ec.app.sequence
Class ExonParser
java.lang.Object
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
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 |
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
ExonParser
public ExonParser()
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