Package fr.ens.biologie.genomique.eoulsan.modules.expression

Class ExpressionCounterUtils

java.lang.Object
fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterUtils
public class ExpressionCounterUtils extends Object
This class define some glue methods between Eoulsan and Kenetre.
Since:
2.6
Author:
Laurent Jourdren

  • Method Summary

    Modifier and Type
    Method
    Description
    static Map<String,Integer>
    count(fr.ens.biologie.genomique.kenetre.bio.expressioncounter.ExpressionCounter counter, DataFile samFile, fr.ens.biologie.genomique.kenetre.util.ReporterIncrementer reporter, String counterGroup)
    Count the the features.
    static void
    init(fr.ens.biologie.genomique.kenetre.bio.expressioncounter.ExpressionCounter counter, DataFile genomeDescFile, DataFile annotationFile, boolean gtfFormat)
    Initialize the counter.
    static void
    init(fr.ens.biologie.genomique.kenetre.bio.expressioncounter.ExpressionCounter counter, fr.ens.biologie.genomique.kenetre.bio.GenomeDescription genomeDesc, DataFile annotationFile, boolean gtfFormat)
    Initialize the counter.

    Methods inherited from class java.lang.Object

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

  • Method Details

    • init

      public static void init(fr.ens.biologie.genomique.kenetre.bio.expressioncounter.ExpressionCounter counter, fr.ens.biologie.genomique.kenetre.bio.GenomeDescription genomeDesc, DataFile annotationFile, boolean gtfFormat) throws IOException, fr.ens.biologie.genomique.kenetre.KenetreException
      Initialize the counter.
      Parameters:
      counter - the counter
      genomeDesc - genome description
      annotationFile - annotation file
      gtfFormat - true if the input format is in GTF format
      Throws:
      fr.ens.biologie.genomique.kenetre.KenetreException - if an error occurs while initialize the counter
      IOException - if an error occurs while reading input files

    • init

      public static void init(fr.ens.biologie.genomique.kenetre.bio.expressioncounter.ExpressionCounter counter, DataFile genomeDescFile, DataFile annotationFile, boolean gtfFormat) throws IOException, fr.ens.biologie.genomique.kenetre.KenetreException
      Initialize the counter.
      Parameters:
      counter - the counter
      genomeDescFile - genome description file
      annotationFile - annotation file
      gtfFormat - true if the input format is in GTF format
      Throws:
      fr.ens.biologie.genomique.kenetre.KenetreException - if an error occurs while initialize the counter
      IOException - if an error occurs while reading input files

    • count

      public static Map<String,Integer> count(fr.ens.biologie.genomique.kenetre.bio.expressioncounter.ExpressionCounter counter, DataFile samFile, fr.ens.biologie.genomique.kenetre.util.ReporterIncrementer reporter, String counterGroup) throws IOException, fr.ens.biologie.genomique.kenetre.KenetreException
      Count the the features.
      Parameters:
      counter - the counter
      samFile - SAM file
      reporter - the reporter
      counterGroup - the counter group of the reporter
      Returns:
      a map with the counts
      Throws:
      fr.ens.biologie.genomique.kenetre.KenetreException - if an error occurs while counting
      IOException - if an error occurs while reading the input file
      fr.ens.biologie.genomique.kenetre.KenetreException - if an errors occurs while counting