Version 1.3.37

* BUGFIX local FDR not working correctly * Forward arguments from command-line to GUI * min number of fragments readable from csv * validity checks can be switched off * gives feedback on what sub-groups got dropped
lutzfischer · Oct 11, 2019 · 8547731 · 8547731
1 parent e51e802
commit 8547731
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Showing 17 changed files with 320 additions and 93 deletions.
diff --git a/nbactions.xml b/nbactions.xml
@@ -10,7 +10,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-Xmx3g -XX:+HeapDumpOnOutOfMemoryError -classpath %classpath org.rappsilber.fdr.CommandLine</exec.args>
+                <exec.args>-classpath %classpath org.rappsilber.fdr.CommandLine --pepfdr=5.0 --boost=link --csvOutDir=/home/lfischer/temp/test --csvBaseName=test_XiVersion1.7.754.RC1_2 --xiconfig=/home/lfischer/temp/test/test_XiVersion1.7.754.RC1.csv.config --fasta=/Users/salman/xi_data/xi/sequenceDB/pool8_BSCL-17_46_41-12_Sep_2019/DATABASE.fasta /home/lfischer/temp/test/test_XiVersion1.7.754.RC1.csv --gui</exec.args>
                 <exec.executable>java</exec.executable>
                 <exec.workingdir>/home/lfischer</exec.workingdir>
             </properties>
@@ -25,7 +25,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address} -Xmx3g -XX:+HeapDumpOnOutOfMemoryError -classpath %classpath org.rappsilber.fdr.CommandLine</exec.args>
+                <exec.args>-agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath org.rappsilber.fdr.CommandLine --pepfdr=5.0 --boost=link --csvOutDir=/home/lfischer/temp/test --csvBaseName=test_XiVersion1.7.754.RC1_2 --xiconfig=/home/lfischer/temp/test/test_XiVersion1.7.754.RC1.csv.config --fasta=/Users/salman/xi_data/xi/sequenceDB/pool8_BSCL-17_46_41-12_Sep_2019/DATABASE.fasta /home/lfischer/temp/test/test_XiVersion1.7.754.RC1.csv --gui</exec.args>
                 <exec.executable>java</exec.executable>
                 <jpda.listen>true</jpda.listen>
                 <exec.workingdir>/home/lfischer</exec.workingdir>
@@ -41,7 +41,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-Xmx3g -XX:+HeapDumpOnOutOfMemoryError -classpath %classpath org.rappsilber.fdr.CommandLine</exec.args>
+                <exec.args>-classpath %classpath org.rappsilber.fdr.CommandLine --pepfdr=5.0 --boost=link --csvOutDir=/home/lfischer/temp/test --csvBaseName=test_XiVersion1.7.754.RC1_2 --xiconfig=/home/lfischer/temp/test/test_XiVersion1.7.754.RC1.csv.config --fasta=/Users/salman/xi_data/xi/sequenceDB/pool8_BSCL-17_46_41-12_Sep_2019/DATABASE.fasta /home/lfischer/temp/test/test_XiVersion1.7.754.RC1.csv --gui</exec.args>
                 <exec.executable>java</exec.executable>
                 <exec.workingdir>/home/lfischer</exec.workingdir>
             </properties>

diff --git a/pom.xml b/pom.xml
@@ -3,7 +3,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.rappsilberlab</groupId>
     <artifactId>xiFDR</artifactId>
-    <version>1.3.36</version>
+    <version>1.3.37</version>
     <packaging>jar</packaging>
     <dependencies>
         <dependency>
@@ -35,11 +35,6 @@
             <artifactId>RUtils</artifactId>
             <version>1.0-SNAPSHOT</version>
         </dependency>
-        <dependency>
-            <groupId>rappsilber</groupId>
-            <artifactId>XiSearch</artifactId>
-            <version>1.6.749</version>
-        </dependency>
         <dependency>
             <groupId>org.rappsilber</groupId>
             <artifactId>XLMOD</artifactId>
@@ -103,6 +98,11 @@
             <artifactId>CSV</artifactId>
             <version>1.0-SNAPSHOT</version>
         </dependency>
+        <dependency>
+            <groupId>rappsilber</groupId>
+            <artifactId>XiSearch</artifactId>
+            <version>1.7.754.dev</version>
+        </dependency>
     </dependencies>
     <build>
 	<plugins>
@@ -145,5 +145,5 @@
     </properties>
     <description>Application for FDR estimation cross-linking massspectrometry data
 </description>
-    <name>xiFDR-1.3.36</name>
+    <name>xiFDR-1.3.37</name>
 </project>
diff --git a/src/main/java/org/rappsilber/fdr/CSVinFDR.java b/src/main/java/org/rappsilber/fdr/CSVinFDR.java
@@ -86,6 +86,8 @@ public class CSVinFDR extends OfflineFDR {
         {"crosslinker mass","cross linker mass","crossLinkerModMass","cross linker mod mass","crosslinkerModMass"},
         {"peptide coverage1", "peptide1 unique matched non lossy coverage", "unique_peak_primary_coverage_p1"},
         {"peptide coverage2", "peptide2 unique matched non lossy coverage", "unique_peak_primary_coverage_p2"},
+        {"peptide1 fragments", "peptide1 unique matched conservative", "conservative_fragsites_p1"},
+        {"peptide2 fragments", "peptide2 unique matched conservative", "conservative_fragsites_p2"},
         {"minimum peptide coverage", "min coverage pp"},
         {"delta", "delta score", "dscore"},
     };
@@ -102,11 +104,6 @@ public CSVinFDR(int[] peptideLengthGroups) {
     @Override
     protected ArrayList<String> getPSMHeader() {
         ArrayList<String> ret = super.getPSMHeader();
-//        String header = "PSMID" + seperator + "run" + seperator + "scan" 
-//                + seperator + "exp charge"  + seperator + "exp m/z" + seperator + "exp mass" + seperator + "exp fractionalmass" 
-//                + seperator + "match charge" + seperator + "match mass" + seperator + "match fractionalmass"   
-//                
-//                + seperator + "Protein1" + seperator + "Description1" + seperator + "Decoy1" + seperator + "Protein2" + seperator + "Description2" + seperator + "Decoy2" + seperator + "Peptide1" + seperator + "Peptide2" + seperator + "PeptidePosition1" + seperator + "PeptidePosition2" + seperator + "PeptideLength1" + seperator + "PeptideLength2" + seperator + "fromSite" + seperator + "ToSite" + seperator + "Charge" + seperator + "Score" + seperator + "isDecoy" + seperator + "isTT" + seperator + "isTD" + seperator + "isDD" + seperator + "fdrGroup" + seperator + "fdr" + seperator + "" + seperator + "PeptidePairFDR" + seperator + "Protein1FDR" + seperator + "Protein2FDR" + seperator + "LinkFDR" + seperator + "PPIFDR" + seperator + seperator + "peptide pair id" + seperator + "link id" + seperator + "ppi id";
         ret.add(5, "exp charge");
         ret.add(6, "exp m/z");
         ret.add(7, "exp mass");
@@ -126,7 +123,6 @@ protected ArrayList<String> getPSMOutputLine(PSM pp) {
         double mass = (mz-1.00727646677)*charge;
         double fraction = mass-Math.floor(mass);
         double calcfraction = pp.getCalcMass()-Math.floor(pp.getCalcMass());
-
 
         ret.add(5,""+ charge);
         ret.add(6, d2s(mz));
@@ -135,7 +131,6 @@ protected ArrayList<String> getPSMOutputLine(PSM pp) {
         ret.add(9,i2s(pp.getCharge()));
         ret.add(10,  d2s(pp.getCalcMass()));
         ret.add(11, d2s(calcfraction));
-
 
         return ret;
     }    

diff --git a/src/main/java/org/rappsilber/fdr/CommandLine.java b/src/main/java/org/rappsilber/fdr/CommandLine.java
@@ -33,7 +33,7 @@ public static void main(String args[]) throws SQLException, FileNotFoundExceptio
         boolean db = false;
         for (String a : args) {
             gui = false;
-            if (a.startsWith("--xiconfig=")) {
+            if (a.startsWith("--xiconfig=") || a.contentEquals("--gui")) {
                 xicsv=true;
             } else if (a.startsWith("--dbids=")) {
                 db = true;

diff --git a/src/main/java/org/rappsilber/fdr/FDRSettings.java b/src/main/java/org/rappsilber/fdr/FDRSettings.java
@@ -165,6 +165,8 @@ public interface FDRSettings {
     public void ppiLocalFDR(Boolean local);
     public boolean combineScoreAndDelta();
     public void combineScoreAndDelta(boolean c);
+    public boolean ignoreValidityChecks();
+    public void ignoreValidityChecks(boolean ignore);
 //    public double getSubScoreCutOff();
 //    public void setSubScoreCutOff(double localfdr);
 

diff --git a/src/main/java/org/rappsilber/fdr/FDRSettingsImpl.java b/src/main/java/org/rappsilber/fdr/FDRSettingsImpl.java
@@ -61,6 +61,7 @@ public class FDRSettingsImpl implements FDRSettings {
     private boolean combineScoreAndDelta;
     private int minFragments;
     private boolean boostMinFragments = false;
+    private boolean ignoreValidityChecks;
 
     @Override
     public void addCalcListener(ActionListener al) {
@@ -318,6 +319,7 @@ public static void transferSettings(FDRSettings from, FDRSettings to) {
         to.boostPepCoverage(from.boostPepCoverage());
         to.boostDeltaScore(from.boostDeltaScore());
         to.combineScoreAndDelta(from.combineScoreAndDelta());
+        to.ignoreValidityChecks(from.ignoreValidityChecks());
     }
 
     public boolean combineScoreAndDelta() {
@@ -516,6 +518,16 @@ public int getMinPeptideFragmentsFilter() {
     public void setMinPeptideFragmentsFilter(int frags) {
         this.minFragments = frags;
     }
+
+    @Override
+    public boolean ignoreValidityChecks() {
+        return this.ignoreValidityChecks;
+    }
+
+    @Override
+    public void ignoreValidityChecks(boolean ignore) {
+        this.ignoreValidityChecks = ignore;
+    }
 
 
 }