util.bio.parsers
Class UCSCGeneModelTableReader

java.lang.Object
  util.bio.parsers.UCSCGeneModelTableReader

public class UCSCGeneModelTableReader

extends java.lang.Object

Parses a UCSC gene model table file, use table options for #hg17.refGene.name hg17.refLink.product hg17.geneName.name hg17.refSeqSummary.summary... example: #refGene.name refGene.chrom refGene.strand refGene.txStart refGene.txEnd refGene.cdsStart refGene.cdsEnd refGene.exonCount refGene.exonStarts refGene.exonEnds refLink.product geneName.name refSeqSummary.summary NM_198576 chr1 + 995569 1031415 995619 1030284 36 995569,997647,1010723,1016111,1016522,1016827,1017258,1018541,1018840,1019125,1019411,1019636,1020463,1020661,1021035,1021266,1021462,1021699,1022122,1022629,1022875,1023078,1023314,1024169,1024538,1024868,1025205,1025535,1025729,1026028,1026555,1026755,1027030,1029055,1029750,1030126, 995820,997909,1010771,1016327,1016747,1017052,1017465,1018760,1019035,1019326,1019560,1019742,1020580,1020826,1021179,1021391,1021568,1022038,1022260,1022757,1022990,1023198,1023668,1024362,1024754,1025098,1025340,1025632,1025894,1026140,1026672,1026948,1027118,1029280,1029854,1031415, agrin AGRIN Agrin is a neuronal aggregating factor that induces the aggregation of ... *

Constructor Summary

UCSCGeneModelTableReader(java.io.File file, int numToSubtractFromEnd)

Method Summary

java.util.HashMap	getChromSpecificGeneLines()
UCSCGeneLine[]	getGeneLines()
static void	main(java.lang.String[] args)
void	parseGeneTableFile(java.io.File file, int numToSubtractFromEnd)
void	readOutHash() To test your hash.
void	splitByChromosome() Splits a UCSCGeneLine[] by chromosome into a HashMap of chromosome:UCSCGeneLine[].

Methods inherited from class java.lang.Object

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

Constructor Detail

UCSCGeneModelTableReader

public UCSCGeneModelTableReader(java.io.File file,
                                int numToSubtractFromEnd)

Parameters:

numToSubtractFromEnd - - UCSC uses interbase numbering, to get to end inclusive numbering you must subtract one from the ends of everything, thus set to 1.

Method Detail

main

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

readOutHash

public void readOutHash()

To test your hash.

splitByChromosome

public void splitByChromosome()

Splits a UCSCGeneLine[] by chromosome into a HashMap of chromosome:UCSCGeneLine[].

parseGeneTableFile

public void parseGeneTableFile(java.io.File file,
                               int numToSubtractFromEnd)

Parameters:

numToSubtractFromEnd - - UCSC uses interbase numbering, to get to end inclusive numbering you must subtract one from the ends of everything, thus set to 1.

getChromSpecificGeneLines

public java.util.HashMap getChromSpecificGeneLines()

getGeneLines

public UCSCGeneLine[] getGeneLines()