Some cleavable cross-linker related columns are read in

* specific grouping for these can be selected Bugfix for spaces in ambiguous accession list Validity check disabled by default but still reports warning Validity check warnings more verbose When writing csv-files from the command line mzIdentML files get writen out as well * a window asking for document-owner will be displayed decoy:psms better marked Improved synchronisation between settings-panel Some adaptation to forward settings from the commandline to the GUI
lutzfischer · Oct 31, 2019 · 5e06093 · 5e06093
1 parent 8547731
commit 5e06093
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Showing 32 changed files with 2,632 additions and 751 deletions.
diff --git a/nbactions-release-profile.xml b/nbactions-release-profile.xml
@@ -1,46 +1,46 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<actions>
-        <action>
-            <actionName>run</actionName>
-            <packagings>
-                <packaging>jar</packaging>
-            </packagings>
-            <goals>
-                <goal>process-classes</goal>
-                <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
-            </goals>
-            <properties>
-                <exec.args>-classpath %classpath org.rappsilber.fdr.gui.FDRGUI</exec.args>
-                <exec.executable>java</exec.executable>
-            </properties>
-        </action>
-        <action>
-            <actionName>debug</actionName>
-            <packagings>
-                <packaging>jar</packaging>
-            </packagings>
-            <goals>
-                <goal>process-classes</goal>
-                <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
-            </goals>
-            <properties>
-                <exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath org.rappsilber.fdr.gui.FDRGUI</exec.args>
-                <exec.executable>java</exec.executable>
-                <jpda.listen>true</jpda.listen>
-            </properties>
-        </action>
-        <action>
-            <actionName>profile</actionName>
-            <packagings>
-                <packaging>jar</packaging>
-            </packagings>
-            <goals>
-                <goal>process-classes</goal>
-                <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
-            </goals>
-            <properties>
-                <exec.args>-classpath %classpath org.rappsilber.fdr.gui.FDRGUI</exec.args>
-                <exec.executable>java</exec.executable>
-            </properties>
-        </action>
-    </actions>
+<?xml version="1.0" encoding="UTF-8"?>
+<actions>
+        <action>
+            <actionName>run</actionName>
+            <packagings>
+                <packaging>jar</packaging>
+            </packagings>
+            <goals>
+                <goal>process-classes</goal>
+                <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
+            </goals>
+            <properties>
+                <exec.args>-classpath %classpath org.rappsilber.fdr.CommandLine</exec.args>
+                <exec.executable>java</exec.executable>
+            </properties>
+        </action>
+        <action>
+            <actionName>debug</actionName>
+            <packagings>
+                <packaging>jar</packaging>
+            </packagings>
+            <goals>
+                <goal>process-classes</goal>
+                <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
+            </goals>
+            <properties>
+                <exec.args>-agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath org.rappsilber.fdr.CommandLine</exec.args>
+                <exec.executable>java</exec.executable>
+                <jpda.listen>true</jpda.listen>
+            </properties>
+        </action>
+        <action>
+            <actionName>profile</actionName>
+            <packagings>
+                <packaging>jar</packaging>
+            </packagings>
+            <goals>
+                <goal>process-classes</goal>
+                <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
+            </goals>
+            <properties>
+                <exec.args>-classpath %classpath org.rappsilber.fdr.CommandLine</exec.args>
+                <exec.executable>java</exec.executable>
+            </properties>
+        </action>
+    </actions>
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>-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.args>-classpath %classpath org.rappsilber.fdr.CommandLine --linkfdr=5.0 --boost=link --csvOutDir=/home/lfischer/temp/test/FDR_rpfdr5.0 --csvBaseName=4pm_dsso_Xi1.7.0.RC1_grouped --xiconfig=/home/lfischer/temp/test/4pm_dsso_Xi1.7.0.RC1.csv.config --fasta=/Users/salman/xi_data/xi/sequenceDB/4_protein_mix-17_59_11-19_Jan_2018/4ProtMix.fasta /home/lfischer/temp/test/4pm_dsso_Xi1.7.0.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=${jpda.address} -classpath %classpath org.rappsilber.fdr.CommandLine --pepfdr=5.0 --boost=link --csvOutDir=/home/lfischer/temp/test --csvBaseName=test_XiVersion1.7.754.RC1_2 --xiconfig=/home/lfischer/temp/test/test_XiVersion1.7.754.RC1.csv.config --fasta=/Users/salman/xi_data/xi/sequenceDB/pool8_BSCL-17_46_41-12_Sep_2019/DATABASE.fasta /home/lfischer/temp/test/test_XiVersion1.7.754.RC1.csv --gui</exec.args>
+                <exec.args>-agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath org.rappsilber.fdr.CommandLine --linkfdr=5.0 --boost=link --csvOutDir=/home/lfischer/temp/test/FDR_rpfdr5.0 --csvBaseName=4pm_dsso_Xi1.7.0.RC1_grouped --xiconfig=/home/lfischer/temp/test/4pm_dsso_Xi1.7.0.RC1.csv.config --fasta=/Users/salman/xi_data/xi/sequenceDB/4_protein_mix-17_59_11-19_Jan_2018/4ProtMix.fasta /home/lfischer/temp/test/4pm_dsso_Xi1.7.0.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>-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.args>-classpath %classpath org.rappsilber.fdr.CommandLine --linkfdr=5.0 --boost=link --csvOutDir=/home/lfischer/temp/test/FDR_rpfdr5.0 --csvBaseName=4pm_dsso_Xi1.7.0.RC1_grouped --xiconfig=/home/lfischer/temp/test/4pm_dsso_Xi1.7.0.RC1.csv.config --fasta=/Users/salman/xi_data/xi/sequenceDB/4_protein_mix-17_59_11-19_Jan_2018/4ProtMix.fasta /home/lfischer/temp/test/4pm_dsso_Xi1.7.0.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>1.3.37</version>
+    <version>1.4.0</version>
     <packaging>jar</packaging>
     <dependencies>
         <dependency>
@@ -145,5 +145,5 @@
     </properties>
     <description>Application for FDR estimation cross-linking massspectrometry data
 </description>
-    <name>xiFDR-1.3.37</name>
+    <name>xiFDR-1.4.0</name>
 </project>
diff --git a/src/main/java/org/rappsilber/fdr/CSVinFDR.java b/src/main/java/org/rappsilber/fdr/CSVinFDR.java
@@ -88,6 +88,8 @@ public class CSVinFDR extends OfflineFDR {
         {"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"},
+        {"peptides with stubs", "fragment CCPepFragment"},
+        {"peptides with doublets", "fragment CCPepDoubletFound"},
         {"minimum peptide coverage", "min coverage pp"},
         {"delta", "delta score", "dscore"},
     };
@@ -193,6 +195,8 @@ public void readCSV(CsvParser csv, CsvCondition filter) throws FileNotFoundExcep
         Integer cDelta = getColumn(csv,"delta",true);
         Integer cPep1Coverage = getColumn(csv,"peptide coverage1",true);
         Integer cPep2Coverage = getColumn(csv,"peptide coverage1",true);
+        Integer cPepStubs = getColumn(csv,"peptides with stubs",true);
+        Integer cPepDoublets = getColumn(csv,"peptides with doublets",true);
         Integer cPepMinCoverage = getColumn(csv,"minimum peptide coverage",true);
         Integer cRank = getColumn(csv,"rank",true);
 
@@ -293,12 +297,12 @@ public void readCSV(CsvParser csv, CsvCondition filter) throws FileNotFoundExcep
                     peptide2score=score*(1-ratio);
                 }
 
-                String[] accessions1 =saccession1.split(";");
-                String[] accessions2 =saccession2.split(";");
-                String[] descriptions1 =sdescription1.split(";",-1);
-                String[] descriptions2 =sdescription2.split(";",-1);
-                String[] pepPositions1 =spepPosition1.split(";",-1);
-                String[] pepPositions2 =spepPosition2.split(";",-1);
+                String[] accessions1 =saccession1.split("\\s*;\\s*");
+                String[] accessions2 =saccession2.split("\\s*;\\s*");
+                String[] descriptions1 =sdescription1.split("\\s*;\\s*",-1);
+                String[] descriptions2 =sdescription2.split("\\s*;\\s*",-1);
+                String[] pepPositions1 =spepPosition1.split("\\s*;\\s*",-1);
+                String[] pepPositions2 =spepPosition2.split("\\s*;\\s*",-1);
 
                 if (!sdescription1.isEmpty()) {
                     if (descriptions1.length != accessions1.length)
@@ -346,7 +350,7 @@ public void readCSV(CsvParser csv, CsvCondition filter) throws FileNotFoundExcep
 
                 int[] ipeppos1 = new int[pepPositions1.length];
                 for (int i = 0; i<pepPositions1.length; i++) {
-                    ipeppos1[i] = Integer.parseInt(pepPositions1[i]);
+                    ipeppos1[i] = Integer.parseInt(pepPositions1[i].trim());
                 }
 
                 int[] ipeppos2 = new int[pepPositions2.length];
@@ -420,6 +424,21 @@ public void readCSV(CsvParser csv, CsvCondition filter) throws FileNotFoundExcep
                 }
                 if (cDelta != null)
                     psm.setDeltaScore(csv.getDouble(cDelta));
+
+                if (cPepStubs != null) {
+                    double s = csv.getDouble(cPepStubs);
+                    psm.addOtherInfo("PeptidesWithStubs", s);
+                    if (s >0)  {
+                        stubsFound(true);
+                    } 
+
+                }
+                if (cPepDoublets != null) {
+
+                    psm.addOtherInfo("PeptidesWithDoublets", csv.getDouble(cPepDoublets));
+
+                }
+
                 if (cPepMinCoverage != null) {
 
                     psm.addOtherInfo("minPepCoverage", csv.getDouble(cPepMinCoverage));

diff --git a/src/main/java/org/rappsilber/fdr/FDRSettings.java b/src/main/java/org/rappsilber/fdr/FDRSettings.java
@@ -169,5 +169,7 @@ public interface FDRSettings {
     public void ignoreValidityChecks(boolean ignore);
 //    public double getSubScoreCutOff();
 //    public void setSubScoreCutOff(double localfdr);
+    public void setGroupByCrosslinkerStubs(boolean group);
+    public boolean getGroupByCrosslinkerStubs();
 
 }
diff --git a/src/main/java/org/rappsilber/fdr/FDRSettingsImpl.java b/src/main/java/org/rappsilber/fdr/FDRSettingsImpl.java
@@ -32,7 +32,7 @@ public class FDRSettingsImpl implements FDRSettings {
     double ProteinGroupFDR;
     double ProteinGroupLinkFDR;
     double ProteinGroupPairFDR;
-    int BoostingSteps;
+    int BoostingSteps = 4;
     boolean BoostBetween;
     boolean LinkDirectional;
     boolean PPIDirectional;
@@ -61,7 +61,8 @@ public class FDRSettingsImpl implements FDRSettings {
     private boolean combineScoreAndDelta;
     private int minFragments;
     private boolean boostMinFragments = false;
-    private boolean ignoreValidityChecks;
+    private boolean ignoreValidityChecks = true;
+    private boolean groubByCrosslinkerStubs;
 
     @Override
     public void addCalcListener(ActionListener al) {
@@ -320,6 +321,7 @@ public static void transferSettings(FDRSettings from, FDRSettings to) {
         to.boostDeltaScore(from.boostDeltaScore());
         to.combineScoreAndDelta(from.combineScoreAndDelta());
         to.ignoreValidityChecks(from.ignoreValidityChecks());
+        to.setGroupByCrosslinkerStubs(from.getGroupByCrosslinkerStubs());
     }
 
     public boolean combineScoreAndDelta() {
@@ -528,6 +530,16 @@ public boolean ignoreValidityChecks() {
     public void ignoreValidityChecks(boolean ignore) {
         this.ignoreValidityChecks = ignore;
     }
+
+    @Override
+    public void setGroupByCrosslinkerStubs(boolean group) {
+        this.groubByCrosslinkerStubs = group;
+    }
+
+    @Override
+    public boolean getGroupByCrosslinkerStubs() {
+        return this.groubByCrosslinkerStubs;
+    }
 
 
 }