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author
William Lai
committed
#18 Feature added
1 parent b0af09e commit 4b20623

4 files changed

Lines changed: 446 additions & 29 deletions

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‎src/main/ScriptManager.java‎

Lines changed: 45 additions & 29 deletions
Original file line numberDiff line numberDiff line change
@@ -33,6 +33,7 @@
3333
import window_interface.File_Utilities.MD5ChecksumWindow;
3434
import window_interface.Coordinate_Analysis.BEDPeakAligntoRefWindow;
3535
import window_interface.Coordinate_Analysis.FilterBEDbyProximityWindow;
36+
import window_interface.Coordinate_Analysis.RandomCoordinateWindow;
3637
import window_interface.Sequence_Analysis.DNAShapefromBEDWindow;
3738
import window_interface.Sequence_Analysis.DNAShapefromFASTAWindow;
3839
import window_interface.Sequence_Analysis.FASTAExtractWindow;
@@ -427,42 +428,57 @@ public void run() {
427428

428429
JButton btnBedPeakAlignment = new JButton("Align BED to Reference");
429430
btnBedPeakAlignment.setToolTipText("Align BED file to Reference file creating CDT file");
430-
pnlPeakAnalysis.add(btnBedPeakAlignment);
431-
432431
btnBedPeakAlignment.addActionListener(new ActionListener() {
433432
public void actionPerformed(ActionEvent e) {
434-
EventQueue.invokeLater(new Runnable() {
435-
public void run() {
436-
try {
437-
BEDPeakAligntoRefWindow frame = new BEDPeakAligntoRefWindow();
438-
frame.setVisible(true);
439-
} catch (Exception e) {
440-
e.printStackTrace();
441-
}
442-
}
443-
});
444-
}
445-
});
446-
433+
EventQueue.invokeLater(new Runnable() {
434+
public void run() {
435+
try {
436+
BEDPeakAligntoRefWindow frame = new BEDPeakAligntoRefWindow();
437+
frame.setVisible(true);
438+
} catch (Exception e) {
439+
e.printStackTrace();
440+
}
441+
}
442+
});
443+
}
444+
});
445+
pnlPeakAnalysis.add(btnBedPeakAlignment);
446+
447447
JButton btnBedFilter = new JButton("Filter BED by Proximity");
448448
btnBedFilter.setToolTipText("Filter BED file by proximity");
449-
pnlPeakAnalysis.add(btnBedFilter);
449+
btnBedFilter.addActionListener(new ActionListener() {
450+
public void actionPerformed(ActionEvent e) {
451+
EventQueue.invokeLater(new Runnable() {
452+
public void run() {
453+
try {
454+
FilterBEDbyProximityWindow frame = new FilterBEDbyProximityWindow();
455+
frame.setVisible(true);
456+
} catch (Exception e) {
457+
e.printStackTrace();
458+
}
459+
}
460+
});
461+
}
462+
});
463+
pnlPeakAnalysis.add(btnBedFilter);
450464

451465

452-
btnBedFilter.addActionListener(new ActionListener() {
453-
public void actionPerformed(ActionEvent e) {
454-
EventQueue.invokeLater(new Runnable() {
455-
public void run() {
456-
try {
457-
FilterBEDbyProximityWindow frame = new FilterBEDbyProximityWindow();
458-
frame.setVisible(true);
459-
} catch (Exception e) {
460-
e.printStackTrace();
466+
JButton btnRandomCoordinateGeneration = new JButton("Generate Random Coordinate");
467+
btnRandomCoordinateGeneration.addActionListener(new ActionListener() {
468+
public void actionPerformed(ActionEvent e) {
469+
EventQueue.invokeLater(new Runnable() {
470+
public void run() {
471+
try {
472+
RandomCoordinateWindow frame = new RandomCoordinateWindow();
473+
frame.setVisible(true);
474+
} catch (Exception e) {
475+
e.printStackTrace();
476+
}
461477
}
462-
}
463-
});
464-
}
465-
});
478+
});
479+
}
480+
});
481+
pnlPeakAnalysis.add(btnRandomCoordinateGeneration);
466482

467483

468484
JPanel pnlTagAnalysis = new JPanel();

‎src/scripts/Coordinate_Analysis/RandomCoordinate.java‎

Lines changed: 56 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,56 @@
1+
package scripts.Coordinate_Analysis;
2+
3+
import java.io.File;
4+
import java.io.IOException;
5+
import java.io.PrintStream;
6+
7+
import javax.swing.JOptionPane;
8+
9+
import objects.CoordinateObjects.BEDCoord;
10+
import objects.CoordinateObjects.GFFCoord;
11+
import objects.CoordinateObjects.GenericCoord;
12+
import util.GenomeSizeReference;
13+
14+
public class RandomCoordinate {
15+
private File OUTPUT = null;
16+
private String GENOME = "";
17+
private int numSites = 0;
18+
private int windowSize = 0;
19+
20+
private boolean BEDout = true;
21+
private String EXTENSION = ".bed";
22+
23+
public RandomCoordinate(String gen, int sites, int size, boolean bed, File out) {
24+
GENOME = gen;
25+
numSites = sites;
26+
windowSize = size;
27+
OUTPUT = out;
28+
BEDout = bed;
29+
if(BEDout) { EXTENSION = ".bed"; }
30+
else { EXTENSION = ".gff"; }
31+
}
32+
33+
public void execute() throws IOException {
34+
GenomeSizeReference coord = new GenomeSizeReference(GENOME);
35+
if(!coord.isSmaller(windowSize)) {
36+
System.err.println("Window size is too large for selected genome!!!\n");
37+
JOptionPane.showMessageDialog(null, "Invalid Window Size Entered!!!");
38+
} else {
39+
String randomName = GENOME + "_" + numSites + "SITES_" + windowSize + "bp" + EXTENSION;
40+
PrintStream OUT = null;
41+
if(OUTPUT == null) OUT = new PrintStream(randomName);
42+
else OUT = new PrintStream(OUTPUT + File.separator + randomName);
43+
for(int x = 0; x < numSites; x++) {
44+
GenericCoord temp = coord.generateRandomCoord(windowSize);
45+
if(BEDout) {
46+
BEDCoord outcoord = new BEDCoord(temp.getChrom(), temp.getStart(), temp.getStop(), temp.getDir(), temp.getName());
47+
OUT.println(outcoord.toString());
48+
} else {
49+
GFFCoord outcoord = new GFFCoord(temp.getChrom(), temp.getStart(), temp.getStop(), temp.getDir(), temp.getName());
50+
OUT.println(outcoord.toString());
51+
}
52+
}
53+
OUT.close();
54+
}
55+
}
56+
}

‎src/util/GenomeSizeReference.java‎

Lines changed: 141 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,141 @@
1+
package util;
2+
3+
import java.util.ArrayList;
4+
import java.util.Arrays;
5+
import java.util.concurrent.ThreadLocalRandom;
6+
7+
import objects.CoordinateObjects.GenericCoord;
8+
9+
public class GenomeSizeReference {
10+
11+
private static String genomeName = "";
12+
private static long genomeSize = 0;
13+
14+
private static ArrayList<String> chromName = null;
15+
private static ArrayList<Long> chromSize = null;
16+
17+
public GenomeSizeReference() {
18+
chromName = new ArrayList<String>();
19+
chromSize = new ArrayList<Long>();
20+
}
21+
22+
public GenomeSizeReference(String build) {
23+
if(build.equals("sacCer3_cegr")) {
24+
initialize_sacCer3_cegr();
25+
} else if(build.equals("hg19")) {
26+
initialize_hg19();
27+
} else if(build.equals("hg19_contigs")) {
28+
initialize_hg19_contig();
29+
} else if(build.equals("mm10")) {
30+
initialize_mm10();
31+
} else {
32+
System.err.println("Non-existent genome build!\n");
33+
}
34+
}
35+
36+
public void setGenome(String build) {
37+
if(build.equals("sacCer3_cegr")) {
38+
initialize_sacCer3_cegr();
39+
} else if(build.equals("hg19")) {
40+
initialize_hg19();
41+
} else if(build.equals("hg19_contigs")) {
42+
initialize_hg19_contig();
43+
} else if(build.equals("mm10")) {
44+
initialize_mm10();
45+
} else {
46+
System.err.println("Non-existent genome build!\n");
47+
}
48+
}
49+
50+
public String getGenome() {
51+
return genomeName;
52+
}
53+
54+
public long getGenomeSize() {
55+
return genomeSize;
56+
}
57+
58+
public static void initialize_sacCer3_cegr() {
59+
genomeName = "sacCer3_cegr";
60+
genomeSize = 12163423;
61+
String[] chrom = {"chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chrM", "2-micron"};
62+
chromName = new ArrayList<String>(Arrays.asList(chrom));
63+
long[] size = new long[] {230218, 813184, 316620, 1531933, 576874, 270161, 1090940, 562643, 439888, 745751, 666816, 1078177, 924431, 784333, 1091291, 948066, 85779, 6318};
64+
chromSize = new ArrayList<Long>();
65+
for(int x = 0; x < size.length; x++) { chromSize.add(new Long(size[x])); }
66+
}
67+
68+
public static void initialize_hg19() {
69+
genomeName = "hg19";
70+
genomeSize = (long) 2.725521370E9;
71+
String[] chrom = {"chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chrX", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr20", "chrY", "chr19", "chr22", "chr21"};
72+
chromName = new ArrayList<String>(Arrays.asList(chrom));
73+
long[] size = new long[] {249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 155270560, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 63025520, 59373566, 59128983, 51304566, 48129895};
74+
chromSize = new ArrayList<Long>();
75+
for(int x = 0; x < size.length; x++) { chromSize.add(new Long(size[x])); }
76+
}
77+
78+
public static void initialize_hg19_contig() {
79+
genomeName = "hg19";
80+
genomeSize = (long) 3.137161264E9;
81+
String[] chrom = {"chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chrX", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr20", "chrY", "chr19", "chr22", "chr21",
82+
"chr6_ssto_hap7", "chr6_mcf_hap5", "chr6_cox_hap2", "chr6_mann_hap4", "chr6_apd_hap1", "chr6_qbl_hap6", "chr6_dbb_hap3", "chr17_ctg5_hap1", "chr4_ctg9_hap1", "chr1_gl000192_random", "chrUn_gl000225", "chr4_gl000194_random", "chr4_gl000193_random", "chr9_gl000200_random",
83+
"chrUn_gl000222", "chrUn_gl000212", "chr7_gl000195_random", "chrUn_gl000223", "chrUn_gl000224", "chrUn_gl000219", "chr17_gl000205_random", "chrUn_gl000215", "chrUn_gl000216", "chrUn_gl000217", "chr9_gl000199_random", "chrUn_gl000211","chrUn_gl000213", "chrUn_gl000220",
84+
"chrUn_gl000218", "chr19_gl000209_random", "chrUn_gl000221", "chrUn_gl000214", "chrUn_gl000228", "chrUn_gl000227", "chr1_gl000191_random", "chr19_gl000208_random", "chr9_gl000198_random", "chr17_gl000204_random", "chrUn_gl000233", "chrUn_gl000237", "chrUn_gl000230",
85+
"chrUn_gl000242", "chrUn_gl000243", "chrUn_gl000241", "chrUn_gl000236", "chrUn_gl000240", "chr17_gl000206_random", "chrUn_gl000232", "chrUn_gl000234", "chr11_gl000202_random", "chrUn_gl000238", "chrUn_gl000244", "chrUn_gl000248", "chr8_gl000196_random", "chrUn_gl000249",
86+
"chrUn_gl000246", "chr17_gl000203_random", "chr8_gl000197_random", "chrUn_gl000245", "chrUn_gl000247", "chr9_gl000201_random", "chrUn_gl000235", "chrUn_gl000239", "chr21_gl000210_random", "chrUn_gl000231", "chrUn_gl000229", "chrM", "chrUn_gl000226", "chr18_gl000207_random"};
87+
88+
chromName = new ArrayList<String>(Arrays.asList(chrom));
89+
long[] size = new long[] {249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 155270560, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 63025520, 59373566, 59128983, 51304566, 48129895,
90+
4928567, 4833398, 4795371, 4683263, 4622290, 4611984, 4610396, 1680828, 590426, 547496, 211173, 191469, 189789, 187035, 186861, 186858, 182896, 180455, 179693, 179198, 174588, 172545, 172294, 172149, 169874, 166566, 164239, 161802, 161147, 159169, 155397, 137718, 129120, 128374,
91+
106433, 92689, 90085, 81310, 45941,45867, 43691, 43523, 43341, 42152, 41934, 41933, 41001, 40652, 40531, 40103, 39939, 39929, 39786, 38914, 38502, 38154, 37498, 37175, 36651, 36422, 36148, 34474, 33824, 27682, 27386, 19913, 16571, 15008, 4262};
92+
chromSize = new ArrayList<Long>();
93+
for(int x = 0; x < size.length; x++) { chromSize.add(new Long(size[x])); }
94+
}
95+
96+
public static void initialize_mm10() {
97+
genomeName = "mm10";
98+
genomeSize = (long) 2.725521370E9;
99+
String[] chrom = {"chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chrX", "chrY"};
100+
chromName = new ArrayList<String>(Arrays.asList(chrom));
101+
long[] size = new long[] { 195471971, 182113224, 160039680, 156508116, 151834684, 149736546, 145441459, 129401213, 124595110, 130694993, 122082543, 120129022, 120421639, 124902244, 104043685, 98207768, 94987271, 90702639, 61431566, 171031299, 91744698};
102+
chromSize = new ArrayList<Long>();
103+
for(int x = 0; x < size.length; x++) { chromSize.add(new Long(size[x])); }
104+
}
105+
106+
public GenericCoord generateRandomCoord(int WINDOW) {
107+
GenericCoord coord = null;
108+
boolean VALID = false;
109+
while(!VALID) {
110+
long location = ThreadLocalRandom.current().nextLong(genomeSize);
111+
long runningTotal = 0;
112+
int chromIndex = 0;
113+
for(int x = 0; x < chromSize.size(); x++) {
114+
if(location < runningTotal + chromSize.get(x).longValue()) {
115+
chromIndex = x;
116+
x = chromSize.size() + 1;
117+
} else { runningTotal += chromSize.get(x).longValue(); }
118+
}
119+
location -= runningTotal;
120+
String CHROM = chromName.get(chromIndex);
121+
long START = location - (WINDOW / 2);
122+
long STOP = location + (WINDOW / 2);
123+
String DIR = "+";
124+
if(ThreadLocalRandom.current().nextBoolean()) { DIR = "-"; }
125+
126+
if(START > 0 && STOP < chromSize.get(chromIndex).longValue()) {
127+
VALID = true;
128+
coord = new GenericCoord(CHROM, START, STOP, DIR);
129+
}
130+
}
131+
return coord;
132+
}
133+
134+
//Check to make sure WINDOW size is smaller than every chromosome to prevent infinite loop
135+
public boolean isSmaller(int WINDOW) {
136+
for(int x = 0; x < chromSize.size(); x++) {
137+
if(WINDOW > chromSize.get(0)) { return false; }
138+
}
139+
return true;
140+
}
141+
}

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