Package 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 Details

  • Constructor Details

  • Method Details

    • 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