Merge the Command Line version to master#44
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WilliamKMLai merged 45 commits intomasterfrom Dec 8, 2020
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Outlining the empty classes for building the command line version. Although the jar file should build sucessfully, the command line version isn't working and the tools just print the tool name for now. build.gradle -change version name to reflect that its devCLI -add Picocli to the libraries to build with src/main/ScriptManagerGUI -moved most of the code from old ScriptManager class to here as the GUI application class src/main/ScriptManager -new main class to call GUI version or CLI version depending on input parameters -multiple classes defined for each tool group based on a generic abstract toolgroup class (SubcommandCLI) that is also defined here -the abstract class prints the usage message for the tool group if the tool name subcommand is not given by the user. src/objects/ToolDescriptions -store tool descriptions in a separate object so the GUI and CLI versions are pulling from the same text--so its easier if we ever want to adjust the text src/cli/* -all classes named to reflect organization of window_interface and scripts files -each implements Callable and contains relevant Picocli imports -each contains an empty `validateInput()` method where parameter formatting and validation will be carried out -executing will just print its class name for now until it is updated to execute its respective tool script
One of the redundant checks in validateInput() methods of the CLI will be to strip the extension off a file name to build default output filenames. The method takes a File object and returns a String object of the file's name without the extension.
This wrapper class wraps the GUI's TextArea output object such that the GUI components are hidden from the CLI version to avoid exceptions being thrown when there is no way of displaying GUI components. Since some of the GUI tools output to a TextArea GUI object, running a CLI version on the terminal of a remote server without adjusting the script object would throw an exception. By wrapping the TextArea in this object, CLI won't know that it contains a GUI object unless this object is instantiated. By writing code to avoid instantiating the object if running as CLI, we've created a workaround for the GUI text components. The class extends OutputStream and takes the TextArea object and saves it in its constructor. The write() method is overriden with the code that uses the TextArea append() method.
Before, this tool was implemented with a JFrame script object so this commit separates out the JFrame elements for CLI implementation. JFrame elements are saved to the src/window_interface/*/BAMtoBEDOutput class while the calculations are kept in the src/scripts/*/BAMtoBED class. window_interface/*Window -adjust import to call *Output class window_interface/*Output -adjust import to call script class -adjust output argument when initializing script class to be full filename and not just directory script/* -strip out JFrame objects -use output as filename rather than directory name cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user
Before, this tool was implemented with a JFrame script object so this commit separates out the JFrame elements for CLI implementation. JFrame elements are saved to the src/window_interface/*/BAMtobedGraphOutput class while the calculations are kept in the src/scripts/*/BAMtobedGraph class. window_interface/*Window -adjust import to call *Output class window_interface/*Output -adjust import to call script class -adjust output argument when initializing script class to be full filename base and not just directory script/* -strip out JFrame objects -use output basename as filename rather than directory name cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user
Before, this tool was implemented with a JFrame script object so this commit separates out the JFrame elements for CLI implementation. JFrame elements are saved to the src/window_interface/*/BAMtoGFFOutput class while the calculations are kept in the src/scripts/*/BAMtoGFF class. window_interface/*Window -adjust import to call *Output class window_interface/*Output -adjust import to call script class -adjust output argument when initializing script class to be full filename and not just directory script/* -strip out JFrame objects -use output as filename rather than directory name cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user
Before, this tool was implemented with a JFrame script object so this commit separates out the JFrame elements for CLI implementation. JFrame elements are saved to the src/window_interface/*/BAMtoscIDXOutput class while the calculations are kept in the src/scripts/*/BAMtoscIDX class. window_interface/*Window -adjust import to call *Output class window_interface/*Output -adjust import to call script class -adjust output argument when initializing script class to be full filename and not just directory script/* -strip out JFrame objects -use output as filename rather than directory name cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user
The prior method for stripping extensions from filenames would throw a java.lang.StringIndexOutOfBoundsException if the File object input had a name without any periods in it. This method for stripping off the extension avoids this.
Before, this tool was implemented with a JFrame script object so this commit separates out the JFrame elements for CLI implementation. JFrame elements are saved to the src/window_interface/*/FilterforPIPseqOutput class while the calculations are kept in the src/scripts/*/FilterforPIPseq class. window_interface/*Window -adjust import to call *Output class window_interface/*Output -adjust import to call script class -adjust output argument when initializing script class to be full filename and not just directory script/* -strip out JFrame objects -use output as filename rather than directory name cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user
This tool was originally written as a wrapper for an existing CLI tool so this commit just writes up the help message if a user attempts to execute this tool from the command line. The help message will redirect the user to the `samtools index` command.
This tool was originally written as a wrapper for an existing CLI tool so this commit just writes up the help message if a user attempts to execute this tool from the command line. The help message will redirect the user to Picard's MarkDuplicates tool.
This tool was originally written as a wrapper for an existing CLI tool so this commit just writes up the help message if a user attempts to execute this tool from the command line. The help message will redirect the user to Picard's MergeSamFiles tool
This tool was originally written as a wrapper for an existing CLI tool so this commit just writes up the help message if a user attempts to execute this tool from the command line. The help message will redirect the user to the `samtools sort` command
Before, this tool was implemented with a JFrame script object so this commit separates out the JFrame elements for CLI implementation. JFrame elements are saved to the src/window_interface/*/SEStatOutput class while the calculations are kept in the src/scripts/*/SEStats class. window_interface/*Window -adjust import to call *Output class window_interface/*Output -adjust import to call script class -adjust output argument when initializing script class to be full filename and not just directory script/* -strip out JFrame objects -use output as filename rather than directory name cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user
This method was added to be used by BAM_Statistics/PEStat to save the duplication graph output as a PNG if a non-null filename is indicated. This is for the CLI implementation of saving the duplication figures shown in the GUI version.
LineChart, a general util class was updated with fixes that are relevant to the bam-statistic's PEStat CLI version. This pulls those updates into bam-statistics so I can finish the PEStat update.
Before, this tool was implemented with a JFrame script object so this commit separates out the JFrame elements for CLI implementation. JFrame elements are saved to the src/window_interface/*/PEStatsOutput class while the calculations are kept in the src/scripts/*/PEStats class. window_interface/*Window -adjust import to call *Output class window_interface/*Output -adjust import to call script class -adjust output argument when initializing script class to be full filename and not just directory script/* -strip out JFrame objects -use output as filename rather than directory name cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user
Before, this tool was implemented with a JFrame script object so this commit separates out the JFrame elements for CLI implementation. JFrame elements are saved to the src/window_interface/*/BAMGenomeCorrelationOutput class while the calculations are kept in the src/scripts/*/BAMGenomeCorrelation class. window_interface/*Window -adjust import to call *Output class window_interface/*Output -adjust import to call script class -adjust output argument when initializing script class to be full filename and not just directory script/* -strip out JFrame objects -use output as filename rather than directory name cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user charts/HeatMap -createCorrelationHeatmap updated to take a File object for saving the chart when executing the CLI version
Before, this tool was implemented with a JFrame script object so this commit separates out the JFrame elements for CLI implementation. JFrame elements are saved to the src/window_interface/*/DNAShapefromBEDOutput class while the calculations are kept in the src/scripts/*/DNAShapefromBED class. window_interface/*Window -adjust import to call *Output class window_interface/*Output -adjust import to call script class -adjust output argument when initializing script class to be full file basename and not just directory script/* -strip out JFrame objects -use output as file basename rather than directory name cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user
Before, this tool was implemented with a JFrame script object so this commit separates out the JFrame elements for CLI implementation. JFrame elements are saved to the src/window_interface/*/DNAShapefromFASTAOutput class while the calculations are kept in the src/scripts/*/DNAShapefromFASTA class. window_interface/*Window -adjust import to call *Output class window_interface/*Output -adjust import to call script class -adjust output argument when initializing script class to be full file basename and not just directory script/* -strip out JFrame objects -use output as file basename rather than directory name cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user
Before, this tool was implemented with a JFrame script object so this commit separates out the JFrame elements for CLI implementation. JFrame elements are saved to the src/window_interface/*/FASTAExtractOutput class while the calculations are kept in the src/scripts/*/FASTAExtract class. window_interface/*Window -adjust import to call *Output class window_interface/*Output -adjust import to call script class -adjust output argument when initializing script class to be full filename and not just directory script/* -strip out JFrame objects -use output as filename rather than directory name cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user
This tool did not implement JFrame elements in the script class so the CLI implementation did not need to create an src/window_interface/*/ RandomizeFASTAOutput class. As a result, fewer files were affected: window_interface/*Window -adjust output argument when initializing script class to be full filename and not just directory script/* -use output as filename rather than directory name cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user
Before, this tool was implemented with a JFrame script object so this commit separates out the JFrame elements for CLI implementation. JFrame elements are saved to the src/window_interface/*/SearchMotifOutput class while the calculations are kept in the src/scripts/*/SearchMotif class. window_interface/*Window -adjust import to call *Output class window_interface/*Output -adjust import to call script class -adjust output argument when initializing script class to be full filename and not just directory script/* -strip out JFrame objects -use output as filename rather than directory name cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user
I meant to replace this class with the RandomizeFASTA class for consistent naming but I forgot to add it to the RandomizeFASTA command line interface commit.
Before, this tool was implemented with a JFrame script object so this commit separates out the JFrame elements for CLI implementation. JFrame elements are saved to the src/window_interface/*/AggregateDataOutput class while the calculations are kept in the src/scripts/*/AggregateData class. window_interface/*Window -adjust import to call *Output class window_interface/*Output -adjust import to call script class -adjust output argument when initializing script class to be full filename and not just directory script/* -strip out JFrame objects -use output as filename rather than directory name cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user
This tool did not implement JFrame elements in the script class so the CLI implementation did not need to create an src/window_interface/*/ ScaleMatrixOutput class. As a result, fewer files were affected: window_interface/*Window -adjust output argument when initializing script class to be full filename and not just directory script/* -use output as filename rather than directory name cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user
Before, this tool was implemented with a JFrame script object so this commit separates out the JFrame elements for CLI implementation. JFrame elements are saved to the src/window_interface/*/ScalingFactorOutput class while the calculations are kept in the src/scripts/*/ScalingFactor class. Note this tool's NCIS method may need deeper testing for other cases that would break the CLI. window_interface/*Window -adjust import to call *Output class window_interface/*Output -adjust import to call script class -adjust output argument when initializing script class to be full filename and not just directory script/* -strip out JFrame objects -use output as filename rather than directory name cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user
This tool's command line development has been skipped to reflect the GUI deactivation of the tool. I also commented out its execution in the main ScriptManager subcommand to mimic the GUI.
Before, this tool was implemented with a JFrame script object so this commit separates out the JFrame elements for CLI implementation. JFrame elements are saved to the src/window_interface/*/TagPileupOutput class while the calculations are kept in the src/scripts/*/TagPileup class. This monster of a tool (at least compared to the others) has extra files to update and they are described following the first few files that relate to the general edit structure for tools so far. window_interface/*Window -adjust import to call *Output class window_interface/*Output -adjust import to call script class -adjust output argument when initializing script class to be full filename and not just directory script/* -strip out JFrame objects -use output as filename rather than directory name cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user objects/PileupParameters -reorganized methods to put get next to set methods -added comments to annotate vars with details about what each variable is for -renamed a couple methods to be more descriptive by appending 'get' to the front of the method name -added a method that would spit out all parameters as a command line execution String. Although unused for now, it may be useful for future features.
This tool did not implement JFrame elements in the script class so with no adjustments to so the script or window classes, this tool was straightforward in implementing a CLI version. cli/* -call appropriate script class -write up picocli parsing objects -skipped validateInput() method for this tool.
This tool did not implement JFrame elements in the script class so the CLI implementation did not need to create an src/window_interface/*/ FourColorPlotOutput class. As a result, only the cli/* file was affected. The script is a public static void method so super easy to implement. cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user
Before, this tool was implemented with a JFrame script object so this commit separates out the JFrame elements for CLI implementation. JFrame elements are saved to the src/window_interface/*/HeatMapOutput class while the calculations are kept in the src/scripts/*/HeatMapPlot class. window_interface/*Window -adjust import to call *Output class window_interface/*Output -adjust import to call script class -adjust output argument when initializing script class to be full filename and not just directory script/* -strip out JFrame objects -use output as filename rather than directory name cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user
Before, this tool was implemented with a JFrame script object so this commit separates out the JFrame elements for CLI implementation. JFrame elements are saved to the src/window_interface/*/MergeHeatMapOutput class while the calculations are kept in the src/scripts/*/MergeHeatMap class. window_interface/*Window -adjust import to call *Output class window_interface/*Output -adjust import to call script class -adjust output argument when initializing script class to be full filename and not just directory script/* -strip out JFrame objects -use output as filename rather than directory name cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user
This tool is unlike the others in that there is no GUI version. It's a straightforward tool to plot the composite output of TagPileup that uses the existing chart/CompositePlot class as the script object. Because the GUI version outputs a composite plot, I created this to retain that functionality so that when this tool is used with the CLI TagPileup, it can do the same things as the GUI version. cli/Figure_Generation/ -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user charts/CompositePlot -createCompositePlot() method updated to reduce redundancy -createChart(3params) was made public so that this tool could take advantage of it, instead of just being an internal helper method -createChart(4params) was updated to optionally include a legend (CLI makes it an optional user-specified value)
Before, this tool was implemented with a JFrame script object so this commit separates out the JFrame elements for CLI implementation. JFrame elements are saved to the src/window_interface/*/BEDPeakAligntoRefOutput class while the calculations are kept in the src/scripts/*/BEDPeakAligntoRef class. window_interface/*Window -adjust import to call *Output class window_interface/*Output -adjust import to call script class -adjust output argument when initializing script class to be full filename and not just directory script/* -strip out JFrame objects -use output as filename rather than directory name cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user
Before, this tool was implemented with a JFrame script object so this commit separates out the JFrame elements for CLI implementation. JFrame elements are saved to the src/window_interface/*/ FilterBEDbyProximityOutput class while the calculations are kept in the src/scripts/*/FilterBEDbyProximity class. window_interface/*Window -adjust import to call *Output class window_interface/*Output -adjust import to call script class -adjust output argument when initializing script class to be full filename and not just directory script/* -strip out JFrame objects -use output as filename rather than directory name cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user
This tool did not implement JFrame elements in the script class so the CLI implementation did not need to create an src/window_interface/*/ RandomCoordinateOutput class. As a result, no need to create an Output window class so fewer edits to be made: window_interface/*Window -adjust output argument when initializing script class to be full filename and not just directory script/* -use output as filename rather than directory name cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user
This tool did not implement JFrame elements in the script class so the CLI implementation did not need to create an src/window_interface/*/ TileGenomeOutput class. As a result, just the following files were affected: window_interface/*Window -adjust output argument when initializing script class to be full filename and not just directory script/* -use output as filename rather than directory name cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user
This tool did not implement JFrame elements in the script class so the CLI implementation did not need to create an src/window_interface/*/ ExpandBEDOutput class. As a result, fewer files were affected: window_interface/*Window -adjust output argument when initializing script class to be full filename and not just directory script/* -use output as filename rather than directory name -add capability to print to STDOUT cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user
This tool did not implement JFrame elements in the script class so the CLI implementation did not need to create an src/window_interface/*/ ExpandGFFOutput class. As a result, fewer files were affected: window_interface/*Window -adjust output argument when initializing script class to be full filename and not just directory script/* -use output as filename rather than directory name -add capability to print to STDOUT cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user
This tool did not implement JFrame elements in the script class so the CLI implementation did not need to create an src/window_interface/*/ BEDtoGFFOutput class. As a result, fewer files were affected: window_interface/*Window -adjust output argument when initializing script class to be full filename and not just directory script/* -use output as filename rather than directory name -add capability to print to STDOUT cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user
This tool did not implement JFrame elements in the script class so the CLI implementation did not need to create an src/window_interface/*/ GFFtoBEDOutput class. As a result, fewer files were affected: window_interface/*Window -adjust output argument when initializing script class to be full filename and not just directory script/* -use output as filename rather than directory name -add capability to print to STDOUT cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user
…to coordinate-manipulation
This tool did not implement JFrame elements in the script class so the CLI implementation did not need to create an src/window_interface/*/ SortGFFOutput class. There is a quirk with the BEDtoGFF tool that adds a semicolon to the end of the last column with the feature ID. To make this tool compatible with the GFF output, I split the last GFF column on the semicolon and took the first token as the ID. I also moved the parseCDT method originally in the window_interface/ Coordinate_Manipulation/*/Sort* classes to the util/CDTUtilities class. The parseCDT method is used to get the number of items in a row of the input CDT file and to check the formatting for consistent row sizes. Since both the SortBED and SortGFF tools use the same method, this commit merges them into the same copy that can be referenced from a general utilities class. This will make updates easier if this method needs to be adjusted in the future. util/CDTUtilities -move parseCDT method from SortGFFWindow class to the CDTUtilities class -add properties to the class to save information on consistent row sizes -add methods to retrieve these values NOTE: static methods of this class appear to be unused or copied into another class, consider retiring window_interface/*Window -adjust output argument when initializing script class to be full file basename and not just directory -lots of differences in this commit are a matter of entabbing -rename BED related variable names to be consistent with GFF variable naming -update CDT file loading to use CDTUtilities validation method -remove parseCDT() method since using CDTUtilities version script/* -use output as file basename rather than directory name -temporary fix using String's split() method on the semicolon cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user -import CDTUtilities and parse CDT input to check consistent rows as a part of validateInput()
Before, this tool was implemented with a JFrame script object so this commit separates out the JFrame elements for CLI implementation. JFrame elements are saved to the src/window_interface/*/SortBEDOutput class while the calculations are kept in the src/scripts/*/SortBED class. window_interface/*Window -adjust output argument when initializing script class to be full filename and not just directory -lots of differences in this commit are a matter of entabbing -rename BED related variable names to be consistent with GFF variable naming -update CDT file loading to use CDTUtilities validation method -remove parseCDT() method since using CDTUtilities version script/* -use output as file basename rather than directory name cli/* -call appropriate script class -write up picocli parsing objects -write up validateInput() method to check inputs and write messages for the user -import CDTUtilities and parse CDT input to check consistent rows as a part of validateInput()
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most of the tools have a command line version built out in the
build-clibranch. This commit merges the CLI version tools into the master branch.