Merge pull request #30 from Integrative-Transcriptomics/dev

Judith Neukamm · web-flow · commit 06ebe31d056e · 2019-05-21T17:08:28.000+02:00
Dev
diff --git a/build.gradle b/build.gradle
@@ -1,5 +1,5 @@
 group 'com.uni-tuebingen.de.it.eager.damageprofiler'
-version '0.4.6'
+version '0.4.7'
 
 buildscript {
     repositories {
diff --git a/src/main/java/GUI/MainGuiFX.java b/src/main/java/GUI/MainGuiFX.java
@@ -143,7 +143,7 @@ private void addListener() {
             communicator.setSpecies_ref_identifier(textfield_specie.getText());
             if(!checkbox_dynamic_y_axis_height.isSelected()){
                 try {
-                    communicator.setyAxis(Double.parseDouble(textfield_y_axis_height.getText()));
+                    communicator.setyAxis_damageplot(Double.parseDouble(textfield_y_axis_height.getText()));
                 } catch (Exception ex){
                     System.out.println("Height value not valid.");
                 }
diff --git a/src/main/java/IO/Communicator.java b/src/main/java/IO/Communicator.java
@@ -14,7 +14,11 @@ public class Communicator {
     // damage calculation
     private int threshold = 25;
 
-    private double yAxis;
+    private double yAxis_damageplot;
+    private double xaxis_histo_id_min =-1;
+    private double xaxis_histo_id_max =-1;
+    private double xaxis_histo_length_min=-1;
+    private double xaxis_histo_length_max=-1;
     private int length = 100;
     private boolean use_merged_and_mapped_reads = false;
     private boolean use_all_reads = false;
@@ -95,12 +99,12 @@ public void setUse_all_reads(boolean use_all_reads) {
         this.use_all_reads = use_all_reads;
     }
 
-    public void setyAxis(double yAxis) {
-        this.yAxis = yAxis;
+    public void setyAxis_damageplot(double yAxis_damageplot) {
+        this.yAxis_damageplot = yAxis_damageplot;
     }
 
-    public double getyAxis() {
-        return yAxis;
+    public double getyAxis_damageplot() {
+        return yAxis_damageplot;
     }
 
     public String getTitle_plots() {
@@ -120,5 +124,35 @@ public void setSpecieslist_filepath(String specieslist_filepath) {
     }
 
 
+    public double getXaxis_histo_id_min() {
+        return xaxis_histo_id_min;
+    }
+
+    public void setXaxis_histo_id_min(double xaxis_histo_id_min) {
+        this.xaxis_histo_id_min = xaxis_histo_id_min;
+    }
+
+    public double getXaxis_histo_id_max() {
+        return xaxis_histo_id_max;
+    }
+
+    public void setXaxis_histo_id_max(double xaxis_histo_id_max) {
+        this.xaxis_histo_id_max = xaxis_histo_id_max;
+    }
 
+    public double getXaxis_histo_length_min() {
+        return xaxis_histo_length_min;
+    }
+
+    public void setXaxis_histo_length_min(double xaxis_histo_length_min) {
+        this.xaxis_histo_length_min = xaxis_histo_length_min;
+    }
+
+    public double getXaxis_histo_length_max() {
+        return xaxis_histo_length_max;
+    }
+
+    public void setXaxis_histo_length_max(double xaxis_histo_length_max) {
+        this.xaxis_histo_length_max = xaxis_histo_length_max;
+    }
 }
diff --git a/src/main/java/IO/Histogram.java b/src/main/java/IO/Histogram.java
@@ -3,6 +3,7 @@
 import org.apache.log4j.Logger;
 import org.jfree.chart.ChartFactory;
 import org.jfree.chart.JFreeChart;
+import org.jfree.chart.axis.ValueAxis;
 import org.jfree.chart.plot.PlotOrientation;
 import org.jfree.chart.plot.XYPlot;
 import org.jfree.chart.renderer.xy.StandardXYBarPainter;
@@ -56,7 +57,8 @@ public HistogramDataset createDataset(String[] title, int max){
     }
 
 
-    public JFreeChart createChart(HistogramDataset dataset, String title, String xlab, String ylab){
+    public JFreeChart createChart(HistogramDataset dataset, String title, String xlab, String ylab,
+                                  double xmin, double xmax){
 
         JFreeChart chart = ChartFactory.createHistogram(
                 title,//"Histogram read length",
@@ -76,6 +78,16 @@ public JFreeChart createChart(HistogramDataset dataset, String title, String xla
         xyplot.setDomainGridlinePaint(new Color(150,150,150));
         xyplot.setRangeGridlinePaint(new Color(150,150,150));
 
+        if(xmin > -1){
+            ValueAxis axis = xyplot.getDomainAxis();
+            axis.setLowerBound(xmin);
+        }
+
+        if(xmax > -1){
+            ValueAxis axis = xyplot.getDomainAxis();
+            axis.setUpperBound(xmax);
+        }
+
         XYBarRenderer xybarrenderer = (XYBarRenderer)xyplot.getRenderer();
         xybarrenderer.setShadowVisible(false);
         xybarrenderer.setBarPainter(new StandardXYBarPainter());
diff --git a/src/main/java/IO/OutputGenerator.java b/src/main/java/IO/OutputGenerator.java
@@ -33,6 +33,10 @@
  */
 public class OutputGenerator {
 
+    private final double x_axis_min_id_histo;
+    private final double x_axis_max_id_histo;
+    private final double x_axis_min_length_histo;
+    private final double x_axis_max_length_histo;
     private int numberOfUsedReads;
     private final double height;
     private final Logger LOG;
@@ -50,7 +54,8 @@ public class OutputGenerator {
 
 
     public OutputGenerator(String outputFolder, DamageProfiler damageProfiler, String specie, int threshold,
-                           int length, double height, String input, Logger LOG) {
+                           int length, double height, double x_axis_min_id_histo, double x_axis_max_id_histo,
+                           double x_axis_min_length_histo, double x_axis_max_length_histo, String input, Logger LOG) {
 
         this.outpath = outputFolder;
         this.frequencies = damageProfiler.getFrequencies();
@@ -59,6 +64,10 @@ public OutputGenerator(String outputFolder, DamageProfiler damageProfiler, Strin
         this.threshold = threshold;
         this.length = length;
         this.height = height;
+        this.x_axis_min_id_histo = x_axis_min_id_histo;
+        this.x_axis_max_id_histo = x_axis_max_id_histo;
+        this.x_axis_min_length_histo = x_axis_min_length_histo;
+        this.x_axis_max_length_histo = x_axis_max_length_histo;
         this.input = input;
         this.LOG = LOG;
 
@@ -425,7 +434,8 @@ public void plotLengthHistogram(List<Double> length_all, List<Double> length_for
         Histogram hist_all = new Histogram(LOG);
         hist_all.addData(length_all);
         HistogramDataset dataset_all = hist_all.createDataset(new String[]{"all reads"}, max_length);
-        JFreeChart chart_all = hist_all.createChart(dataset_all, "Read length distribution", "Read length", "Occurrences");
+        JFreeChart chart_all = hist_all.createChart(dataset_all, "Read length distribution", "Read length",
+                "Occurrences",  x_axis_min_length_histo, x_axis_max_length_histo);
 
         Histogram hist_separated = new Histogram(LOG);
         if(length_forward.size()>0){
@@ -435,7 +445,8 @@ public void plotLengthHistogram(List<Double> length_all, List<Double> length_for
             hist_separated.addData(length_reverse);
         }
         HistogramDataset dataset_separated = hist_separated.createDataset(new String[]{"+ strand", "- strand"}, max_length);
-        JFreeChart chart_separated = hist_separated.createChart(dataset_separated, "Read length distribution", "Read length", "Occurrences");
+        JFreeChart chart_separated = hist_separated.createChart(dataset_separated, "Read length distribution",
+                "Read length", "Occurrences",  x_axis_min_length_histo, x_axis_max_length_histo);
 
         createPdf("/Length_plot.pdf", new JFreeChart[]{chart_all, chart_separated}, file);
 
@@ -455,7 +466,8 @@ public void plotIdentitiyHistogram(ArrayList distances, String title, String fil
         Histogram hist_all = new Histogram(LOG);
         hist_all.addData(distances);
         HistogramDataset dataset = hist_all.createDataset(new String[]{title}, 100);
-        JFreeChart chart_all = hist_all.createChart(dataset,  "Read identity distribution", "Identity", "Occurrences");
+        JFreeChart chart_all = hist_all.createChart(dataset,  "Read identity distribution", "Identity", "Occurrences",
+                x_axis_min_id_histo, x_axis_max_id_histo);
         createPdf("/identity_histogram.pdf", new JFreeChart[]{chart_all}, file);
 
     }
diff --git a/src/main/java/IO/SpeciesListParser.java b/src/main/java/IO/SpeciesListParser.java
@@ -24,7 +24,7 @@ public SpeciesListParser(String speciesListFile, Logger LOG) {
     }
 
 
-    public String getSingleSpecie(String rname) throws IOException {
+    public String getSingleSpecie(String rname) {
 
         specieHandler.getSpecie(rname);
         return specieHandler.getSpecie_name();
diff --git a/src/main/java/IO/UserOptionsParser.java b/src/main/java/IO/UserOptionsParser.java
@@ -69,12 +69,35 @@ private void parse(){
                 .hasArg()
                 .create("title"));
 
-        options.addOption(OptionBuilder.withLongOpt("yaxis")
-                .withArgName("YAXIS")
-                .withDescription("Maximal value on y axis.")
+        options.addOption(OptionBuilder.withLongOpt("yaxis_damageplot")
+                .withArgName("YAXIS_DAMAGEPLOT")
+                .withDescription("Maximal value on y axis of damage plot.")
                 .hasArg()
-                .create("yaxis"));
+                .create("yaxis_damageplot"));
 
+        options.addOption(OptionBuilder.withLongOpt("xaxis_histo_id_min")
+                .withArgName("XAXIS_HISTO_ID_MIN")
+                .withDescription("Minimal value x-axis of identity histogram.")
+                .hasArg()
+                .create("xaxis_histo_id_min"));
+
+        options.addOption(OptionBuilder.withLongOpt("xaxis_histo_id_max")
+                .withArgName("XAXIS_HISTO_ID_MAX")
+                .withDescription("Maximal value x-axis of identity histogram.")
+                .hasArg()
+                .create("xaxis_histo_id_max"));
+
+        options.addOption(OptionBuilder.withLongOpt("xaxis_histo_length_min")
+                .withArgName("XAXIS_HISTO_LENGTH_MIN")
+                .withDescription("Minimal value x-axis of length histogram.")
+                .hasArg()
+                .create("xaxis_histo_length_min"));
+
+        options.addOption(OptionBuilder.withLongOpt("xaxis_histo_length_max")
+                .withArgName("XAXIS_HISTO_LENGTH_MAX")
+                .withDescription("Maximal value x-axis of length histogram.")
+                .hasArg()
+                .create("xaxis_histo_length_max"));
 
         Option mapped_and_merged = new Option("merged", "all_mapped_and_merged_reads", false,
                 "Use all mapped and merged reads to calculate damage plot instead of using all mapped reads. The SAM/BAM entry must start with 'M_', otherwise " +
@@ -144,10 +167,29 @@ private void parse(){
                 communicator.setTitle_plots(cmd.getOptionValue("title"));
             }
 
-            if(cmd.hasOption("yaxis")) {
-                communicator.setyAxis(Double.parseDouble(cmd.getOptionValue("yaxis")));
+            if(cmd.hasOption("yaxis_damageplot")) {
+                communicator.setyAxis_damageplot(Double.parseDouble(cmd.getOptionValue("yaxis_damageplot")));
+            }
+
+            if(cmd.hasOption("xaxis_histo_id_min")) {
+                communicator.setXaxis_histo_id_min(Double.parseDouble(cmd.getOptionValue("xaxis_histo_id_min")));
             }
 
+
+            if(cmd.hasOption("xaxis_histo_id_max")) {
+                communicator.setXaxis_histo_id_max(Double.parseDouble(cmd.getOptionValue("xaxis_histo_id_max")));
+            }
+
+            if(cmd.hasOption("xaxis_histo_length_min")) {
+                communicator.setXaxis_histo_length_min(Double.parseDouble(cmd.getOptionValue("xaxis_histo_length_min")));
+            }
+
+
+            if(cmd.hasOption("xaxis_histo_length_max")) {
+                communicator.setXaxis_histo_length_max(Double.parseDouble(cmd.getOptionValue("xaxis_histo_length_max")));
+            }
+
+
             if (cmd.hasOption('t')) {
                 communicator.setThreshold(Integer.parseInt(cmd.getOptionValue('t')));
             }
diff --git a/src/main/java/RunDamageProfiler.java b/src/main/java/RunDamageProfiler.java
@@ -8,7 +8,7 @@
  */
 public class RunDamageProfiler {
 
-    private static final String VERSION = "0.4.6";
+    private static final String VERSION = "0.4.7";
 
 
     @SuppressWarnings("static-access")
diff --git a/src/main/java/calculations/DamageProfiler.java b/src/main/java/calculations/DamageProfiler.java
@@ -214,10 +214,17 @@ private void processRecord(SAMRecord record) throws Exception{
         } else if(record.getStringAttribute(SAMTag.MD.name()) != null){
             // get reference corresponding to the record
             if(record.getCigar().getReadLength() != 0 && record.getCigar().getReadLength() == record.getReadLength()){
-
+//                if(record.getCigarString().contains("S")){
+//                    System.out.println("Cigar contains soft clipping");
+//                } else if(record.getCigarString().contains("D")){
+//                    System.out.println("Cigar contains deletion");
+//                } else {
                     byte[] ref_seq = SequenceUtil.makeReferenceFromAlignment(record, false);
                     reference_aligned = new String(ref_seq, "UTF-8");
                     record_aligned = record.getReadString();
+               // }
+
+
 
             } else {
                 LOG.info("Skipped record (length does not match): " + record.getReadName());
@@ -282,7 +289,7 @@ public int getNumberOfAllReads() {
     }
     public ArrayList<Double> getIdentity() { return identity; }
 
-    public String getSpeciesname(File file, String ref) throws IOException {
+    public String getSpeciesname(File file, String ref) {
 
         SamReader input = SamReaderFactory.make().enable(SamReaderFactory.Option.DONT_MEMORY_MAP_INDEX).
                 validationStringency(ValidationStringency.LENIENT).open(file);
diff --git a/src/main/java/calculations/SpecieHandler.java b/src/main/java/calculations/SpecieHandler.java
@@ -1,6 +1,7 @@
 package calculations;
 
 import java.io.*;
+import java.util.Random;
 
 import IO.DOMParser;
 import org.apache.log4j.Logger;
@@ -19,7 +20,7 @@ public SpecieHandler(){
     }
 
 
-    public void getSpecie(String rname) throws IOException{
+    public void getSpecie(String rname){
         if (rname != null) {
             String tax = "";
 
@@ -62,28 +63,39 @@ public void getSpecie(String rname) throws IOException{
      * @return species name as string
      * @throws IOException
      */
-    private String getSpeciesByID(int id) throws IOException {
-        String species;
+    private String getSpeciesByID(int id) {
+        String species="";
+        Random rand = new Random();
+
+        // Obtain a number between [0 - 1000].
+        int n = rand.nextInt(1000);
 
         // run command line call to get XML file from
         // ncbi with information about the ncbiID of our species
-        Runtime rt = Runtime.getRuntime();
-        Process proc = rt.exec("curl https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=taxonomy&amp;id=" + id);
 
-        BufferedReader stdInput = new BufferedReader(new InputStreamReader(proc.getInputStream()));
-        BufferedWriter xmlOutput = new BufferedWriter(new FileWriter("ncbiID.xml"));
+        // try to call 'curl'. If not possible, do not set species name but only ID
+        try {
+            Runtime rt = Runtime.getRuntime();
+            Process proc = rt.exec("curl https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=taxonomy&amp;id=" + id);
+
+            BufferedReader stdInput = new BufferedReader(new InputStreamReader(proc.getInputStream()));
+            BufferedWriter xmlOutput = new BufferedWriter(new FileWriter("ncbiID" + n + ".xml"));
 
-        // read the output from the command and write it in xml file
-        String s = null;
-        while ((s = stdInput.readLine()) != null) {
-            xmlOutput.write(s);
+            // read the output from the command and write it in xml file
+            String s = null;
+            while ((s = stdInput.readLine()) != null) {
+                xmlOutput.write(s);
+            }
+            xmlOutput.close();
+
+            DOMParser domparser = new DOMParser(LOG);
+            species = domparser.parse("ncbiID" + n + ".xml");
+            File f = new File("ncbiID" + n + ".xml");
+            f.delete();
+        } catch (Exception e){
+            System.out.println("'Curl' is not installed. If you would like to use this option, please install it.");
         }
-        xmlOutput.close();
 
-        DOMParser domparser = new DOMParser(LOG);
-        species = domparser.parse("ncbiID.xml");
-        File f = new File("ncbiID.xml");
-        f.delete();
 
 
         return species;
diff --git a/src/main/java/calculations/StartCalculations.java b/src/main/java/calculations/StartCalculations.java

Original file line number	Diff line number	Diff line change
`@@ -143,7 +143,7 @@ private void addListener() {`
`143`	`143`	`communicator.setSpecies_ref_identifier(textfield_specie.getText());`
`144`	`144`	`if(!checkbox_dynamic_y_axis_height.isSelected()){`
`145`	`145`	`try {`
`146`		`- communicator.setyAxis(Double.parseDouble(textfield_y_axis_height.getText()));`
	`146`	`+ communicator.setyAxis_damageplot(Double.parseDouble(textfield_y_axis_height.getText()));`
`147`	`147`	`} catch (Exception ex){`
`148`	`148`	`System.out.println("Height value not valid.");`
`149`	`149`	`}`
Original file line number	Diff line number	Diff line change
`@@ -24,7 +24,7 @@ public SpeciesListParser(String speciesListFile, Logger LOG) {`
`24`	`24`	`}`
`25`	`25`
`26`	`26`
`27`		`- public String getSingleSpecie(String rname) throws IOException {`
	`27`	`+ public String getSingleSpecie(String rname) {`
`28`	`28`
`29`	`29`	`specieHandler.getSpecie(rname);`
`30`	`30`	`return specieHandler.getSpecie_name();`