.ReferenceSequenceFileFactory;
+import htsjdk.samtools.util.CloseableIterator;
+import htsjdk.samtools.util.Locatable;
+import htsjdk.samtools.util.SequenceUtil;
+import htsjdk.variant.variantcontext.Allele;
+import htsjdk.variant.variantcontext.VariantContext;
+import htsjdk.variant.vcf.VCFHeader;
+import htsjdk.variant.vcf.VCFReader;
+
+@Program(name="vcf2html",
+description="Produce a html view of eah interval from a VCF file",
+keywords={"vcf","html"},
+creationDate="20211012",
+modificationDate="20211012",
+generate_doc=false
+)
+public class VcfToHtml extends Launcher {
+	private static final Logger LOG = Logger.build(VcfToHtml.class).make();
+
+	@Parameter(names={"-o","--output"},description=ArchiveFactory.OPT_DESC,required=true)
+	private Path archiveOutput = null ;
+
+	@Parameter(names={"-R","--reference"},description=INDEXED_FASTA_REFERENCE_DESCRIPTION,required=true)
+	private Path faidx = null ;
+	@Parameter(names={"-r","--region","--regions","--interval"},description=IntervalListProvider.OPT_DESC,required=true)
+	private String regionsStr = null;
+
+	@Override
+	public int doWork(final List<String> args) {
+		try {
+			try(VCFReader reader  = VCFReaderFactory.makeDefault().open(Paths.get(oneAndOnlyOneFile(args)),true)) {
+				final VCFHeader header= reader.getHeader();
+				final SAMSequenceDictionary dict = SequenceDictionaryUtils.extractRequired(header);
+				try( ReferenceSequenceFile reference = ReferenceSequenceFileFactory.getReferenceSequenceFile(this.faidx)) {
+					SequenceUtil.assertSequenceDictionariesEqual(SequenceDictionaryUtils.extractRequired(reference),dict);
+					final List<Locatable> locs = IntervalListProvider.from(this.regionsStr).dictionary(dict).stream().
+						sorted(new ContigDictComparator(dict).createLocatableComparator()).
+						collect(Collectors.toList());
+					if(locs.isEmpty()) {
+						LOG.error("no region was defined");
+						return -1;
+						}
+					final XMLOutputFactory xof = XMLOutputFactory.newFactory();
+
+					try(ArchiveFactory archive = ArchiveFactory.open(archiveOutput)) {
+						final OutputStream index_os = archive.openOuputStream("index.html");
+						XMLStreamWriter index_html = xof.createXMLStreamWriter(index_os, "UTF-8");
+						index_html.writeStartDocument("UTF-8", "1.0");
+						index_html.writeStartElement("html");
+						index_html.writeStartElement("body");
+
+
+
+						for(final Locatable loc:locs) {
+							final List<VariantContext> variants;
+							try(CloseableIterator<VariantContext> iter = reader.query(loc)) {
+								variants = iter.stream().collect(Collectors.toList());
+								}
+
+							StringWriter sw = new StringWriter();
+
+							sw.append("var g = ");
+							JsonWriter jsw = new JsonWriter(sw);
+							jsw.beginObject();
+							jsw.name("contig").value(loc.getContig());
+							jsw.name("start").value(loc.getStart());
+							jsw.name("end").value(loc.getEnd());
+							jsw.name("len").value(loc.getLengthOnReference());
+							jsw.name("sequence").value(reference.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getEnd()).getBaseString());
+							jsw.name("variants");
+							jsw.beginArray();
+							for(VariantContext ctx:variants) {
+								jsw.beginObject();
+								jsw.name("start").value(ctx.getStart());
+								jsw.name("end").value(ctx.getEnd());
+								jsw.name("id").value(ctx.hasID()?ctx.getID():"");
+								jsw.name("ref").value(ctx.getReference().getDisplayString());
+								jsw.name("alts");
+								jsw.beginArray();
+								for(Allele alt:ctx.getAlternateAlleles()) {
+									jsw.value(alt.getDisplayString());
+									}
+								jsw.endArray();
+								jsw.endObject();
+								}
+							jsw.endArray();
+							jsw.endObject();
+							jsw.flush();
+							jsw.close();
+							sw.append(";");
+
+
+
+
+
+							final String filename = loc.getContig()+"_"+loc.getStart()+"_"+loc.getEnd()+".html";
+
+							final String title= new SimpleInterval(loc).toNiceString();
+							OutputStream os = archive.openOuputStream(filename);
+							XMLStreamWriter out = xof.createXMLStreamWriter(os, "UTF-8");
+							out.writeStartDocument("UTF-8", "1.0");
+							out.writeStartElement("html");
+							out.writeStartElement("head");
+							out.writeStartElement("script");
+							out.writeCharacters(sw.toString());	
+
+							out.writeCharacters(
+									"function subref(start,end) {}" +
+									"function createCtx(ith) {}" +
+									"function repaint() {}"
+								);
+
+							out.writeEndElement();//script
+							out.writeStartElement("title");
+							out.writeCharacters(title+" N="+StringUtils.niceInt(variants.size()));
+							out.writeEndElement();//title
+							out.writeEndElement();//head
+							out.writeStartElement("body");
+
+							out.writeEmptyElement("input");
+
+
+							out.writeStartElement("div");
+							out.writeEndElement();//div
+
+							out.writeEndElement();//body
+							out.writeEndElement();//html
+							os.flush();
+							os.close();
+
+							index_html.writeStartElement("li");
+							index_html.writeStartElement("a");
+							index_html.writeAttribute("a", filename);
+							index_html.writeCharacters(title+" N="+StringUtils.niceInt(variants.size()));
+							index_html.writeEndElement();//a
+							index_html.writeEndElement();//li
+							}
+						index_html.writeEndElement();//body
+						index_html.writeEndElement();//html
+						index_html.writeEndDocument();
+						index_html.close();
+						index_os.flush();
+						index_os.close();
+						}
+					}
+
+				}
+			return 0;
+			}
+		catch(final Throwable err) {
+			LOG.error(err);
+			return -1;
+			}
+		}
+
+	public static void main(String[] args) {
+		new VcfToHtml().instanceMainWithExit(args);
+
+	}
+
+}