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Added new DNA shapes to DNAShape tools addressing issue #152 #179

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Added new DNA shapes to DNAShape tools addressing issue #152 #179

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5a9a514
added data from DNAshapeR
benjaminbeer256 Aug 14, 2024
a74dc1c
Added correct values for shift and tilt
benjaminbeer256 Aug 16, 2024
df86654
Merge pull request #173 from CEGRcode/main
benjaminbeer256 Aug 17, 2024
0538f5e
DNAshapeFromFASTA cli is functional
benjaminbeer256 Oct 20, 2024
ea251cb
DNAshapefromFASTA window interface is functional
benjaminbeer256 Oct 29, 2024
1fe8376
Added DNAShapefromBED
benjaminbeer256 Nov 4, 2024
ec9bd08
Rearranged window and simplified script
benjaminbeer256 Nov 8, 2024
ca6ca1a
fixed typos before pull request
benjaminbeer256 Nov 8, 2024
6677158
prevent "AWT-EventQueue-0" excpetion
benjaminbeer256 Nov 12, 2024
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148 changes: 87 additions & 61 deletions src/main/java/scriptmanager/cli/Sequence_Analysis/DNAShapefromBEDCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -5,15 +5,15 @@
import picocli.CommandLine.Option;
import picocli.CommandLine.Parameters;

import java.util.ArrayList;
import java.util.concurrent.Callable;

import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.PrintStream;

import scriptmanager.objects.ToolDescriptions;
import scriptmanager.objects.Exceptions.OptionException;
import scriptmanager.util.DNAShapeReference;
import scriptmanager.util.ExtensionFileFilter;
import scriptmanager.scripts.Sequence_Analysis.DNAShapefromBED;

Expand Down Expand Up @@ -56,21 +56,43 @@ public DNAShapefromBEDCLI(){}

@ArgGroup(validate = false, heading = "Shape Options%n")
ShapeType shape = new ShapeType();
ArrayList<Integer> OUTPUT_TYPES;

static class ShapeType {
public static class ShapeType {
@Option(names = { "-g", "--groove" }, description = "output minor groove width")
private boolean groove = false;
public boolean groove = false;
@Option(names = { "-r", "--roll" }, description = "output roll")
private boolean roll = false;
public boolean roll = false;
@Option(names = { "-p", "--propeller" }, description = "output propeller twist")
private boolean propeller = false;
public boolean propeller = false;
@Option(names = { "-l", "--helical" }, description = "output helical twist")
private boolean helical = false;
@Option(names = { "-a", "--all" }, description = "output groove, roll, propeller twist, and helical twist (equivalent to -grpl).")
private boolean all = false;
public boolean helical = false;
@Option(names = { "--electrostatic-potential" }, description = "output electrostatic potential")
public boolean ep = false;
@Option(names = { "--stretch" }, description = "output stretch")
public boolean stretch = false;
@Option(names = { "--buckle" }, description = "output buckle")
public boolean buckle = false;
@Option(names = { "--shear" }, description = "output shear")
public boolean shear = false;
@Option(names = { "--opening" }, description = "output opening")
public boolean opening = false;
@Option(names = { "--stagger" }, description = "output stagger")
public boolean stagger = false;
@Option(names = { "--tilt" }, description = "output tilt")
public boolean tilt = false;
@Option(names = { "--slide" }, description = "output slide")
public boolean slide = false;
@Option(names = { "--rise" }, description = "output rise")
public boolean rise = false;
@Option(names = { "--shift" }, description = "output shift")
public boolean shift = false;
@Option(names = { "--2013" }, description = "output groove, roll, propeller twist, and helical twist (equivalent to -grpl).")
public boolean originalAll = false;
@Option(names = { "-a", "--2021" }, description = "output all 14 shapes")
public boolean all = false;
}

private boolean[] OUTPUT_TYPE = new boolean[] { false, false, false, false };
private short outputMatrix = DNAShapefromBED.NO_MATRIX;

/**
Expand All @@ -88,29 +110,9 @@ public Integer call() throws Exception {
}

// Generate Composite Plot
DNAShapefromBED script_obj = new DNAShapefromBED(genomeFASTA, bedFile, outputBasename, OUTPUT_TYPE,
DNAShapefromBED script_obj = new DNAShapefromBED(genomeFASTA, bedFile, outputBasename, OUTPUT_TYPES,
forceStrand, composite, outputMatrix, gzOutput);
script_obj.run();
// Print Composite Scores
if (composite) {
String[] headers = new String[] { "AVG_MGW", "AVG_PropT", "AVG_HelT", "AVG_Roll" };
for (int t = 0; t < OUTPUT_TYPE.length; t++) {
if (OUTPUT_TYPE[t]) {
PrintStream COMPOSITE = new PrintStream(new File(outputBasename + "_" + headers[t] + ".out"));
double[] AVG = script_obj.getAvg(t);
// position vals
for (int z = 0; z < AVG.length; z++) {
COMPOSITE.print("\t" + z);
}
COMPOSITE.print("\n" + ExtensionFileFilter.stripExtension(bedFile) + "_" + headers[t]);
// score vals
for (int z = 0; z < AVG.length; z++) {
COMPOSITE.print("\t" + AVG[z]);
}
COMPOSITE.println();
}
}
}
System.err.println("Shapes Calculated.");
return (0);
}
Expand Down Expand Up @@ -144,36 +146,47 @@ private String validateInput() throws IOException {
// no extension check
// check directory
if (outParent == null) {
// System.err.println("default to current directory");
System.err.println("default to current directory");
} else if (!new File(outParent).exists()) {
r += "(!)Check output directory exists: " + outParent + "\n";
}
}

// Check & set output_type
if (!(shape.groove || shape.propeller || shape.helical || shape.roll || shape.all)) {
r += "(!)Please select at least one of the shape flags.\n";
} else if ((shape.groove || shape.propeller || shape.helical || shape.roll) && shape.all) {
r += "(!)Please avoid mixing the \"-a\" flag with the other shape flags.\n";
}

if (shape.groove) {
OUTPUT_TYPE[0] = true;
}
if (shape.propeller) {
OUTPUT_TYPE[1] = true;
}
if (shape.helical) {
OUTPUT_TYPE[2] = true;
}
if (shape.roll) {
OUTPUT_TYPE[3] = true;
OUTPUT_TYPES = new ArrayList<>();
if (shape.groove) { OUTPUT_TYPES.add(DNAShapeReference.MGW); }
if (shape.propeller) { OUTPUT_TYPES.add(DNAShapeReference.PROPT); }
if (shape.helical) { OUTPUT_TYPES.add(DNAShapeReference.HELT); }
if (shape.roll) { OUTPUT_TYPES.add(DNAShapeReference.ROLL); }
if (shape.ep) { OUTPUT_TYPES.add(DNAShapeReference.EP); }
if (shape.stretch) { OUTPUT_TYPES.add(DNAShapeReference.STRETCH); }
if (shape.buckle) { OUTPUT_TYPES.add(DNAShapeReference.BUCKLE); }
if (shape.shear) { OUTPUT_TYPES.add(DNAShapeReference.SHEAR); }
if (shape.opening) { OUTPUT_TYPES.add(DNAShapeReference.OPENING); }
if (shape.stagger) { OUTPUT_TYPES.add(DNAShapeReference.STAGGER); }
if (shape.tilt) { OUTPUT_TYPES.add(DNAShapeReference.TILT); }
if (shape.slide) { OUTPUT_TYPES.add(DNAShapeReference.SLIDE); }
if (shape.rise) { OUTPUT_TYPES.add(DNAShapeReference.RISE); }
if (shape.shift) { OUTPUT_TYPES.add(DNAShapeReference.SHIFT); }
if (shape.all){
for (int i = 0; i < 14; i++){
if (OUTPUT_TYPES.contains(i)){
r += "(!)Please avoid mixing the \"-a\" flag with the other shape flags.\n";
}
else {
OUTPUT_TYPES.add(i);
}
}
}

if (shape.all) {
OUTPUT_TYPE = new boolean[] { true, true, true, true };
else if (shape.originalAll){
for (int i = 0; i < 5; i++){
if (OUTPUT_TYPES.contains(i)){
r += "(!)Please avoid mixing the \"--2013\" flag with the other shape flags.\n";
}
else {
OUTPUT_TYPES.add(i);
}
}
}

if (matrix && cdt) {
r += "(!)Please select either the matrix or the cdt flag.\n";
} else if (matrix) {
Expand All @@ -194,23 +207,36 @@ private String validateInput() throws IOException {
* sequence from
* @param out the output file name base (to add
* _&lt;shapetype&gt;.cdt suffix to)
* @param type a four-element boolean list for specifying shape type
* to output (no enforcement on size)
* @param type An ArrayList specifying the shape type of the output with integers
* @param str force strandedness (true=forced, false=not forced)
* @param outputComposite whether to output a composite average output
* @param outputMatrix value encoding not to write output matrix data, write
* matrix in CDT format, and write matrix in tab format
* @param gzOutput whether or not to gzip output
* @return command line to execute with formatted inputs
*/
public static String getCLIcommand(File gen, File input, File out, boolean[] type, boolean str, boolean outputComposite, short outputMatrix, boolean gzOutput) throws OptionException {
public static String getCLIcommand(File gen, File input, File out, ArrayList<Integer> type, boolean str, boolean outputComposite, short outputMatrix, boolean gzOutput) throws OptionException {
String command = "java -jar $SCRIPTMANAGER sequence-analysis dna-shape-bed";
command += " -o " + out.getAbsolutePath();
command += gzOutput ? " -z " : "";
command += type[0] ? " --groove" : "";
command += type[1] ? " --propeller" : "";
command += type[2] ? " --helical" : "";
command += type[3] ? " --roll" : "";
if (type.size() == 14){
command += type.size() == 14? "-a" : "";
} else {
command += type.contains(0)? "--groove" : "";
command += type.contains(1)? "--propeller" : "";
command += type.contains(2)? "--helical" : "";
command += type.contains(3)? "--roll" : "";
command += type.contains(4)? "--electrostatic-potential" : "";
command += type.contains(5)? "--stretch" : "";
command += type.contains(6)? "--buckle" : "";
command += type.contains(7)? "--shear" : "";
command += type.contains(8)? "--opening" : "";
command += type.contains(9)? "--stagger" : "";
command += type.contains(10)? "--tilt" : "";
command += type.contains(11)? "--slide" : "";
command += type.contains(12)? "--rise" : "";
command += type.contains(13)? "--shift" : "";
}
command += str ? "" : "--no-force";
command += outputComposite ? "--composite" : "";
switch (outputMatrix) {
Expand Down
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