From 4a7cd4d4aced97bdb6df45226d8b59eb00e20bb4 Mon Sep 17 00:00:00 2001
From: Luan Nguyen <l.nguyen@hartwigmedicalfoundation.nl>
Date: Wed, 2 Oct 2024 20:04:15 +1000
Subject: [PATCH] Chord: Implemented extractSigsSnv() R function in java

---
 .../hartwig/hmftools/chord/prep/SnvPrep.java  | 123 ++++++++++++++++++
 1 file changed, 123 insertions(+)
 create mode 100644 chord/src/main/java/com/hartwig/hmftools/chord/prep/SnvPrep.java

diff --git a/chord/src/main/java/com/hartwig/hmftools/chord/prep/SnvPrep.java b/chord/src/main/java/com/hartwig/hmftools/chord/prep/SnvPrep.java
new file mode 100644
index 0000000000..d5cb82c448
--- /dev/null
+++ b/chord/src/main/java/com/hartwig/hmftools/chord/prep/SnvPrep.java
@@ -0,0 +1,123 @@
+package com.hartwig.hmftools.chord.prep;
+
+import static com.hartwig.hmftools.chord.ChordConstants.CHORD_LOGGER;
+
+import java.nio.file.NoSuchFileException;
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+import com.hartwig.hmftools.chord.ChordConfig;
+import com.hartwig.hmftools.chord.variant.VcfFile;
+import com.hartwig.hmftools.common.sigs.SnvSigUtils;
+import com.hartwig.hmftools.common.variant.SageVcfTags;
+
+import htsjdk.variant.variantcontext.VariantContext;
+
+public class SnvPrep
+{
+    private final ChordConfig mConfig;
+
+    public SnvPrep(ChordConfig config)
+    {
+        mConfig = config;
+    }
+
+    private List<VariantContext> loadVariants(String sampleId) throws NoSuchFileException
+    {
+        VcfFile vcfFile = new VcfFile(mConfig.purpleSomaticVcfFile(sampleId), mConfig.IncludeNonPass);
+        return vcfFile.loadVariants();
+    }
+
+    private static Map<String,Integer> countTriNucContexts(List<VariantContext> variantContexts)
+    {
+        // Get bin names
+        // Returns: C>A_ACA -> 0, C>A_ACC -> 1, C>A_ACG -> 2, etc. We only need the name (i.e. key)
+        Map<String,Integer> triNucNameIndexMap = new LinkedHashMap<>();
+        SnvSigUtils.populateBucketMap(triNucNameIndexMap);
+
+        // Initialize count vector
+        Map<String,Integer> triNucNameCountsMap = new LinkedHashMap<>();
+        triNucNameIndexMap.keySet().forEach(i -> triNucNameCountsMap.put(i, 0));
+
+        // Count trinucleotide contexts
+        int snvCount = 0;
+        for(VariantContext variantContext : variantContexts)
+        {
+            String refSeq = variantContext.getReference().getBaseString();
+            String altSeq = variantContext.getAlternateAllele(0).getDisplayString();
+
+            boolean isSnv = refSeq.length()==1 && altSeq.length()==1;
+            if(!isSnv)
+                continue;
+
+            String triNucSequence = variantContext.getAttributeAsString(SageVcfTags.TRINUCLEOTIDE_CONTEXT, null);
+            String triNucContext = SnvSigUtils.variantContext(refSeq, altSeq, triNucSequence);
+
+            // CHORD_LOGGER.trace("{}:{}:{}:{} {}",
+            //       variantContext.getContig(), variantContext.getStart(), refSeq, altSeq, renameTriNucBin(triNucContext));
+
+            triNucNameCountsMap.compute(triNucContext, (k,v) -> v + 1);
+
+            snvCount++;
+        }
+
+        CHORD_LOGGER.debug("Counted trinucleotide contexts for {} SNVs", snvCount);
+
+        return triNucNameCountsMap;
+    }
+
+    private static String renameTriNucBin(String bucketName)
+    {
+        // Convert e.g. "C>A_ACA" to "A[C>A]A"
+        // The latter is the format required by the CHORD random forest model
+
+        String[] bucketNameSplit = bucketName.split("_");
+
+        String substitutionType = bucketNameSplit[0];
+        char[] triNucSequence = bucketNameSplit[1].toCharArray();
+
+        return String.format("%s[%s]%s", triNucSequence[0], substitutionType, triNucSequence[2]);
+    }
+
+    private static List<MutTypeCount> makeCountsList(Map<String,Integer> triNucCounts)
+    {
+        List<MutTypeCount> counts = new ArrayList<>();
+
+        for(String binName : triNucCounts.keySet())
+        {
+            String newBinName = renameTriNucBin(binName);
+            int count = triNucCounts.get(binName);
+
+            MutTypeCount mutTypeCount = new MutTypeCount(newBinName, count);
+
+            CHORD_LOGGER.trace(mutTypeCount);
+
+            counts.add(new MutTypeCount(newBinName, count));
+        }
+
+        return counts;
+    }
+
+    public List<MutTypeCount> extractSampleData(String sampleId)
+    {
+        try
+        {
+            CHORD_LOGGER.info("Counting SNV 96 trinucleotide contexts");
+
+            List<VariantContext> variantContexts = loadVariants(sampleId);
+            Map<String,Integer> triNucCountsMap = countTriNucContexts(variantContexts);
+            List<MutTypeCount> triNucCountsList = makeCountsList(triNucCountsMap);
+
+            return triNucCountsList;
+        }
+        catch(Exception e)
+        {
+            CHORD_LOGGER.error("sample({}) failed to count SNV trinucleotide contexts:", sampleId);
+            e.printStackTrace();
+            System.exit(1);
+            return null;
+        }
+    }
+}