-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
ad1fa18
commit a6682d5
Showing
8 changed files
with
581 additions
and
22 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,145 @@ | ||
| package cnv_compare; | ||
|
|
||
| import java.io.BufferedReader; | ||
| import java.io.File; | ||
| import java.io.FileNotFoundException; | ||
| import java.io.FileReader; | ||
| import java.io.IOException; | ||
| import java.io.PrintWriter; | ||
| import java.nio.file.Path; | ||
| import java.nio.file.Paths; | ||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
|
|
||
| import liftoverutils.Interval; | ||
| import liftoverutils.IntervalNode;; | ||
|
|
||
| public class CnvCompare { | ||
|
|
||
|
|
||
| public static void main(String[] args) { | ||
| File cnvFile1 = new File("C:\\Users\\manojkumar_bhosale\\Desktop\\ToDelete\\forCNV\\test1.txt"); | ||
| File cnvFile2 = new File("C:\\Users\\manojkumar_bhosale\\Desktop\\ToDelete\\forCNV\\test2.txt"); | ||
| Path outDir = Paths.get("C:\\Users\\manojkumar_bhosale\\Desktop\\ToDelete\\forCNV"); | ||
| } | ||
|
|
||
| public static void compareCnvFilesToFolder(File cnvFile1, File cnvFile2, Path outDir) { | ||
| CnvCompare cc = new CnvCompare(); | ||
| cc.compareCnv(cnvFile1, cnvFile2, outDir); | ||
| } | ||
|
|
||
|
|
||
| void compareCnv(File cnvFile1, File cnvFile2, Path outDir) { | ||
| List<Interval<CnvInterval>> intervalList = new ArrayList<Interval<CnvInterval>>(); | ||
| File comparisonFile = outDir.resolve(cnvFile1.getName().replace(".", "_")+""+cnvFile2.getName()).toFile(); | ||
| int leftNumIntervals = 0; | ||
| int rightNumIntervals = 0; | ||
| int leftOverlap = 0; | ||
| int rightOverlap = 0; | ||
| int exactMatch = 0; | ||
| int within = 0; | ||
| int covering = 0; | ||
| int noMatch = 0; | ||
|
|
||
| try(BufferedReader br = new BufferedReader(new FileReader(cnvFile1));BufferedReader br1 = new BufferedReader(new FileReader(cnvFile2)); PrintWriter pw = new PrintWriter(comparisonFile)){ | ||
| String line = ""; | ||
| while((line = br1.readLine()) != null) { | ||
| if(line.startsWith("#")) | ||
| continue; | ||
| leftNumIntervals++; | ||
| String[] splitedRec = line.split("\t"); | ||
| String chr = splitedRec[0]; | ||
| int start = Integer.parseInt(splitedRec[1]); | ||
| int stop = Integer.parseInt(splitedRec[2]); | ||
| String type = splitedRec[6]; | ||
| CnvInterval cnvInterval = new CnvInterval(chr, start, stop, type); | ||
| Interval<CnvInterval> interval = new Interval<CnvInterval>(start, stop, cnvInterval); | ||
| intervalList.add(interval); | ||
| } | ||
|
|
||
| IntervalNode<CnvInterval> masterNode = new IntervalNode<>(intervalList); | ||
| line = ""; | ||
|
|
||
| while((line = br.readLine()) != null) { | ||
| if(line.startsWith("#")) | ||
| continue; | ||
| rightNumIntervals++; | ||
| String[] splitedRec = line.split("\t"); | ||
| String chr = splitedRec[0]; | ||
| int start = Integer.parseInt(splitedRec[1]); | ||
| int stop = Integer.parseInt(splitedRec[2]); | ||
| String type = splitedRec[6]; | ||
| CnvInterval cnvInterval = new CnvInterval(chr, start, stop, type); | ||
| Interval<CnvInterval> interval = new Interval<CnvInterval>(start, stop, cnvInterval); | ||
| List<Interval<CnvInterval>> intersectList = masterNode.query(interval); | ||
| boolean noMatchFlag = true; | ||
| for(Interval<CnvInterval> intersect : intersectList){ | ||
| int res = getVerdict(cnvInterval, intersect.getData()); | ||
| if(res == 0) { | ||
| exactMatch++; | ||
| noMatchFlag = false; | ||
| }else if(res == 1) { | ||
| covering++; | ||
| noMatchFlag = false; | ||
| }else if(res == 2) { | ||
| within++; | ||
| noMatchFlag = false; | ||
| }else if(res == 3) { | ||
| leftOverlap++; | ||
| noMatchFlag = false; | ||
| }else if(res == 4){ | ||
| rightOverlap++; | ||
| noMatchFlag = false; | ||
| } | ||
| } | ||
|
|
||
| if(noMatchFlag) | ||
| noMatch++; | ||
|
|
||
| } | ||
|
|
||
| pw.println("File1\tFile2\t#Intervals in File1\t#Intervals in File2\tExact matches\tCovering\tWithin\tLeft overlap\tRight Overlap\tNo overlap"); | ||
| pw.println(cnvFile1+"\t"+cnvFile2+"\t"+rightNumIntervals+"\t"+leftNumIntervals+"\t"+exactMatch+"\t"+covering+"\t"+within+"\t"+leftOverlap+"\t"+rightOverlap+"\t"+noMatch); | ||
|
|
||
| } catch (FileNotFoundException e) { | ||
| // TODO Auto-generated catch block | ||
| e.printStackTrace(); | ||
| } catch (IOException e) { | ||
| // TODO Auto-generated catch block | ||
| e.printStackTrace(); | ||
| } | ||
| } | ||
|
|
||
| int getVerdict(CnvInterval inter1, CnvInterval inter2){ | ||
| if(cnvOfSameType(inter1, inter2) && isSameChr(inter1, inter2)) { | ||
| if(inter1.getStartPosition() == inter2.getStartPosition() && inter1.getStopPosition() == inter2.getStopPosition()) { | ||
| return 0; //exact match | ||
| }else if(inter1.getStartPosition() <= inter2.getStartPosition() && inter1.getStopPosition() >= inter2.getStopPosition()) { | ||
| return 1; //covering | ||
| }else if(inter1.getStartPosition() >= inter2.getStartPosition() && inter1.getStopPosition() <= inter2.getStopPosition()){ | ||
| return 2; //within | ||
| }else if(inter1.getStartPosition() <= inter2.getStartPosition() && inter1.getStopPosition() <= inter2.getStopPosition()){ | ||
| return 3; //left overlap | ||
| }else if(inter1.getStartPosition() >= inter2.getStartPosition() && inter1.getStopPosition() >= inter2.getStopPosition()){ | ||
| return 4; //right overlap | ||
| } | ||
| } | ||
| return 5; | ||
| } | ||
|
|
||
| boolean cnvOfSameType(CnvInterval inter1, CnvInterval inter2) { | ||
| return (inter1.getType()).equals(inter2.getType()); | ||
| } | ||
|
|
||
| boolean isSameChr(CnvInterval inter1, CnvInterval inter2) { | ||
| return (inter1.getChromosome()).equals(inter2.getChromosome()); | ||
| } | ||
|
|
||
|
|
||
| public static void readCnvFile(File cnvFile) { | ||
|
|
||
|
|
||
|
|
||
| } | ||
|
|
||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,91 @@ | ||
| package cnv_compare; | ||
|
|
||
| public class CnvInterval { | ||
|
|
||
| private String chromosome; | ||
| private int startPosition; | ||
| private int stopPosition; | ||
| private String type; | ||
| private float logRatio; | ||
| private int copyNumber; | ||
|
|
||
| public CnvInterval(String chromosome, int startPosition, int stopPosition, String type, float logRatio, | ||
| int copyNumber) { | ||
| super(); | ||
| this.chromosome = chromosome; | ||
| this.startPosition = startPosition; | ||
| this.stopPosition = stopPosition; | ||
| this.type = type; | ||
| this.logRatio = logRatio; | ||
| this.copyNumber = copyNumber; | ||
| } | ||
|
|
||
| public CnvInterval(String chromosome, int startPosition, int stopPosition, String type) { | ||
| super(); | ||
| this.chromosome = chromosome.toUpperCase(); | ||
| this.startPosition = startPosition; | ||
| this.stopPosition = stopPosition; | ||
| this.type = type.toUpperCase(); | ||
| this.logRatio = 0; | ||
| this.copyNumber = 0; | ||
| } | ||
|
|
||
| public CnvInterval(String chromosome, int startPosition, int stopPosition) { | ||
| super(); | ||
| this.chromosome = chromosome; | ||
| this.startPosition = startPosition; | ||
| this.stopPosition = stopPosition; | ||
| this.type = ""; | ||
| this.logRatio = 0; | ||
| this.copyNumber = 0; | ||
| } | ||
|
|
||
| public String getChromosome() { | ||
| return chromosome; | ||
| } | ||
|
|
||
| public void setChromosome(String chromosome) { | ||
| this.chromosome = chromosome; | ||
| } | ||
|
|
||
| public int getStartPosition() { | ||
| return startPosition; | ||
| } | ||
|
|
||
| public void setStartPosition(int startPosition) { | ||
| this.startPosition = startPosition; | ||
| } | ||
|
|
||
| public int getStopPosition() { | ||
| return stopPosition; | ||
| } | ||
|
|
||
| public void setStopPosition(int stopPosition) { | ||
| this.stopPosition = stopPosition; | ||
| } | ||
|
|
||
| public String getType() { | ||
| return type; | ||
| } | ||
|
|
||
| public void setType(String type) { | ||
| this.type = type; | ||
| } | ||
|
|
||
| public float getLogRatio() { | ||
| return logRatio; | ||
| } | ||
|
|
||
| public void setLogRatio(float logRatio) { | ||
| this.logRatio = logRatio; | ||
| } | ||
|
|
||
| public int getCopyNumber() { | ||
| return copyNumber; | ||
| } | ||
|
|
||
| public void setCopyNumber(int copyNumber) { | ||
| this.copyNumber = copyNumber; | ||
| } | ||
|
|
||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.