biolockj.node.wgs

Class MetaphlanNode

java.lang.Object

biolockj.node.OtuNodeImpl

biolockj.node.wgs.MetaphlanNode

All Implemented Interfaces:

OtuNode, Comparable<OtuNode>

public class MetaphlanNode
extends OtuNodeImpl

This class represents one line of Metaphlan2Classifier output. For a full description of the output file format https://bitbucket.org/biobakery/biobakery/wiki/metaphlan2#rst-header-output-files 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.

3 sample lines of Metaphlan output (2 header rows + 1st row):
#SampleID Metaphlan2_Analysis
#clade_name relative_abundance coverage average_genome_length_in_the_clade estimated_number_of_reads_from_the_clade
k__Bacteria|p__Bacteroidetes 14.68863 0.137144143537 4234739 580770

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
MetaphlanNode(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

MetaphlanNode

public MetaphlanNode(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. The number of reads matching the line taxonomy is extracted from the last column (estimated_number_of_reads_from_the_clade)

Parameters:

id - Sample ID

line - Metaphlan output line

Throws:

Exception - if an invalid line format is found