org.biojava.nbio.genome.util

Class ChromosomeMappingTools

java.lang.Object

org.biojava.nbio.genome.util.ChromosomeMappingTools

public class ChromosomeMappingTools
extends Object

A class that can map chromosomal positions to mRNA (coding sequence) positions.

Author:

Andreas Prlic

Field Summary

Fields

Modifier and Type	Field and Description
static String	CDS
static String	CHROMOSOME

Constructor Summary

Constructors

Constructor and Description
ChromosomeMappingTools()

Method Summary

Modifier and Type	Method and Description
static String	formatExonStructure(GeneChromosomePosition chromosomePosition) Pretty print the details of a GeneChromosomePosition to a String
static List<com.google.common.collect.Range<Integer>>	getCDSExonRanges(GeneChromosomePosition chromPos) Extracts the exon boundaries in CDS coordinates.
static int	getCDSLength(GeneChromosomePosition chromPos) Get the length of the CDS in nucleotides.
static int	getCDSLengthForward(List<Integer> exonStarts, List<Integer> exonEnds, int cdsStart, int cdsEnd) Get the length of the coding sequence
static int	getCDSLengthReverse(List<Integer> exonStarts, List<Integer> exonEnds, int cdsStart, int cdsEnd) Get the length of the coding sequence
static int	getCDSPosForChromosomeCoordinate(int coordinate, GeneChromosomePosition chromosomePosition) I have a genomic coordinate, where is it on the mRNA
static int	getCDSPosForward(int chromPos, List<Integer> exonStarts, List<Integer> exonEnds, int cdsStart, int cdsEnd) Converts the genetic coordinate to the position of the nucleotide on the mRNA sequence for a gene living on the forward DNA strand.
static int	getCDSPosReverse(int chromPos, List<Integer> exonStarts, List<Integer> exonEnds, int cdsStart, int cdsEnd) Converts the genetic coordinate to the position of the nucleotide on the mRNA sequence for a gene living on the reverse DNA strand.
static List<com.google.common.collect.Range<Integer>>	getCDSRegions(List<Integer> origExonStarts, List<Integer> origExonEnds, int cdsStart, int cdsEnd) Extracts the exons boundaries in CDS coordinates corresponding to the forward DNA strand.
static List<com.google.common.collect.Range<Integer>>	getChromosomalRangesForCDS(GeneChromosomePosition chromPos) Extracts the boundaries of the coding regions in chromosomal coordinates
static ChromPos	getChromosomePosForCDScoordinate(int cdsNucleotidePosition, GeneChromosomePosition chromPos) Maps the position of a CDS nucleotide back to the genome
static ChromPos	getChromPosForward(int cdsPos, List<Integer> exonStarts, List<Integer> exonEnds, int cdsStart, int cdsEnd) Get the CDS position mapped onto the chromosome position
static ChromPos	getChromPosReverse(int cdsPos, List<Integer> exonStarts, List<Integer> exonEnds, int cdsStart, int cdsEnd) Get the CDS position mapped on the chromosome position
static DNASequence	getTranscriptDNASequence(TwoBitFacade twoBitFacade, GeneChromosomePosition gcp) Extracts the DNA sequence transcribed from the input genetic coordinates.
static DNASequence	getTranscriptDNASequence(TwoBitFacade twoBitFacade, String chromosome, List<Integer> exonStarts, List<Integer> exonEnds, int cdsStart, int cdsEnd, Character orientation) Extracts the DNA sequence transcribed from the input genetic coordinates.
static void	setCoordinateSystem(int baseInt)

Methods inherited from class java.lang.Object

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

Field Detail

CHROMOSOME

public static final String CHROMOSOME

See Also:

Constant Field Values

CDS

public static final String CDS

See Also:

Constant Field Values

Constructor Detail

ChromosomeMappingTools

public ChromosomeMappingTools()

Method Detail

setCoordinateSystem

public static void setCoordinateSystem(int baseInt)

formatExonStructure

public static String formatExonStructure(GeneChromosomePosition chromosomePosition)

Pretty print the details of a GeneChromosomePosition to a String

Parameters:

chromosomePosition -

Returns:

getCDSLength

public static int getCDSLength(GeneChromosomePosition chromPos)

Get the length of the CDS in nucleotides.

Parameters:

chromPos -

Returns:

length of the CDS in nucleotides.

getChromosomePosForCDScoordinate

public static ChromPos getChromosomePosForCDScoordinate(int cdsNucleotidePosition,
                                                        GeneChromosomePosition chromPos)

Maps the position of a CDS nucleotide back to the genome

Parameters:

cdsNucleotidePosition -

Returns:

a ChromPos object

getChromPosReverse

public static ChromPos getChromPosReverse(int cdsPos,
                                          List<Integer> exonStarts,
                                          List<Integer> exonEnds,
                                          int cdsStart,
                                          int cdsEnd)

Get the CDS position mapped on the chromosome position

Parameters:

exonStarts -

exonEnds -

cdsStart -

cdsEnd -

Returns:

getChromPosForward

public static ChromPos getChromPosForward(int cdsPos,
                                          List<Integer> exonStarts,
                                          List<Integer> exonEnds,
                                          int cdsStart,
                                          int cdsEnd)

Get the CDS position mapped onto the chromosome position

Parameters:

exonStarts -

exonEnds -

cdsStart -

cdsEnd -

Returns:

getCDSLengthReverse

public static int getCDSLengthReverse(List<Integer> exonStarts,
                                      List<Integer> exonEnds,
                                      int cdsStart,
                                      int cdsEnd)

Get the length of the coding sequence

Parameters:

exonStarts -

exonEnds -

cdsStart -

cdsEnd -

Returns:

getCDSLengthForward

public static int getCDSLengthForward(List<Integer> exonStarts,
                                      List<Integer> exonEnds,
                                      int cdsStart,
                                      int cdsEnd)

Get the length of the coding sequence

Parameters:

exonStarts -

exonEnds -

cdsStart -

cdsEnd -

Returns:

getCDSExonRanges

public static List<com.google.common.collect.Range<Integer>> getCDSExonRanges(GeneChromosomePosition chromPos)

Extracts the exon boundaries in CDS coordinates. (needs to be divided by 3 to get AA positions)

Parameters:

chromPos -

Returns:

getChromosomalRangesForCDS

public static List<com.google.common.collect.Range<Integer>> getChromosomalRangesForCDS(GeneChromosomePosition chromPos)

Extracts the boundaries of the coding regions in chromosomal coordinates

Parameters:

chromPos -

Returns:

getCDSPosForChromosomeCoordinate

public static int getCDSPosForChromosomeCoordinate(int coordinate,
                                                   GeneChromosomePosition chromosomePosition)

I have a genomic coordinate, where is it on the mRNA

Parameters:

coordinate -

chromosomePosition -

Returns:

getCDSPosForward

public static int getCDSPosForward(int chromPos,
                                   List<Integer> exonStarts,
                                   List<Integer> exonEnds,
                                   int cdsStart,
                                   int cdsEnd)

Converts the genetic coordinate to the position of the nucleotide on the mRNA sequence for a gene living on the forward DNA strand.

Parameters:

chromPos - The genetic coordinate on a chromosome

exonStarts - The list holding the genetic coordinates pointing to the start positions of the exons (including UTR regions)

exonEnds - The list holding the genetic coordinates pointing to the end positions of the exons (including UTR regions)

cdsStart - The start position of a coding region

cdsEnd - The end position of a coding region

Returns:

the position of the nucleotide base on the mRNA sequence corresponding to the input genetic coordinate (base 1)

getCDSPosReverse

public static int getCDSPosReverse(int chromPos,
                                   List<Integer> exonStarts,
                                   List<Integer> exonEnds,
                                   int cdsStart,
                                   int cdsEnd)

Converts the genetic coordinate to the position of the nucleotide on the mRNA sequence for a gene living on the reverse DNA strand.

Parameters:

chromPos - The genetic coordinate on a chromosome

exonStarts - The list holding the genetic coordinates pointing to the start positions of the exons (including UTR regions)

exonEnds - The list holding the genetic coordinates pointing to the end positions of the exons (including UTR regions)

cdsStart - The start position of a coding region

cdsEnd - The end position of a coding region

Returns:

the position of the nucleotide base on the mRNA sequence corresponding to the input genetic coordinate (base 1)

getCDSRegions

public static List<com.google.common.collect.Range<Integer>> getCDSRegions(List<Integer> origExonStarts,
                                                                           List<Integer> origExonEnds,
                                                                           int cdsStart,
                                                                           int cdsEnd)

Extracts the exons boundaries in CDS coordinates corresponding to the forward DNA strand.

Parameters:

origExonStarts - The list holding the genetic coordinates pointing to the start positions of the exons (including UTR regions)

origExonEnds - The list holding the genetic coordinates pointing to the end positions of the exons (including UTR regions)

cdsStart - The start position of a coding region

cdsEnd - The end position of a coding region

Returns:

the list of genetic positions corresponding to the exons boundaries in CDS coordinates

getTranscriptDNASequence

public static DNASequence getTranscriptDNASequence(TwoBitFacade twoBitFacade,
                                                   GeneChromosomePosition gcp)
                                            throws Exception

Extracts the DNA sequence transcribed from the input genetic coordinates.

Parameters:

twoBitFacade - the facade that provide an access to a 2bit file

gcp - The container with chromosomal positions

Returns:

the DNA sequence transcribed from the input genetic coordinates

Throws:

Exception

getTranscriptDNASequence

public static DNASequence getTranscriptDNASequence(TwoBitFacade twoBitFacade,
                                                   String chromosome,
                                                   List<Integer> exonStarts,
                                                   List<Integer> exonEnds,
                                                   int cdsStart,
                                                   int cdsEnd,
                                                   Character orientation)
                                            throws Exception

Extracts the DNA sequence transcribed from the input genetic coordinates.

Parameters:

chromosome - the name of the chromosome

exonStarts - The list holding the genetic coordinates pointing to the start positions of the exons (including UTR regions)

exonEnds - The list holding the genetic coordinates pointing to the end positions of the exons (including UTR regions)

cdsStart - The start position of a coding region

cdsEnd - The end position of a coding region

orientation - The orientation of the strand where the gene is living

Returns:

the DNA sequence transcribed from the input genetic coordinates

Throws:

Exception