Version 1.2.0

Luciphor's score (pep1score) incorporated
proteomicsyates · Mar 2, 2021 · 47c6670 · 47c6670
1 parent b95e53e
commit 47c6670
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Showing 3 changed files with 31 additions and 9 deletions.
diff --git a/pom.xml b/pom.xml
@@ -10,7 +10,7 @@
 	</parent>
 	<groupId>edu.scripps.yates</groupId>
 	<artifactId>luciphor_dtaselect_integrator</artifactId>
-	<version>1.1.0</version>
+	<version>1.2.0</version>
 	<name>luciphor_dtaselect_integrator</name>
 	<description>Program that takes output from luciphor and some thresholds on its scores and integrates the results into a DTASelect-filter.txt file.</description>
 

diff --git a/...ain/java/edu/scripps/yates/luciphor_dtaselect_integrator/LuciphorDtaselectIntegrator.java b/...ain/java/edu/scripps/yates/luciphor_dtaselect_integrator/LuciphorDtaselectIntegrator.java
@@ -31,6 +31,7 @@ public class LuciphorDtaselectIntegrator {
 	private static final String COL_LOCAL_FLR = "localFLR";
 	private static final String DTA_COL_PSMID = "FileName";
 	private static final String DTA_COL_SEQUENCE = "Sequence";
+	private static final String COL_PEP1SCORE = "pep1score";
 
 	public LuciphorDtaselectIntegrator(String luciphorPath, String dtaselectPath, Double lflrThreshold,
 			Double gflrThreshold) {
@@ -91,7 +92,8 @@ private void processDTASelect(Map<String, LuciphorEntry> filteredLuciphorEntries
 					// get the indexes of the headers
 					indexByHeader = getIndexByHeader(line);
 					// add new columns for the original sequence and the luciphor scores
-					fw.write(line + "\toriginal_sequence\t" + COL_GLOBAL_FLR + "\t" + COL_LOCAL_FLR + "\n");
+					fw.write(line + "\toriginal_sequence\tluciphor_score\t" + COL_GLOBAL_FLR + "\t" + COL_LOCAL_FLR
+							+ "\n");
 					continue;
 				}
 				if (!isPSMLine) {
@@ -108,7 +110,7 @@ private void processDTASelect(Map<String, LuciphorEntry> filteredLuciphorEntries
 						final String originalSequence = split[indexByHeader.get(DTA_COL_SEQUENCE)];
 						final String sequenceToReplace = luciphorEntry.getFormattedPredictedSequence(originalSequence);
 //						if (originalSequence.equals(sequenceToReplace)) {
-//							fw.write(line + "\t\t\t\n");
+//							fw.write(line + "\t\t\t\t\n");
 //							continue;
 //						}
 						// create new array of values
@@ -127,8 +129,10 @@ private void processDTASelect(Map<String, LuciphorEntry> filteredLuciphorEntries
 							numChanged++;
 							newLineValues.add(originalSequence);
 						}
+						newLineValues.add(String.valueOf(luciphorEntry.getScore()));
 						newLineValues.add(String.valueOf(luciphorEntry.getGlobalFLR()));
 						newLineValues.add(String.valueOf(luciphorEntry.getLocalFLR()));
+
 						// get the new line as string
 						final StringBuilder newLine = new StringBuilder();
 						int i = 0;
@@ -144,7 +148,7 @@ private void processDTASelect(Map<String, LuciphorEntry> filteredLuciphorEntries
 
 						continue;
 					} else {
-						fw.write(line + "\t\t\t\n");
+						fw.write(line + "\t\t\t\t\n");
 					}
 				}
 			}
@@ -213,12 +217,24 @@ private List<LuciphorEntry> readLuciphorFile() throws IOException {
 		for (int numLine = 1; numLine < lines.size(); numLine++) {
 			final String line = lines.get(numLine);
 			final String[] split = line.split("\t");
+			if (!indexByHeader.containsKey(COL_SPEC_ID) || !indexByHeader.containsKey(COL_PRED_PEP1)) {
+				continue;
+			}
 			final String psmID = split[indexByHeader.get(COL_SPEC_ID)];
 			final String predictedSequence = split[indexByHeader.get(COL_PRED_PEP1)];
-			final double localFLR = Double.valueOf(split[indexByHeader.get(COL_LOCAL_FLR)]);
-			final double globalFLR = Double.valueOf(split[indexByHeader.get(COL_GLOBAL_FLR)]);
-			final LuciphorEntry luciphorEntry = new LuciphorEntry(psmID, predictedSequence, localFLR, globalFLR);
-
+			double localFLR = Double.NaN;
+			if (indexByHeader.containsKey(COL_LOCAL_FLR)) {
+				localFLR = Double.valueOf(split[indexByHeader.get(COL_LOCAL_FLR)]);
+			}
+			double globalFLR = Double.NaN;
+			if (indexByHeader.containsKey(COL_GLOBAL_FLR)) {
+				globalFLR = Double.valueOf(split[indexByHeader.get(COL_GLOBAL_FLR)]);
+			}
+			double score = Double.NaN;
+			if (indexByHeader.containsKey(COL_PEP1SCORE)) {
+				score = Double.valueOf(split[indexByHeader.get(COL_PEP1SCORE)]);
+			}
+			final LuciphorEntry luciphorEntry = new LuciphorEntry(psmID, predictedSequence, localFLR, globalFLR, score);
 			ret.add(luciphorEntry);
 		}
 		System.out.println(ret.size() + " PSMs read from Luciphor file");

diff --git a/src/main/java/edu/scripps/yates/luciphor_dtaselect_integrator/LuciphorEntry.java b/src/main/java/edu/scripps/yates/luciphor_dtaselect_integrator/LuciphorEntry.java
@@ -14,13 +14,15 @@ public class LuciphorEntry {
 	private final String predictedSequence;
 	private final double localFLR;
 	private final double globalFLR;
+	private final double score;
 	private static Set<Character> modifiedAAs = new THashSet<Character>();
 
-	public LuciphorEntry(String psmID, String predictedSequence, double localFLR, double globalFLR) {
+	public LuciphorEntry(String psmID, String predictedSequence, double localFLR, double globalFLR, double score) {
 		this.psmID = psmID;
 		this.predictedSequence = predictedSequence;
 		this.localFLR = localFLR;
 		this.globalFLR = globalFLR;
+		this.score = score;
 		findModifiedAAs(predictedSequence);
 	}
 
@@ -123,4 +125,8 @@ private TIntObjectMap<PTMInPeptide> getPTMsByPosition(List<PTMInPeptide> ptms) {
 		return ret;
 	}
 
+	public double getScore() {
+		return score;
+	}
+
 }