biolockj.node.wgs

Class Kraken2Node

java.lang.Object

biolockj.node.OtuNodeImpl

biolockj.node.wgs.Kraken2Node

All Implemented Interfaces:

OtuNode, Comparable<OtuNode>

public class Kraken2Node
extends OtuNodeImpl

This class represents one line of Kraken2Classifier output. Each line can represent multiple reads since the estimated_number_of_reads_from_the_clade column is used to approximate the number of reads with the given OTU in the sample.

Sample Kraken report line (head 7A_1_reported.tsv) :
d__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales 20094

Field Summary

Fields inherited from class biolockj.node.OtuNodeImpl

CLASS_DELIM, DOMAIN_DELIM, FAMILY_DELIM, GENUS_DELIM, ORDER_DELIM, PHYLUM_DELIM, SPECIES_DELIM

Constructor Summary

Constructors

Constructor and Description
Kraken2Node(String id, String line) Build the OtuNode by extracting the OTU names for each level from the line.

Method Summary

Methods inherited from class biolockj.node.OtuNodeImpl

addTaxa, compareTo, delimToLevelMap, getCount, getLine, getOtuName, getSampleId, getTaxaMap, populateInBetweenTaxa, setCount, setLine, setSampleId

Methods inherited from class java.lang.Object

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

Constructor Detail

Kraken2Node

public Kraken2Node(String id,
                   String line)
            throws Exception

Build the OtuNode by extracting the OTU names for each level from the line. Sample ID is passed as a parameter pulled from the file name.

Parameters:

id - Sample ID

line - Kraken2 output line

Throws:

Exception - if an invalid line format is found