trans.anno
Class AnnotateRegions

java.lang.Object
  trans.anno.AnnotateRegions

public class AnnotateRegions

extends java.lang.Object

For annotating Intervals or binding regions with gene information, proximity, neighbors, and bias based on random trials. Specific for dmel release 4.0 gff3. Each gff3 file needs careful reworking to get it into a form for making gene models.

See Also:

AnnotateRegionsWithGeneList

Constructor Summary

AnnotateRegions(java.lang.String[] args)

Method Summary

static void	compareBindingRegionsVsGeneGrps(GeneGroup[] geneGroups, BindingRegion[] bindingRegions) Does a complete scan, could be optimized.
static int[]	countGenes(BindingRegion[] br) Returns the number of genes where the binding region is on the 5' end and the number of genes where the binding region is on the 3' end of the respective gene, the number of genes that overlap a binding region on their 5' end and 3' end, lastly the number of regions entirely contained by a gene, the number of binding regions with neighbors, the number of regions with no neighbors as defined by the neighborhood, the number of regions in non coding DNA, the number of regions in coding DNA, the number of regions that overlap coding and nonCoding DNA
static int	countNumberBindingRegionsWithNeighbors(BindingRegion[] br)
static int	countNumberNeighbors(BindingRegion[] br)
static java.util.ArrayList	extractCGNames(java.util.ArrayList geneGroups) Extracts the names of each gene group returning an ArrayList of Strings.
static GeneGroup[]	filterGeneGroups(GeneGroup[] genes, java.util.HashSet cgNames) Returns an array of GeneGroup whose names were found in the Hash
int	findDistanceToATG(BindingRegion br, GeneGroup gp) Finds the distance to conservative estimate of an ATG, returns 0 if overlaps.
int	findDistToClosestATG(BindingRegion br) Finds the distance to the closest ATG translation start site.
int	findDistToClosestATG(BindingRegion br, java.util.ArrayList geneGroups)
int	findDistToClosestTranscript(BindingRegion br) Finds the distance to the closest ATG translation start site.
int	findDistToClosestTranscript(BindingRegion br, java.util.ArrayList geneGroups)
int	findDistToClosestTranscript(BindingRegion br, GeneGroup gp) Finds the distance to conservative estimate of start of first exon, returns 0 if overlaps.
static void	main(java.lang.String[] args)
static BindingRegion[]	makeRandomBindingRegions(BindingRegion[] br, java.util.HashMap chromLengths, int sizeNeighborhood) For each binding region this will make another binding region from the same chromosome with the same length, yet at a random location.
static boolean	overlap(java.util.ArrayList ints, int startRegion, int endRegion) Tests whether any startEnd int[] in the ArrayList of ints ovelaps a region defined by the startRegion and endRegion.
static BindingRegion[]	parseIntervalFile(java.io.File intervalFile, int sizeNeighborhood) Attempts to fetch a serialized array of Interval[], then sorts/ ranks the intervals by the median ratio of the sub window.
static BindingRegion[]	parsePicksFile(java.io.File picksFile, int sizeNeighborhood)
void	printDistToClosestATGAndTranscript(BindingRegion[] br) Prints rank, chrom, start, stop, distance to closest ATG, to closest transcript start.
static void	printDocs()
void	processArgs(java.lang.String[] args) This method will process each argument and assign new varibles

Methods inherited from class java.lang.Object

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

Constructor Detail

AnnotateRegions

public AnnotateRegions(java.lang.String[] args)

Method Detail

makeRandomBindingRegions

public static BindingRegion[] makeRandomBindingRegions(BindingRegion[] br,
                                                       java.util.HashMap chromLengths,
                                                       int sizeNeighborhood)

For each binding region this will make another binding region from the same chromosome with the same length, yet at a random location.

printDistToClosestATGAndTranscript

public void printDistToClosestATGAndTranscript(BindingRegion[] br)

Prints rank, chrom, start, stop, distance to closest ATG, to closest transcript start.

findDistToClosestATG

public int findDistToClosestATG(BindingRegion br)

Finds the distance to the closest ATG translation start site.

findDistToClosestATG

public int findDistToClosestATG(BindingRegion br,
                                java.util.ArrayList geneGroups)

findDistToClosestTranscript

public int findDistToClosestTranscript(BindingRegion br)

Finds the distance to the closest ATG translation start site.

findDistToClosestTranscript

public int findDistToClosestTranscript(BindingRegion br,
                                       java.util.ArrayList geneGroups)

findDistanceToATG

public int findDistanceToATG(BindingRegion br,
                             GeneGroup gp)

Finds the distance to conservative estimate of an ATG, returns 0 if overlaps.

findDistToClosestTranscript

public int findDistToClosestTranscript(BindingRegion br,
                                       GeneGroup gp)

Finds the distance to conservative estimate of start of first exon, returns 0 if overlaps.

countNumberNeighbors

public static int countNumberNeighbors(BindingRegion[] br)

countNumberBindingRegionsWithNeighbors

public static int countNumberBindingRegionsWithNeighbors(BindingRegion[] br)

countGenes

public static int[] countGenes(BindingRegion[] br)

Returns the number of genes where the binding region is on the 5' end and the number of genes where the binding region is on the 3' end of the respective gene, the number of genes that overlap a binding region on their 5' end and 3' end, lastly the number of regions entirely contained by a gene, the number of binding regions with neighbors, the number of regions with no neighbors as defined by the neighborhood, the number of regions in non coding DNA, the number of regions in coding DNA, the number of regions that overlap coding and nonCoding DNA

Returns:

int[9] {num 5', num 3', overlap 5', overlap 3', contained, no neighbors, non coding, coding, overlap coding and non coding}

overlap

public static boolean overlap(java.util.ArrayList ints,
                              int startRegion,
                              int endRegion)

Tests whether any startEnd int[] in the ArrayList of ints ovelaps a region defined by the startRegion and endRegion. Assumes start is always <= end.

extractCGNames

public static java.util.ArrayList extractCGNames(java.util.ArrayList geneGroups)

Extracts the names of each gene group returning an ArrayList of Strings.

compareBindingRegionsVsGeneGrps

public static void compareBindingRegionsVsGeneGrps(GeneGroup[] geneGroups,
                                                   BindingRegion[] bindingRegions)

Does a complete scan, could be optimized.

parsePicksFile

public static BindingRegion[] parsePicksFile(java.io.File picksFile,
                                             int sizeNeighborhood)

parseIntervalFile

public static BindingRegion[] parseIntervalFile(java.io.File intervalFile,
                                                int sizeNeighborhood)

Attempts to fetch a serialized array of Interval[], then sorts/ ranks the intervals by the median ratio of the sub window. It then uses it to build an array of BindingRegion. Will return null if it cannot fetch an Interval[].

printDocs

public static void printDocs()

processArgs

public void processArgs(java.lang.String[] args)

This method will process each argument and assign new varibles

filterGeneGroups

public static GeneGroup[] filterGeneGroups(GeneGroup[] genes,
                                           java.util.HashSet cgNames)

Returns an array of GeneGroup whose names were found in the Hash

main

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