Merge branch 'dev' into gzip-support

Author: owlang

.classpath

@@ -29,4 +29,4 @@
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8/"/>
 	<classpathentry kind="con" path="org.eclipse.buildship.core.gradleclasspathcontainer"/>
 	<classpathentry kind="output" path="bin/default"/>
-</classpath>
+</classpath>

.github/workflows/gradle.yml

@@ -38,4 +38,3 @@ jobs:
       uses: gradle/gradle-build-action@67421db6bd0bf253fb4bd25b31ebb98943c375e1
       with:
         arguments: build
-  

.gitignore

@@ -3,4 +3,4 @@
 /.gradle/
 /build/
 .metadata
-.idea
+.idea

.project

@@ -20,4 +20,4 @@
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.eclipse.buildship.core.gradleprojectnature</nature>
 	</natures>
-</projectDescription>
+</projectDescription>

.settings/org.eclipse.buildship.core.prefs

@@ -1,2 +1,2 @@
 connection.project.dir=
-eclipse.preferences.version=1
+eclipse.preferences.version=1

docusaurus/docs/Guides/command-line.md

@@ -68,6 +68,7 @@ refer the user to the appropriate tool.
 | | [scaling-factor](https://github.com/CEGRcode/scriptmanager/wiki/Read-Analysis#scaling-factor) |
 | | [similarity-matrix](https://github.com/CEGRcode/scriptmanager/wiki/Read-Analysis#similarity-matrix-suspended) |
 | | [tag-pileup](https://github.com/CEGRcode/scriptmanager/wiki/Read-Analysis#tag-pileup) |
+| | [transpose-matrix](https://github.com/CEGRcode/scriptmanager/wiki/Read-Analysis#transpose-matrix) |
 | **seq-analysis** | [dna-shape-bed](https://github.com/CEGRcode/scriptmanager/wiki/Sequence-Analysis#dna-shape-bed) |
 | | [dna-shape-fasta](https://github.com/CEGRcode/scriptmanager/wiki/Sequence-Analysis#dna-shape-fasta) |
 | | [fasta-extract](https://github.com/CEGRcode/scriptmanager/wiki/Sequence-Analysis#fasta-extract) |

docusaurus/docs/Guides/tool-group.md

@@ -108,7 +108,7 @@ Others manipulate files to calculate normalization factors, normalize the data,
 | [`scaling-factor`][scaling-factor] | [BAM][bam-format] | [TXT][txt-format] | Calculate the factor as either total tag normalization or normalization of ChIP-seq data with control. (PMID:22883957) |
 | [`scale-matrix`][scale-matrix] | \[[CDT][cdt-format]\|[TAB][mat-format]\] | [TAB][mat-format]\[..\] | Apply a user-specified scaling factor to tab-delimited matrix data. |
 | [`aggregate-data`][aggregate-data] | \[[CDT][cdt-format]\|[TAB][mat-format]\]\[..\] | [TAB][mat-format]\[..\] | The AggregateData tool is used to process a bunch of matrix files into one matrix file. |
-
+| [`transpose-matrix`][scale-matrix] | \[[CDT][cdt-format]\|[TAB][mat-format]\] | \[[CDT][cdt-format]\|[TAB][mat-format]\] | Interchange the rows and columns of a matrix |
 
 ## Sequence Analysis
 
@@ -165,6 +165,7 @@ _Sequence Analysis tools description_
 [scaling-factor]:read-analysis/scaling-factor.md
 [similarity-matrix]:read-analysis/similarity-matrix.md
 [tag-pileup]:read-analysis/tag-pileup.md
+[transpose-matrix]:read-analysis/transpose-matrix.md
 
 [dna-shape-bed]:sequence-analysis/dna-shape-bed.md
 [dna-shape-fasta]:sequence-analysis/dna-shape-fasta.md

docusaurus/docs/References/toolIndex.table.js

@@ -268,6 +268,13 @@ export const toolIndex = [
 		command: "-",
 		url: "docs/peak-analysis/tile-genome",
 	},
+  {
+		name: "Transpose Matrix",
+		group: "RA",
+		description: "Interchange the rows and columns of a matrix.",
+		command: "-",
+		url: "docs/read-analysis/transpose-matrix",
+	},
 ];
 
 

docusaurus/docs/file-formats.md

@@ -120,6 +120,7 @@ Related Tools:
 | [`heatmap`][heatmap] |  |
 |  | [`peak-align-ref`][peak-align-ref] |
 | [`scale-matrix`][scale-matrix] | [`scale-matrix`][scale-matrix] |
+| [`transpose-matrix`][transpose-matrix] | [`transpose-matrix`][transpose-matrix] |
 | [`sort-bed`][sort-bed] |  |
 |  | [`tag-pileup`][tag-pileup] |
 
@@ -203,6 +204,7 @@ Related Tools:
 [`randomize-fasta`][randomize-fasta]
 [`remove-duplicates`][remove-duplicates]
 [`scale-matrix`][scale-matrix]
+[`transpose-matrix`][transpose-matrix]
 [`scaling-factor`][scaling-factor]
 [`se-stat`][se-stat]
 [`search-motif`][search-motif]
@@ -256,6 +258,7 @@ Related Tools:
 [randomize-fasta]:sequence-analysis/randomize-fasta
 [remove-duplicates]:bam-manipulation/remove-duplicates
 [scale-matrix]:read-analysis/scale-matrix
+[transpose-matrix]:read-analysis/transpose-matrix
 [scaling-factor]:read-analysis/scaling-factor
 [se-stat]:bam-statistics/se-stat
 [search-motif]:sequence-analysis/search-motif

docusaurus/docs/read-analysis/scale-matrix.md

@@ -44,7 +44,7 @@ This tool takes a single matrix file for input.
 
 | Option | Description |
 | ------ | ----------- |
-| `-r, --start-row` |  |
-| `-l, --start-col` |  |
+| `-r, --start-row` | row to start scaling the matrix (zero indexed) |
+| `-l, --start-col` | column to start scaling the matrix (zero indexed) |
 
 [file-format]:file-formats.md

docusaurus/docs/read-analysis/transpose-matrix.md

@@ -0,0 +1,41 @@
+---
+id: transpose-matrix
+title: Transpose Matrix
+sidebar_label: transpose-matrix
+---
+
+![transpose-matrix](/../static/icons/Read_Analysis/TransposeMatrix_square.svg)
+
+Interchange the rows and columns of a matrix, while optionally preserving labels.
+
+<img src={require('/../static/md-img/Read_Analysis/TransposeMatrixWindow.png').default} style={{width:70+'%'}}/> 
+
+## Command Line Interface
+
+Usage:
+```bash
+java -jar ScriptManager.jar read-analysis transpose-matrix [-hV] [-z] [-l=<startCOL>]
+[-o=<output>] [-r=<startROW>] <matrix>
+```
+
+## Positional Input
+
+This tool takes a single matrix file for input.
+
+
+### Output Options
+
+| Option | Description |
+| ------ | ----------- |
+| `-o, --output=<output>` | specify output filename |
+| `-z, --compress` | output compressed .gz file |
+
+
+### Coord Start Options
+
+| Option | Description |
+| ------ | ----------- |
+| `-r, --start-row` | row to start transposing the matrix (zero indexed) |
+| `-l, --start-col` | column to start transposing the matrix (zero indexed) |
+
+[file-format]:file-formats.md

docusaurus/sidebars.js

@@ -57,6 +57,7 @@ module.exports = {
       "read-analysis/scaling-factor",
       "read-analysis/scale-matrix",
       "read-analysis/aggregate-data",
+      "read-analysis/transpose-matrix"
     ],
     "Sequence Analysis": [
       "sequence-analysis/fasta-extract",

docusaurus/static/icons/Read_Analysis/TransposeMatrix_square.svg

@@ -241,4 +241,4 @@ eval "set -- $(
         tr '\n' ' '
     )" '"$@"'
 
-exec "$JAVACMD" "$@"
+exec "$JAVACMD" "$@"

docusaurus/static/md-img/Read_Analysis/TransposeMatrixWindow.png

@@ -89,4 +89,4 @@ exit /b %EXIT_CODE%
 :mainEnd
 if "%OS%"=="Windows_NT" endlocal
 
-:omega
+:omega

gradlew

@@ -28,6 +28,11 @@
  */
 public class CompositePlot {
 
+	/** 
+	* Creates a new CompositePlot object
+	*/
+	public CompositePlot(){}
+
 	/**
 	 * Create a two-line plot (sense and antisense composites) with a title and
 	 * custom colors. There are no checks on input array lengths (line plot

gradlew.bat

@@ -31,7 +31,7 @@ public class Histogram {
 	 * @param y the list of frequencies
 	 * @param x the list of values that have frequencies (same len as y)
 	 * @return the bar-style histogram chart
-	 * @throws IOException
+	 * @throws IOException Invalid file or parameters
 	 */
 	public static ChartPanel createBarChart(double[] y, int[] x) throws IOException {
 		final XYSeries series = new XYSeries("Frequency");
@@ -54,7 +54,7 @@ public static ChartPanel createBarChart(double[] y, int[] x) throws IOException
 	 * @param x the list of values that have frequencies (same len as y)
 	 * @param output the path of the PNG file to save the chart image to
 	 * @return the bar-style histogram chart
-	 * @throws IOException
+	 * @throws IOException Invalid file or parameters
 	 */
 	public static ChartPanel createBarChart(double[] y, int[] x, File output) throws IOException {
 		final XYSeries series = new XYSeries("Frequency");
@@ -82,7 +82,7 @@ public static ChartPanel createBarChart(double[] y, int[] x, File output) throws
 	 * 
 	 * @param dataset the formatted dataset to plot
 	 * @return the formatted and configured histogram chart
-	 * @throws IOException
+	 * @throws IOException Invalid file or parameters
 	 */
 	private static JFreeChart createChart(IntervalXYDataset dataset) throws IOException {
         final JFreeChart chart = ChartFactory.createXYBarChart(

src/main/java/scriptmanager/charts/CompositePlot.java

@@ -31,7 +31,7 @@ public class LineChart {
 	 * @param y the duplication rate values
 	 * @param x the domain values
 	 * @return the line plot chart
-	 * @throws IOException
+	 * @throws IOException Invalid file or parameters
 	 */
 	public static ChartPanel createLineChart(ArrayList<Double> y, String[] x) throws IOException {
 		DefaultCategoryDataset dataset = new DefaultCategoryDataset();
@@ -53,7 +53,7 @@ public static ChartPanel createLineChart(ArrayList<Double> y, String[] x) throws
 	 * @param y2 the genome duplication rate values
 	 * @param x  the domain values
 	 * @return the line plot chart
-	 * @throws IOException
+	 * @throws IOException Invalid file or parameters
 	 */
 	public static ChartPanel createLineChart(ArrayList<Double> y1, ArrayList<Double> y2, String[] x) throws IOException {
 		DefaultCategoryDataset dataset = new DefaultCategoryDataset();
@@ -75,7 +75,7 @@ public static ChartPanel createLineChart(ArrayList<Double> y1, ArrayList<Double>
 	 * @param x the domain values
 	 * @param output the path of the PNG file to save the chart image to
 	 * @return the line plot chart
-	 * @throws IOException
+	 * @throws IOException Invalid file or parameters
 	 */
 	public static ChartPanel createLineChart(ArrayList<Double> y, String[] x, File output) throws IOException {
 		DefaultCategoryDataset dataset = new DefaultCategoryDataset();
@@ -102,7 +102,7 @@ public static ChartPanel createLineChart(ArrayList<Double> y, String[] x, File o
 	 * 
 	 * @param dataset the formatted dataset to plot
 	 * @return the line plot chart
-	 * @throws IOException
+	 * @throws IOException Invalid file or parameters
 	 */
 	private static JFreeChart createChart(CategoryDataset dataset) throws IOException {
         final JFreeChart chart = ChartFactory.createLineChart(

src/main/java/scriptmanager/charts/Histogram.java

@@ -0,0 +1,7 @@
+/**
+ * Collection of classes containing static methods to generate Components with a
+ * variety of visualizations for data. Used by graphical interfaces
+ * (`window_interface`) and figure making scripts in
+ * {@link scriptmanager.scripts.BAM_Format_Converter}
+ */
+package scriptmanager.charts;

src/main/java/scriptmanager/charts/LineChart.java

@@ -15,15 +15,23 @@
 import scriptmanager.scripts.BAM_Format_Converter.BAMtoBED;
 
 /**
-	BAM_Format_ConverterCLI/SEStatsCLI
-*/
+ * Command line interface for
+ * {@link scriptmanager.scripts.BAM_Format_Converter.BAMtoBED}
+ * 
+ * @author Olivia Lang
+ */
 @Command(name = "bam-to-bed", mixinStandardHelpOptions = true,
 	description = ToolDescriptions.bam_to_bed_description,
 	version = "ScriptManager "+ ToolDescriptions.VERSION,
 	sortOptions = false,
 	exitCodeOnInvalidInput = 1,
 	exitCodeOnExecutionException = 1)
 public class BAMtoBEDCLI implements Callable<Integer> {
+
+	/**
+	 * Creates a new BAMtoBEDCLI object
+	 */
+	public BAMtoBEDCLI(){}
 
 	@Parameters( index = "0", description = "The BAM file from which we generate a new file.")
 	private File bamFile;
@@ -61,6 +69,10 @@ static class ReadType {
 	private int STRAND = -9999;
 	private int PAIR;
 
+	/**
+	 * Runs when this subcommand is called, running script in respective script package with user defined arguments
+	 * @throws IOException Invalid file type 
+	 */
 	@Override
 	public Integer call() throws Exception {
 		System.err.println( ">BAMtoBEDCLI.call()" );
@@ -96,10 +108,6 @@ private String validateInput() throws IOException {
 			r += "(!)BAM file does not exist: " + bamFile.getName() + "\n";
 			return(r);
 		}
-		//check input extensions
-		if(!"bam".equals(ExtensionFileFilter.getExtension(bamFile))){
-			r += "(!)Is this a BAM file? Check extension: " + bamFile.getName() + "\n";
-		}
 		//check BAI exists
 		File f = new File(bamFile+".bai");
 		if(!f.exists() || f.isDirectory()){
@@ -117,13 +125,7 @@ private String validateInput() throws IOException {
 		}else if(stdout){
 			if(output!=null){ r += "(!)Cannot use -s flag with -o.\n"; }
 		//check output filename is valid
-		}else{
-			//check ext
-			try{
-				if(!"bed".equals(ExtensionFileFilter.getExtensionIgnoreGZ(output))){
-					r += "(!)Use BED extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) + ".bed\n";
-				}
-			} catch( NullPointerException e){ r += "(!)Output filename must have extension: use BED extension for output filename. Try: " + output + ".bed\n"; }
+		} else {
 			//check directory
 			if(output.getParent()==null){
 	// 			System.err.println("default to current directory");

src/main/java/scriptmanager/charts/package-info.java

@@ -15,15 +15,23 @@
 import scriptmanager.scripts.BAM_Format_Converter.BAMtoGFF;
 
 /**
-	BAM_Format_ConverterCLI/SEStatsCLI
-*/
+ * Command line interface for
+ * {@link scriptmanager.scripts.BAM_Format_Converter.BAMtoGFF}
+ * 
+ * @author Olivia Lang
+ */
 @Command(name = "bam-to-gff", mixinStandardHelpOptions = true,
 	description = ToolDescriptions.bam_to_gff_description,
 	version = "ScriptManager "+ ToolDescriptions.VERSION,
 	sortOptions = false,
 	exitCodeOnInvalidInput = 1,
 	exitCodeOnExecutionException = 1)
 public class BAMtoGFFCLI implements Callable<Integer> {
+
+	/**
+	 * Creates a new BAMtoGFFCLI object
+	 */
+	public BAMtoGFFCLI(){}
 
 	@Parameters( index = "0", description = "The BAM file from which we generate a new file.")
 	private File bamFile;
@@ -61,6 +69,10 @@ static class ReadType {
 	private int STRAND = -9999;
 	private int PAIR;
 
+	/**
+	 * Runs when this subcommand is called, running script in respective script package with user defined arguments
+	 * @throws IOException Invalid file type 
+	 */
 	@Override
 	public Integer call() throws Exception {
 		System.err.println( ">BAMtoGFFCLI.call()" );
@@ -96,10 +108,6 @@ private String validateInput() throws IOException {
 			r += "(!)BAM file does not exist: " + bamFile.getName() + "\n";
 			return(r);
 		}
-		//check input extensions
-		if(!"bam".equals(ExtensionFileFilter.getExtension(bamFile))){
-			r += "(!)Is this a BAM file? Check extension: " + bamFile.getName() + "\n";
-		}
 		//check BAI exists
 		File f = new File(bamFile+".bai");
 		if(!f.exists() || f.isDirectory()){
@@ -118,12 +126,6 @@ private String validateInput() throws IOException {
 			if(output!=null){ r += "(!)Cannot use -s flag with -o.\n"; }
 		//check output filename is valid
 		}else{
-			//check ext
-			try{
-				if(!"gff".equals(ExtensionFileFilter.getExtension(output))){
-					r += "(!)Use GFF extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) + ".gff\n";
-				}
-			} catch( NullPointerException e){ r += "(!)Output filename must have extension: use GFF extension for output filename. Try: " + output + ".gff\n"; }
 			//check directory
 			if(output.getParent()==null){
 	// 			System.err.println("default to current directory");