Mercurial > repos > greg > paired_end_cross_plot
changeset 0:8055f3f619a1 draft default tip
Uploaded
| author | greg |
|---|---|
| date | Thu, 10 Mar 2016 10:34:37 -0500 |
| parents | |
| children | |
| files | paired_end_cross_plot.xml pairedendCrossPlot.jar src/pairedendCrossPlot.java test-data/input1.scidx test-data/input2.scidx test-data/input3.scidx test-data/input4.scidx test-data/output1.tabular test-data/output2.tabular |
| diffstat | 9 files changed, 513 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/paired_end_cross_plot.xml Thu Mar 10 10:34:37 2016 -0500 @@ -0,0 +1,58 @@ +<tool id="paired_end_cross_plot" name="Paired-end cross plot" version="1.0.0"> + <description></description> + <command> + <![CDATA[ + java -jar $__tool_directory__/pairedendCrossPlot.jar + -f "$input1" + -r "$input2" + -w $window_size + -o "$output" 1>/dev/null + ]]> + </command> + <inputs> + <param name="input1" type="data" format="scidx" label="Read 1 ScIdx file" /> + <param name="input2" type="data" format="scidx" label="Read 2 ScIdx file" /> + <param name="window_size" type="integer" value="500" min="1" label="Size of window upstream and downstream around the reference point in base pairs" /> + </inputs> + <outputs> + <data name="output" format="tabular" /> + </outputs> + <tests> + <test> + <param name="input1" value="input1.scidx" ftype="scidx"/> + <param name="input2" value="input2.scidx" ftype="scidx"/> + <param name="window_size" value="500"/> + <output name="output" file="output1.tabular" ftype="tabular"/> + </test> + <test> + <param name="input1" value="input3.scidx" ftype="scidx"/> + <param name="input2" value="input4.scidx" ftype="scidx"/> + <param name="window_size" value="500"/> + <output name="output" file="output2.tabular" ftype="tabular"/> + </test> + </tests> + <help> + +**What it does** + +Produces a frequency histogram of the relative occurrence of Read2 5' ends relative to the +start of every Read1 5' end in a user-specified coordinate window. + +----- + +**Options** + +* **Window Size** - sets the size of the window upstream and downstream around the reference point in base pairs. + + </help> + <citations> + <citation type="bibtex"> + @unpublished{None, + author = {Lai, William}, + title = {None}, + year = {None}, + eprint = {None}, + url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation} + }</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/src/pairedendCrossPlot.java Thu Mar 10 10:34:37 2016 -0500 @@ -0,0 +1,241 @@ +package pairedendCrossPlot; + +import java.io.File; +import java.io.FileNotFoundException; +import java.io.PrintStream; +import java.sql.Timestamp; +import java.util.ArrayList; +import java.util.Date; +import java.util.Scanner; + +public class pairedendCrossPlot { + + private static File READ1 = null; + private static File READ2 = null; + private static File OUTPUT = null; + private static int WINDOW = 500; + + private static int[] BP = null; + private static int[] FOR = null; + private static int[] REV = null; + + private static ArrayList<String> chrName = null; + private static ArrayList<Integer> chrStart = null; + + private static int[] FHIST = null; + private static int[] RHIST = null; + + public static void main(String[] args) throws FileNotFoundException { + loadConfig(args); //Load configuration data + FHIST = new int[(WINDOW * 2) + 1]; //Initialize master histograms + RHIST = new int[(WINDOW * 2) + 1]; //Initialize master histograms + System.out.println("\n" + getTimeStamp()); + + //Pass through the Read2 file once in order to identify the start and stops of all chromosomes present in file + System.out.println("Indexing Read 2 File..."); + indexFile(READ2); + System.out.println("Indexing Complete\n" + getTimeStamp()); + + //Parse read 1 + System.out.println("\n" + getTimeStamp() + "\nParsing Read 1 File..."); + parseRead1(READ1); + System.out.println("\nRead 1 Parsed\n" + getTimeStamp()); + + //Output histogram + System.out.println("\nOutputing final histogram..."); + outputHist(OUTPUT); + System.out.println("Program Complete\n" + getTimeStamp()); + + } + + public static void outputHist(File out) throws FileNotFoundException { + PrintStream OUT = new PrintStream(out); + for(int x = WINDOW * -1; x <= WINDOW; x++) { + OUT.print("\t" + x); + } + OUT.print("\nForward_Tags"); + for(int x = 0; x < FHIST.length; x++) { + OUT.print("\t" + FHIST[x]); + } + OUT.print("\nReverse_Tags"); + for(int x = 0; x < RHIST.length; x++) { + OUT.print("\t" + RHIST[x]); + } + OUT.close(); + } + + public static void parseRead1(File input) throws FileNotFoundException { + Scanner scan = new Scanner(READ1); + String currentChrom = ""; + int currentIndex = 0; + while (scan.hasNextLine()) { + String temp = scan.nextLine(); + if(!temp.contains("index") && !temp.contains("#")) { + String[] array = temp.split("\t"); + int POS = Integer.parseInt(array[1]); + int F = Integer.parseInt(array[2]); + int R = Integer.parseInt(array[3]); + + //Check if newline's chrom is equal to current chrom in memory, reload new chrom if unequal + if(!currentChrom.equals(array[0])) { + BP = null; //reset BP immediately + int newIndex = chrName.indexOf(array[0]); + if(newIndex >= 0) { + System.out.println("\nLoading: " + chrName.get(newIndex)); + loadRead2(READ2, chrName.get(newIndex), chrStart.get(newIndex), chrStart.get(newIndex + 1)); + currentChrom = array[0]; + currentIndex = 0; + System.out.println("Loading Complete\n" + getTimeStamp()); + } + } + if(BP != null) { + //Update local indexes to only upload data from local tag region defined by window + while(POS - WINDOW > BP[currentIndex] && currentIndex < BP.length - 1) { currentIndex++; } //Find furthest upstream index in read2 + int currentStop = currentIndex; + while(POS + WINDOW > BP[currentStop] && currentStop < BP.length - 1) { currentStop++; } //Find furthest downstream index in read2 + + //Populate histogram based on read2 tags flanking current position + int[] temp_F = new int[(WINDOW * 2) + 1]; + int[] temp_R = new int[(WINDOW * 2) + 1]; + for(int x = currentIndex; x <= currentStop; x++) { + int index = BP[x] - POS + WINDOW; + if(index >= 0 && index < temp_F.length) { + temp_F[index] += FOR[x]; + temp_R[index] += REV[x]; + } + } + + //Populate master histogram based on score + for(int x = 0; x < temp_F.length; x++) { + FHIST[x] += (temp_F[x] * F); + RHIST[x] += (temp_R[x] * F); + } + //Reverse arrays + for(int x = 0; x < FHIST.length / 2; x++) { + int tempF = temp_F[x]; + int tempR = temp_R[x]; + temp_F[x] = temp_F[temp_F.length - x - 1]; + temp_F[temp_F.length - x - 1] = tempF; + temp_R[x] = temp_R[temp_R.length - x - 1]; + temp_R[temp_R.length - x - 1] = tempR; + } + for(int x = 0; x < FHIST.length; x++) { + FHIST[x] += (temp_R[x] * R); + RHIST[x] += (temp_F[x] * R); + } + } + } + } + scan.close(); + } + + private static void loadRead2(File input, String currentChrom, int lineStart, int lineStop) throws FileNotFoundException { + BP = new int[lineStop - lineStart - 1]; + FOR = new int[lineStop - lineStart - 1]; + REV = new int[lineStop - lineStart - 1]; + + int counter = 0; + Scanner scan = new Scanner(READ2); + while (scan.hasNextLine()) { + String temp = scan.nextLine(); + if(counter > lineStart) { + String[] array = temp.split("\t"); + if(array[0].equals(currentChrom)) { + BP[counter - lineStart - 1] = Integer.parseInt(array[1]); + FOR[counter - lineStart - 1] = Integer.parseInt(array[2]); + REV[counter - lineStart - 1] = Integer.parseInt(array[3]); + } + } + counter++; + } + scan.close(); + //System.out.println(BP.length + "\t" + FOR.length + "\t" + REV.length); + } + + //Index Read 2 file for faster processing of chromosomes + public static void indexFile(File input) throws FileNotFoundException { + chrName = new ArrayList<String>(); + chrStart = new ArrayList<Integer>(); + Scanner scan = new Scanner(input); + int linenumber = 0; + while (scan.hasNextLine()) { + String temp = scan.nextLine(); + if(!temp.contains("index") && !temp.contains("#")) { + String[] array = temp.split("\t"); + if(!chrName.contains(array[0])) { + chrName.add(array[0]); + chrStart.add(new Integer(linenumber)); + } + } + linenumber++; + } + chrStart.add(new Integer(linenumber)); + scan.close(); + } + + public static void loadConfig(String[] command){ + for (int i = 0; i < command.length; i++) { + switch (command[i].charAt((1))) { + case 'f': + READ1 = new File(command[i + 1]); + i++; + break; + case 'r': + READ2 = new File(command[i + 1]); + i++; + break; + case 'o': + OUTPUT = new File(command[i + 1]); + i++; + break; + case 'w': + WINDOW = Integer.parseInt(command[i + 1]); + i++; + break; + } + } + if(READ1 == null) { + System.out.println("No Read 1 File loaded!!!\n"); + printUsage(); + System.exit(0); + } + if(READ2 == null) { + System.out.println("No Read 2 File loaded!!!\n"); + printUsage(); + System.exit(0); + } + if(WINDOW < 1) { + System.out.println("Invalid Window Size Selected!!!\n"); + printUsage(); + System.exit(0); + } + + if(OUTPUT == null) { + OUTPUT = new File(READ1.getName().split("\\.")[0] + ".out"); + } + + System.out.println("-----------------------------------------\nCommand Line Arguments:"); + System.out.println("Read 1 file: " + READ1); + System.out.println("Read 2 file: " + READ2); + System.out.println("Output: " + OUTPUT); + System.out.println("Window Size: " + WINDOW); + } + + public static void printUsage() { + System.out.println("Usage: java -jar pairedendCrossPlot.jar -f [Read1File] -r [Read2File] [Options]"); + System.out.println("-----------------------------------------"); + System.out.println("\nRequired Parameter:"); + System.out.println("Read 1 File:\t\t\t-f\tRead 1 scIDX file"); + System.out.println("Read 2 File:\t\t\t-r\tRead 1 scIDX file"); + System.out.println("\nOptional Parameters:"); + System.out.println("Output File Name:\t\t-o\tOutput file"); + System.out.println("Window Size +/- Reference:\t-w\t(Default = 500)"); + } + + private static String getTimeStamp() { + Date date= new Date(); + String time = new Timestamp(date.getTime()).toString(); + return time; + } + +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input1.scidx Thu Mar 10 10:34:37 2016 -0500 @@ -0,0 +1,52 @@ +#2016-02-20 12:39:39.157;60801hg19_dedup.bam;READ1 +chrom index forward reverse value +chr1 10078 1 0 1 +chr1 10159 1 0 1 +chr1 10265 0 1 1 +chr1 12868 1 0 1 +chr1 15660 0 1 1 +chr1 16215 1 0 1 +chr1 20260 0 1 1 +chr1 40108 0 1 1 +chr1 48948 1 0 1 +chr1 51494 0 1 1 +chr1 53355 0 1 1 +chr1 55400 0 1 1 +chr1 55822 1 0 1 +chr1 58576 0 1 1 +chr1 62398 0 1 1 +chr1 62705 1 0 1 +chr1 64824 1 0 1 +chr1 65976 1 0 1 +chr1 68141 1 0 1 +chr1 70624 0 1 1 +chr1 73623 1 0 1 +chr1 78938 0 1 1 +chr1 85921 1 0 1 +chr1 87726 1 0 1 +chr1 88204 0 1 1 +chr1 88233 0 1 1 +chr1 88379 0 1 1 +chr1 91427 0 1 1 +chr1 91457 0 1 1 +chr1 93257 1 0 1 +chr1 101793 1 0 1 +chr1 105059 0 1 1 +chr1 105123 0 1 1 +chr1 107434 0 1 1 +chr1 108344 0 1 1 +chr1 108379 1 0 1 +chr1 114132 0 1 1 +chr1 114185 0 1 1 +chr1 114880 0 1 1 +chr1 115833 0 1 1 +chr1 115855 0 1 1 +chr1 122855 1 0 1 +chr1 123638 1 0 1 +chr1 126113 1 0 1 +chr1 129701 0 1 1 +chr1 133553 1 0 1 +chr1 136171 1 0 1 +chr1 137141 0 1 1 +chr1 138859 1 0 1 +chr1 138873 1 0 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input2.scidx Thu Mar 10 10:34:37 2016 -0500 @@ -0,0 +1,52 @@ +#2016-02-20 12:40:06.46;60801hg19_dedup.bam;READ2 +chrom index forward reverse value +chr1 10086 1 0 1 +chr1 10214 0 1 1 +chr1 10434 0 1 1 +chr1 13094 0 1 1 +chr1 15520 1 0 1 +chr1 16372 0 1 1 +chr1 20100 1 0 1 +chr1 39825 1 0 1 +chr1 49250 0 1 1 +chr1 51281 1 0 1 +chr1 53199 1 0 1 +chr1 55183 1 0 1 +chr1 56094 0 1 1 +chr1 58443 1 0 1 +chr1 62162 1 0 1 +chr1 62943 0 1 1 +chr1 64938 0 1 1 +chr1 66052 0 1 1 +chr1 68343 0 1 1 +chr1 70509 1 0 1 +chr1 73854 0 1 1 +chr1 78839 1 0 1 +chr1 85960 0 1 1 +chr1 87867 0 1 1 +chr1 88031 1 0 1 +chr1 88077 1 0 1 +chr1 88326 1 0 1 +chr1 91334 1 0 1 +chr1 91345 1 0 1 +chr1 93500 0 1 1 +chr1 101929 0 1 1 +chr1 104967 1 0 1 +chr1 104971 1 0 1 +chr1 107305 1 0 1 +chr1 108130 1 0 1 +chr1 108552 0 1 1 +chr1 113807 1 0 1 +chr1 113928 1 0 1 +chr1 114757 1 0 1 +chr1 115711 1 0 1 +chr1 115727 1 0 1 +chr1 123015 0 1 1 +chr1 123803 0 1 1 +chr1 126334 0 1 1 +chr1 129534 1 0 1 +chr1 133854 0 1 1 +chr1 136440 0 1 1 +chr1 137063 1 0 1 +chr1 138941 1 0 1 +chr1 138942 1 0 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input3.scidx Thu Mar 10 10:34:37 2016 -0500 @@ -0,0 +1,52 @@ +#2016-02-20 12:39:39.157;CTCF_CS_60801hg19_dedup;READ1 +chrom index forward reverse value +chr1 10078 1 0 1 +chr1 10159 1 0 1 +chr1 10265 0 1 1 +chr1 12868 1 0 1 +chr1 15660 0 1 1 +chr1 16215 1 0 1 +chr1 20260 0 1 1 +chr1 40108 0 1 1 +chr1 48948 1 0 1 +chr1 51494 0 1 1 +chr1 53355 0 1 1 +chr1 55400 0 1 1 +chr1 55822 1 0 1 +chr1 58576 0 1 1 +chr1 62398 0 1 1 +chr1 62705 1 0 1 +chr1 64824 1 0 1 +chr1 65976 1 0 1 +chr1 68141 1 0 1 +chr1 70624 0 1 1 +chr1 73623 1 0 1 +chr1 78938 0 1 1 +chr1 85921 1 0 1 +chr1 87726 1 0 1 +chr1 88204 0 1 1 +chr1 88233 0 1 1 +chr1 88379 0 1 1 +chr1 91427 0 1 1 +chr1 91457 0 1 1 +chr1 93257 1 0 1 +chr1 101793 1 0 1 +chr1 105059 0 1 1 +chr1 105123 0 1 1 +chr1 107434 0 1 1 +chr1 108344 0 1 1 +chr1 108379 1 0 1 +chr1 114132 0 1 1 +chr1 114185 0 1 1 +chr1 114880 0 1 1 +chr1 115833 0 1 1 +chr1 115855 0 1 1 +chr1 122855 1 0 1 +chr1 123638 1 0 1 +chr1 126113 1 0 1 +chr1 129701 0 1 1 +chr1 133553 1 0 1 +chr1 136171 1 0 1 +chr1 137141 0 1 1 +chr1 138859 1 0 1 +chr1 138873 1 0 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input4.scidx Thu Mar 10 10:34:37 2016 -0500 @@ -0,0 +1,52 @@ +#2016-02-20 12:39:39.157;CTCF_CS_60801hg19_dedup;READ2 +chrom index forward reverse value +chr1 10086 1 0 1 +chr1 10214 0 1 1 +chr1 10434 0 1 1 +chr1 13094 0 1 1 +chr1 15520 1 0 1 +chr1 16372 0 1 1 +chr1 20100 1 0 1 +chr1 39825 1 0 1 +chr1 49250 0 1 1 +chr1 51281 1 0 1 +chr1 53199 1 0 1 +chr1 55183 1 0 1 +chr1 56094 0 1 1 +chr1 58443 1 0 1 +chr1 62162 1 0 1 +chr1 62943 0 1 1 +chr1 64938 0 1 1 +chr1 66052 0 1 1 +chr1 68343 0 1 1 +chr1 70509 1 0 1 +chr1 73854 0 1 1 +chr1 78839 1 0 1 +chr1 85960 0 1 1 +chr1 87867 0 1 1 +chr1 88031 1 0 1 +chr1 88077 1 0 1 +chr1 88326 1 0 1 +chr1 91334 1 0 1 +chr1 91345 1 0 1 +chr1 93500 0 1 1 +chr1 101929 0 1 1 +chr1 104967 1 0 1 +chr1 104971 1 0 1 +chr1 107305 1 0 1 +chr1 108130 1 0 1 +chr1 108552 0 1 1 +chr1 113807 1 0 1 +chr1 113928 1 0 1 +chr1 114757 1 0 1 +chr1 115711 1 0 1 +chr1 115727 1 0 1 +chr1 123015 0 1 1 +chr1 123803 0 1 1 +chr1 126334 0 1 1 +chr1 129534 1 0 1 +chr1 133854 0 1 1 +chr1 136440 0 1 1 +chr1 137063 1 0 1 +chr1 138941 1 0 1 +chr1 138942 1 0 1
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