ec.app.sequence
Class ExonParser

java.lang.Object
  extended by ec.app.sequence.ExonParser

public class ExonParser
extends java.lang.Object

This is generic Utility to parse RNA sequences, with exons data given, to find the exact locations of Acceptors and Donors. This is useful for generating 'true sequences' when exons are known. The Data file needs to be in format of sequenceId \t Sequence. Exons data file need to be in format of sequenceId start1 end1 \n, sequenceId start2 end2 etc

Author:
udaykamath

Field Summary
static java.lang.String AG_SEQUENCE
           
static java.lang.String GT_SEQUENCE
           
static java.util.HashMap<java.lang.String,java.util.List<int[]>> organismToExonPositions
           
 
Constructor Summary
ExonParser()
           
 
Method Summary
static void addToMap(java.lang.String organismId, java.lang.String start, java.lang.String end)
           
static java.lang.String getFillers(int size)
           
static void main(java.lang.String[] args)
           
static void parseSequence(java.lang.String chromosomeId, java.lang.String sequence)
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

organismToExonPositions

public static java.util.HashMap<java.lang.String,java.util.List<int[]>> organismToExonPositions

AG_SEQUENCE

public static java.lang.String AG_SEQUENCE

GT_SEQUENCE

public static java.lang.String GT_SEQUENCE
Constructor Detail

ExonParser

public ExonParser()
Method Detail

addToMap

public static void addToMap(java.lang.String organismId,
                            java.lang.String start,
                            java.lang.String end)

getFillers

public static java.lang.String getFillers(int size)

parseSequence

public static void parseSequence(java.lang.String chromosomeId,
                                 java.lang.String sequence)

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception
Throws:
java.lang.Exception