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owlangowlang
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create SortBED command line 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/*/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()
1 parent 2562bc6 commit 3ab7ea0

3 files changed

Lines changed: 139 additions & 78 deletions

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‎src/cli/Coordinate_Manipulation/BED_Manipulation/SortBEDCLI.java‎

Lines changed: 80 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -12,8 +12,9 @@
1212
import java.io.FileNotFoundException;
1313

1414
import objects.ToolDescriptions;
15+
import util.CDTUtilities;
1516
import util.ExtensionFileFilter;
16-
//import scripts.Coordinate_Manipulation.BED_Manipulation.SortBED;
17+
import scripts.Coordinate_Manipulation.BED_Manipulation.SortBED;
1718

1819
/**
1920
Coordinate_ManipulationCLI/SortBEDCLI
@@ -25,6 +26,22 @@
2526
exitCodeOnExecutionException = 1)
2627
public class SortBEDCLI implements Callable<Integer> {
2728

29+
@Parameters( index = "0", description = "the BED file to sort")
30+
private File bedFile;
31+
@Parameters( index = "1", description = "the reference CDT file to sort the input by")
32+
private File cdtFile;
33+
34+
@Option(names = {"-o", "--output"}, description = "specify output file basename with no .cdt/.bed/.jtv extension (default=<bedFile>_SORT")
35+
private String outputBasename = null;
36+
@Option(names = {"-c", "--center"}, description = "sort by center on the input size of expansion in bins (default=100)")
37+
private int center = -999;
38+
@Option(names = {"-x", "--index"}, description = "sort by index from the specified start to the specified stop (0-indexed and half-open interval)",
39+
arity = "2")
40+
private int[] index = {-999, -999};
41+
42+
private int CDT_SIZE = -999;
43+
private boolean byCenter = false;
44+
2845
@Override
2946
public Integer call() throws Exception {
3047
System.err.println( ">SortBEDCLI.call()" );
@@ -35,16 +52,73 @@ public Integer call() throws Exception {
3552
System.exit(1);
3653
}
3754

38-
//SEStats.getSEStats( output, bamFile, null );
55+
if( byCenter ){
56+
index[0] = (CDT_SIZE / 2) - (center / 2);
57+
index[1] = (CDT_SIZE / 2) + (center / 2);
58+
}
59+
60+
SortBED.sortBEDbyCDT(outputBasename, bedFile, cdtFile, index[0], index[1]);
3961

40-
//System.err.println("Calculations Complete");
62+
System.err.println("Sort Complete");
4163
return(0);
4264
}
4365

4466
private String validateInput() throws IOException {
4567
String r = "";
46-
//validate input here
47-
//append messages to the user to `r`
68+
69+
//check inputs exist
70+
if(!bedFile.exists()){
71+
r += "(!)BED file does not exist: " + bedFile.getName() + "\n";
72+
}
73+
if(!cdtFile.exists()){
74+
r += "(!)CDT file does not exist: " + cdtFile.getName() + "\n";
75+
}
76+
if(!"".equals(r)){ return(r); }
77+
//check input extensions
78+
if(!"bed".equals(ExtensionFileFilter.getExtension(bedFile))){
79+
r += "(!)Is this a BED file? Check extension: " + bedFile.getName() + "\n";
80+
}
81+
if(!"cdt".equals(ExtensionFileFilter.getExtension(cdtFile))){
82+
r += "(!)Is this a CDT file? Check extension: " + cdtFile.getName() + "\n";
83+
}
84+
// validate CDT as file, with consistent row size, and save row_size value
85+
try {
86+
CDTUtilities cdt_obj = new CDTUtilities();
87+
cdt_obj.parseCDT(cdtFile);
88+
if( cdt_obj.isValid() ){ CDT_SIZE = cdt_obj.getSize(); }
89+
else{ r += "(!)CDT file doesn't have consistent row sizes. " + cdt_obj.getInvalidMessage(); }
90+
}catch (FileNotFoundException e1){ e1.printStackTrace(); }
91+
92+
//set default output filename
93+
if(outputBasename==null){
94+
outputBasename = ExtensionFileFilter.stripExtension(bedFile) + "_SORT";
95+
//check output filename is valid
96+
}else{
97+
//no extension check
98+
//check directory
99+
File BASEFILE = new File(outputBasename);
100+
if(BASEFILE.getParent()==null){
101+
// System.err.println("default to current directory");
102+
} else if(!new File(BASEFILE.getParent()).exists()){
103+
r += "(!)Check output directory exists: " + BASEFILE.getParent() + "\n";
104+
}
105+
}
106+
107+
// Set Center if Index not given
108+
if( index[0]==-999 && index[1]==-999 ) { byCenter = true; }
109+
// Center Specified
110+
if( byCenter ){
111+
if( center==-999 ){ center = 100; }
112+
else if( center<0 ){
113+
r += "(!)Invalid --center input, must be a positive integer value.";
114+
}
115+
// Index Specified
116+
}else{
117+
if( index[0]<0 || index[1]>CDT_SIZE || index[0]>index[1] ){
118+
r += "(!)Invalid --index value input, check that start>0, stop<CDT row size, and start<stop.";
119+
}
120+
}
121+
48122
return(r);
49123
}
50-
}
124+
}

‎src/scripts/Coordinate_Manipulation/BED_Manipulation/SortBED.java‎

Lines changed: 14 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
11
package scripts.Coordinate_Manipulation.BED_Manipulation;
22

33
import java.io.File;
4+
import java.io.FileNotFoundException;
45
import java.io.IOException;
56
import java.io.PrintStream;
67
import java.util.ArrayList;
@@ -36,12 +37,11 @@ public static void sortBEDbyCDT(String outname, File bed, File cdt, int START_IN
3637

3738
//Output sorted CDT File
3839
String newCDT = outname + ".cdt";
39-
PrintStream OUT = null;
40-
OUT = new PrintStream(newCDT);
41-
OUT.println(CDTHeader);
42-
for(int x = 0; x < SORT.size(); x++) {
43-
OUT.println(CDTFile.get(SORT.get(x).getName()));
44-
}
40+
PrintStream OUT = new PrintStream(newCDT);
41+
OUT.println(CDTHeader);
42+
for(int x = 0; x < SORT.size(); x++) {
43+
OUT.println(CDTFile.get(SORT.get(x).getName()));
44+
}
4545
OUT.close();
4646
CDTFile = null; //Free up memory by getting CDT file out of memory
4747
JTVOutput.outputJTV(outname, "green");
@@ -58,11 +58,12 @@ public static void sortBEDbyCDT(String outname, File bed, File cdt, int START_IN
5858
}
5959
scan.close();
6060
//Output sorted BED File
61-
String newBED = outname +".bed";
62-
OUT = new PrintStream(newBED);
63-
for(int x = 0; x < SORT.size(); x++) {
64-
OUT.println(BEDFile.get(SORT.get(x).getName()));
65-
}
66-
OUT.close();
61+
String newBED = outname +".bed";
62+
OUT = new PrintStream(newBED);
63+
for(int x = 0; x < SORT.size(); x++) {
64+
OUT.println(BEDFile.get(SORT.get(x).getName()));
65+
}
66+
OUT.close();
6767
}
68-
}
68+
69+
}

‎src/window_interface/Coordinate_Manipulation/BED_Manipulation/SortBEDWindow.java‎

Lines changed: 45 additions & 59 deletions
Original file line numberDiff line numberDiff line change
@@ -31,6 +31,7 @@
3131
import javax.swing.SwingWorker;
3232
import javax.swing.border.EmptyBorder;
3333

34+
import util.CDTUtilities;
3435
import util.FileSelection;
3536
import scripts.Coordinate_Manipulation.BED_Manipulation.SortBED;
3637

@@ -74,42 +75,42 @@ public class SortBEDWindow extends JFrame implements ActionListener, PropertyCha
7475
private JLabel lblIndexStop;
7576

7677
class Task extends SwingWorker<Void, Void> {
77-
@Override
78-
public Void doInBackground() throws IOException {
79-
try {
80-
if(rdbtnSortbyCenter.isSelected() && Integer.parseInt(txtMid.getText()) > CDT_SIZE) {
81-
JOptionPane.showMessageDialog(null, "Sort Size is larger than CDT File!!!");
82-
} else if(rdbtnSortbyIndex.isSelected() && Integer.parseInt(txtStart.getText()) < 0) {
83-
JOptionPane.showMessageDialog(null, "Start Index is smaller than 0!!!");
84-
} else if(rdbtnSortbyIndex.isSelected() && Integer.parseInt(txtStop.getText()) > CDT_SIZE) {
85-
JOptionPane.showMessageDialog(null, "Start Index is smaller than 0!!!");
86-
} else {
87-
if(rdbtnSortbyCenter.isSelected()) {
88-
START_INDEX = (CDT_SIZE / 2) - (Integer.parseInt(txtMid.getText()) / 2);
89-
STOP_INDEX = (CDT_SIZE / 2) + (Integer.parseInt(txtMid.getText()) / 2);
90-
} else {
91-
START_INDEX = Integer.parseInt(txtStart.getText());
92-
STOP_INDEX = Integer.parseInt(txtStop.getText());
93-
}
94-
95-
String OUTPUT = txtOutput.getText();
96-
if(OUTPUT_PATH != null) { OUTPUT = OUTPUT_PATH.getCanonicalPath() + File.separator + txtOutput.getText(); }
97-
98-
setProgress(0);
99-
SortBED.sortBEDbyCDT(OUTPUT, BED_File, CDT_File, START_INDEX, STOP_INDEX);
78+
@Override
79+
public Void doInBackground() throws IOException {
80+
try {
81+
if(rdbtnSortbyCenter.isSelected() && Integer.parseInt(txtMid.getText()) > CDT_SIZE) {
82+
JOptionPane.showMessageDialog(null, "Sort Size is larger than CDT File!!!");
83+
} else if(rdbtnSortbyIndex.isSelected() && Integer.parseInt(txtStart.getText()) < 0) {
84+
JOptionPane.showMessageDialog(null, "Start Index is smaller than 0!!!");
85+
} else if(rdbtnSortbyIndex.isSelected() && Integer.parseInt(txtStop.getText()) > CDT_SIZE) {
86+
JOptionPane.showMessageDialog(null, "Stop Index is larger than CDT row size!!!");
87+
} else {
88+
if(rdbtnSortbyCenter.isSelected()) {
89+
START_INDEX = (CDT_SIZE / 2) - (Integer.parseInt(txtMid.getText()) / 2);
90+
STOP_INDEX = (CDT_SIZE / 2) + (Integer.parseInt(txtMid.getText()) / 2);
91+
} else {
92+
START_INDEX = Integer.parseInt(txtStart.getText());
93+
STOP_INDEX = Integer.parseInt(txtStop.getText());
94+
}
95+
96+
String OUTPUT = txtOutput.getText();
97+
if(OUTPUT_PATH != null) { OUTPUT = OUTPUT_PATH.getCanonicalPath() + File.separator + txtOutput.getText(); }
98+
99+
setProgress(0);
100+
SortBED.sortBEDbyCDT(OUTPUT, BED_File, CDT_File, START_INDEX, STOP_INDEX);
100101
setProgress(100);
101102
JOptionPane.showMessageDialog(null, "Sort Complete");
102-
}
103-
} catch(NumberFormatException nfe){
103+
}
104+
} catch(NumberFormatException nfe){
104105
JOptionPane.showMessageDialog(null, "Invalid Input in Fields!!!");
105106
}
106107
return null;
107-
}
108-
109-
public void done() {
110-
massXable(contentPane, true);
111-
setCursor(null); //turn off the wait cursor
112-
}
108+
}
109+
110+
public void done() {
111+
massXable(contentPane, true);
112+
setCursor(null); //turn off the wait cursor
113+
}
113114
}
114115

115116
public SortBEDWindow() {
@@ -284,7 +285,7 @@ public void actionPerformed(ActionEvent e) {
284285
BED_File = newBEDFile;
285286
lblBEDFile.setText(BED_File.getName());
286287
txtOutput.setEnabled(true);
287-
String sortName = (BED_File.getName()).substring(0,BED_File.getName().length() - 4) + "_SORT";
288+
String sortName = (BED_File.getName()).substring(0, BED_File.getName().length() - 4) + "_SORT";
288289
txtOutput.setText(sortName);
289290
}
290291
}
@@ -300,11 +301,19 @@ public void actionPerformed(ActionEvent e) {
300301
public void actionPerformed(ActionEvent e) {
301302
File newCDTFile = FileSelection.getFile(fc,"cdt");
302303
if(newCDTFile != null) {
303-
CDT_File = newCDTFile;
304-
lblCDTFile.setText(CDT_File.getName());
305-
306-
try { CDT_VALID = parseCDTFile(CDT_File);
304+
try {
305+
CDT_File = newCDTFile;
306+
lblCDTFile.setText(CDT_File.getName());
307+
308+
CDTUtilities cdt_obj = new CDTUtilities();
309+
cdt_obj.parseCDT(CDT_File);
310+
CDT_SIZE = cdt_obj.getSize();
311+
CDT_VALID = cdt_obj.isValid();
312+
String message = cdt_obj.getInvalidMessage();
313+
System.err.println(CDT_File.getCanonicalPath() + ": " + message);
314+
if(!message.equals("")) { JOptionPane.showMessageDialog(null, message);}
307315
} catch (FileNotFoundException e1) { e1.printStackTrace(); }
316+
catch (IOException e2) { e2.printStackTrace(); }
308317

309318
if(CDT_VALID) {
310319
lblColumnCount.setText("Column Count: " + CDT_SIZE);
@@ -362,27 +371,4 @@ public void massXable(Container con, boolean status) {
362371
}
363372
}
364373

365-
public boolean parseCDTFile(File CDT) throws FileNotFoundException {
366-
Scanner scan = new Scanner(CDT);
367-
int currentSize = -999;
368-
boolean consistentSize = true;
369-
int currentRow = 1;
370-
while (scan.hasNextLine()) {
371-
String[] temp = scan.nextLine().split("\t");
372-
if(!temp[0].contains("YORF") && !temp[0].contains("NAME")) {
373-
int tempsize = temp.length - 2;
374-
if(currentSize == -999) { currentSize = tempsize; }
375-
else if(currentSize != tempsize) {
376-
JOptionPane.showMessageDialog(null, "Invalid Row at Index: " + currentRow);
377-
consistentSize = false;
378-
scan.close();
379-
}
380-
currentRow++;
381-
}
382-
}
383-
scan.close();
384-
CDT_SIZE = currentSize;
385-
if(consistentSize) { return true; }
386-
else { return false; }
387-
}
388374
}

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