Package fr.ens.biologie.genomique.eoulsan.design

Class DesignUtils

java.lang.Object
fr.ens.biologie.genomique.eoulsan.design.DesignUtils
public final class DesignUtils extends Object
Utils methods for Design.
Since:
1.0
Author:
Laurent Jourdren, Xavier Bauquet

  • Method Details

    • showDesign

      public static void showDesign(Design design)
      Show a design
      Parameters:
      design - Design to show

    • getAllSamplesMetadataKeys

      public static List<String> getAllSamplesMetadataKeys(Design design)
      Get all the sample metadata keys of the samples of a design.
      Parameters:
      design - the design
      Returns:
      a list with the sample metadata keys of the samples of a design

    • getExperimentSampleAllMetadataKeys

      public static List<String> getExperimentSampleAllMetadataKeys(Experiment experiment)
      Get all the experiment metadata keys of the samples of a design.
      Parameters:
      experiment - the experiment
      Returns:
      a list with the experiment metadata keys of the samples of a design

    • checkSamples

      public static boolean checkSamples(Design design)
      Check if there are duplicate samples in the design.
      Parameters:
      design - Design to test
      Returns:
      if there are no duplicate

    • checkGenomes

      public static boolean checkGenomes(Design design)
      Check if there is more than one genome in the design
      Parameters:
      design - Design to test
      Returns:
      true if there is more than one genome in the genome

    • checkAnnotations

      public static boolean checkAnnotations(Design design)
      Check if there is more than one annotation in the design
      Parameters:
      design - Design to test
      Returns:
      true if there is more than one annotation in the genome

    • readAndCheckDesign

      public static Design readAndCheckDesign(InputStream is) throws EoulsanException
      Read and Check design
      Parameters:
      is - InputStream for the design
      Returns:
      a Design object
      Throws:
      EoulsanException - if an error occurs while reading the design

    • obfuscate

      public static void obfuscate(Design design, boolean removeReplicateInformation)
      Remove optional description fields and obfuscate condition field.
      Parameters:
      design - design object to obfuscate
      removeReplicateInformation - if replicate information must be removed

    • replaceLocalPathBySymlinks

      public static void replaceLocalPathBySymlinks(Design design, DataFile symlinksDir) throws IOException
      Replace the local paths in the design by paths to symbolic links in a directory.
      Parameters:
      design - Design object to modify
      symlinksDir - path to the directory where create symbolic links
      Throws:
      IOException - if an error occurs while creating symbolic links of if a path the design file does not exists

    • getCondition

      public static String getCondition(Experiment experiment, Sample sample)
      Get the Condition metadata value for an experimentSample. First look in
      Parameters:
      experiment - the experiment
      sample - the sample
      Returns:
      the Condition value

    • getCondition

      public static String getCondition(ExperimentSample experimentSample)
      Get the Condition metadata value for an experimentSample. First look in
      Parameters:
      experimentSample - the experiment sample
      Returns:
      the Condition value

    • getRepTechGroup

      public static String getRepTechGroup(Experiment experiment, Sample sample)
      Get the RepTechGroup metadata value for an experimentSample. First look in
      Parameters:
      experiment - the experiment
      sample - the sample
      Returns:
      the Condition value

    • getRepTechGroup

      public static String getRepTechGroup(ExperimentSample experimentSample)
      Get the Condition metadata value for an experimentSample. First look in
      Parameters:
      experimentSample - the experiment sample
      Returns:
      the Condition value

    • getMetadata

      public static String getMetadata(Experiment experiment, Sample sample, String key)
      Get a metadata value for an experiment and a sample. First look in
      Parameters:
      experiment - the experiment
      sample - the sample
      key - the metadata key to get
      Returns:
      the Condition value

    • getMetadata

      public static String getMetadata(ExperimentSample experimentSample, String key)
      Get a metadata value for an experimentSample. First look in
      Parameters:
      experimentSample - the experiment sample
      key - the metadata key to get
      Returns:
      the Condition value

    • isSkipped

      public static boolean isSkipped(Experiment experiment)
      Test if an experiement is skipped.
      Parameters:
      experiment - the experiment
      Returns:
      true if the experiment must be skipped

    • containsReferenceField

      public static boolean containsReferenceField(Experiment experiment)
      Test if an experiment contains reference fields.
      Parameters:
      experiment - the experiment object
      Returns:
      true if an experiment contains reference fields

    • getReference

      public static String getReference(Experiment experiment, Sample sample)
      Get the reference of a sample.
      Parameters:
      experiment - the experiment
      sample - the sample
      Returns:
      the reference of a sample

    • getReference

      public static String getReference(ExperimentSample experimentSample)
      Get the reference of a sample.
      Parameters:
      experimentSample - the experiment sample
      Returns:
      the reference of a sample

    • referenceValueToInt

      public static int referenceValueToInt(String value, String experiementReference)
      Convert a reference value to an integer.
      Parameters:
      value - the reference value
      experiementReference - experiment reference
      Returns:
      an integer

    • getModelColumns

      public static Set<String> getModelColumns(Experiment experiment)
      Get the column names used in DESeq2 model.
      Parameters:
      experiment - the experiment
      Returns:
      a set with the column names