trans.anno
Class RandomRegions

java.lang.Object
  trans.anno.RandomRegions

public class RandomRegions

extends java.lang.Object

Use to generate random regions of a defined length from a file of regions (chrom, start, stop). No attention is paid to the chromosome so if you want chromosome matching then split the regions file by chromosome and make a seperate RandomRegions object.

Constructor Summary

RandomRegions(java.io.File regionsFile)

RandomRegions(java.io.File regionsFile, java.io.File genomicSequenceDirectory)

Method Summary

int	countLengths(Region[] rs)
boolean[][]	fetchGCContent(Region[] r) Converts the Region[] sequences into boolean[]s, everything not g or c are recorded as false.
int[][]	fetchRandomCoordinates(int length, int number) Given a desired length of sequence, returns multiple random region start stop coordinates.
int[][]	fetchRandomCoordinates(int length, int number, double fractionGCContent) Given a desired length of sequence, returns multiple random region start stop coordinates.
Region	findRandomRegion(int minimumLength) Attempt to find a random Region of the appropriate minimum length.
int[]	findRandomSegment(Region region, int length) Returns a random segment of the appropriate length within the region.
static Region[]	loadBinaryCoordinatesAsRegionArray(java.io.File file) Reads binary chrom start stop file into Region[]
static Region[]	loadWriteBinaryCoordinates(java.io.File regionsFile) Looks for a binary version of the file xxx.corr, if found loads binary, otherwise it parses the txt file and then writes the binary for future use.
static void	main(java.lang.String[] args)
void	makeRegions(java.io.File regionsFile) Parses the regions file but then adds a pointer per base pair length/ divider to the Region[] for every region.
static void	saveRegionsAsCoordinatesArray(java.io.File file, Region[] r) Writes the chrom start stop of a Region[] as a binary file.
void	setGenomicSequenceDirectory(java.io.File genomicSequenceDirectory)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

RandomRegions

public RandomRegions(java.io.File regionsFile)

RandomRegions

public RandomRegions(java.io.File regionsFile,
                     java.io.File genomicSequenceDirectory)

Method Detail

main

public static void main(java.lang.String[] args)

loadWriteBinaryCoordinates

public static Region[] loadWriteBinaryCoordinates(java.io.File regionsFile)

Looks for a binary version of the file xxx.corr, if found loads binary, otherwise it parses the txt file and then writes the binary for future use.

loadBinaryCoordinatesAsRegionArray

public static Region[] loadBinaryCoordinatesAsRegionArray(java.io.File file)

Reads binary chrom start stop file into Region[]

saveRegionsAsCoordinatesArray

public static void saveRegionsAsCoordinatesArray(java.io.File file,
                                                 Region[] r)

Writes the chrom start stop of a Region[] as a binary file.

fetchRandomCoordinates

public int[][] fetchRandomCoordinates(int length,
                                      int number)

Given a desired length of sequence, returns multiple random region start stop coordinates.

Returns:

int[number of random regions][start stop], will return null if random regions of a given length could not be found.

fetchRandomCoordinates

public int[][] fetchRandomCoordinates(int length,
                                      int number,
                                      double fractionGCContent)

Given a desired length of sequence, returns multiple random region start stop coordinates.

Returns:

int[number of random regions][start stop], will return null if random regions of a given length could not be found.

findRandomSegment

public int[] findRandomSegment(Region region,
                               int length)

Returns a random segment of the appropriate length within the region. Assumes the Region is larger than the length.

findRandomRegion

public Region findRandomRegion(int minimumLength)

Attempt to find a random Region of the appropriate minimum length. Will return null after regions.length attempts.

fetchGCContent

public boolean[][] fetchGCContent(Region[] r)

Converts the Region[] sequences into boolean[]s, everything not g or c are recorded as false.

makeRegions

public void makeRegions(java.io.File regionsFile)

Parses the regions file but then adds a pointer per base pair length/ divider to the Region[] for every region. This is to prevent bias in randomly selecting regions.

countLengths

public int countLengths(Region[] rs)

setGenomicSequenceDirectory

public void setGenomicSequenceDirectory(java.io.File genomicSequenceDirectory)