public class ClassifierTraineeMaker
extends java.lang.Object
Constructor and Description |
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ClassifierTraineeMaker(java.lang.String taxFile,
java.lang.String seqFile,
java.lang.String cnFile,
int trainset_no,
java.lang.String version,
java.lang.String modification,
java.lang.String outdir)
Creates a new ClassifierTraineeMaker
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Modifier and Type | Method and Description |
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static void |
main(java.lang.String[] args)
This is the main method to create training files from raw taxonomic information.
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static void |
printLicense()
Prints the license information to std err.
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public ClassifierTraineeMaker(java.lang.String taxFile, java.lang.String seqFile, java.lang.String cnFile, int trainset_no, java.lang.String version, java.lang.String modification, java.lang.String outdir) throws java.io.FileNotFoundException, java.io.IOException
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;
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.java.io.FileNotFoundException
java.io.IOException
public static void printLicense()
public static void main(java.lang.String[] args) throws java.io.FileNotFoundException, java.io.IOException
Usage: java ClassifierTraineeMaker tax_file rawseq.fa trainsetNo version version_modification output_directory. See the ClassifierTraineeMaker constructor for more detail.
args
- java.io.FileNotFoundException
java.io.IOException