Class ClassifierTraineeMaker

java.lang.Object
edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker

public class ClassifierTraineeMaker extends Object
A command line class to create training information from the raw data.
  • Constructor Details

    • ClassifierTraineeMaker

      public ClassifierTraineeMaker(String taxFile, String seqFile, String cnFile, int trainset_no, String version, String modification, String outdir) throws FileNotFoundException, IOException
      Creates a new ClassifierTraineeMaker
      Parameters:
      taxFile - contains the hierarchical taxonomy information in the following format: taxid*taxon name*parent taxid*depth*rank". taxid, the parent taxid and depth should be in integer format. depth indicates the depth from the root taxon.
      seqFile - contains the raw training sequences in fasta format. The header of this fasta file starts with ">", followed by the sequence name, white space(s) and a list taxon names seperated by ';' with highest rank taxon first. For example: >seq1 ROOT;Ph1;Fam1;G1;
      Note: a sequence can only be assigned to the lowest rank taxon.
      trainset_no - is used to mark the training files generated.
      version - indicates the version of the hierarchical taxonomy.
      modification - holds the modification information of the taxonomy if any.
      outdir - specifies the output directory. The parsed training information will be saved into four files in the given output directory.
      Throws:
      FileNotFoundException
      IOException
  • Method Details

    • printLicense

      public static void printLicense()
      Prints the license information to std err.
    • main

      public static void main(String[] args) throws FileNotFoundException, IOException
      This is the main method to create training files from raw taxonomic information.

      Usage: java ClassifierTraineeMaker tax_file rawseq.fa trainsetNo version version_modification output_directory. See the ClassifierTraineeMaker constructor for more detail.

      Parameters:
      args -
      Throws:
      FileNotFoundException
      IOException