biolockj.util

Class OtuUtil

java.lang.Object

biolockj.util.OtuUtil

public class OtuUtil
extends Object

This utility helps work with OTU count files as formatted by the ParserModule.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	OtuUtil.OtuCountLine This inner class is used to hold a single line from an OTU count file.

Method Summary

Modifier and Type	Method and Description
static String	buildOtuTaxa(String level, String taxa) Build taxa name into OTU path, returns: level + "__" + taxa
static TreeMap<String,Long>	compileSampleOtuCounts(File file) Compile OTU counts from an individual sample OTU count file
static TreeSet<String>	findUniqueOtus(TreeMap<String,TreeMap<String,Long>> sampleOtuCounts) Find every unique OTU across all samples.
static File	getOtuCountFile(File dir, String sampleId, String prefix) Build OTU count file using a standard format in the directory given. Format: pipeline_name + prefix + "otuCount" + sampleId + ".tsv"
static String	getSampleId(File otuCountFile) Extract the sampleId from the OTU count file name. Input files should include a file name just before the .tsv file extension.
static TreeMap<String,TreeMap<String,Long>>	getSampleOtuCounts(Collection<File> files) TreeMap OTU counts for each sample file formatted and named as in ParserModule output.
static boolean	isOtuFile(File file) Check the file name and contents to determine if file is an OTU count file.

Methods inherited from class java.lang.Object

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

Method Detail

buildOtuTaxa

public static String buildOtuTaxa(String level,
                                  String taxa)

Build taxa name into OTU path, returns: level + "__" + taxa

Parameters:

level - Taxonomy level

taxa - Taxa name

Returns:

level + "__" + taxa

compileSampleOtuCounts

public static TreeMap<String,Long> compileSampleOtuCounts(File file)
                                                   throws OtuFileException,
                                                          FileNotFoundException,
                                                          IOException

Compile OTU counts from an individual sample OTU count file

Parameters:

file - OTU count file

Returns:

TreeMap(OTU, count)

Throws:

OtuFileException - If the file is not formatted as an OTU file.

IOException - if unable to parse the input file

FileNotFoundException - if the file path is not found in the file system

findUniqueOtus

public static TreeSet<String> findUniqueOtus(TreeMap<String,TreeMap<String,Long>> sampleOtuCounts)

Find every unique OTU across all samples.

Parameters:

sampleOtuCounts - TreeMap(SampleId, TreeMap(OTU, count)) OTU counts for every sample

Returns:

Ordered TreeSet of unique OTUs

getOtuCountFile

public static File getOtuCountFile(File dir,
                                   String sampleId,
                                   String prefix)

Build OTU count file using a standard format in the directory given.
Format: pipeline_name + prefix + "otuCount" + sampleId + ".tsv"

Parameters:

dir - File directory

sampleId - Sample ID

prefix - File prefix (after pipeline name)

Returns:

OTU count file

getSampleId

public static String getSampleId(File otuCountFile)
                          throws OtuFileException

Extract the sampleId from the OTU count file name.
Input files should include a file name just before the .tsv file extension.

Parameters:

otuCountFile - "otuCount" file

Returns:

Sample ID

Throws:

OtuFileException - if the OTU count file name is improperly formatted

getSampleOtuCounts

public static TreeMap<String,TreeMap<String,Long>> getSampleOtuCounts(Collection<File> files)
                                                               throws Exception

TreeMap OTU counts for each sample file formatted and named as in ParserModule output.

Parameters:

files - Collection of OTU count files

Returns:

TreeMap(SampleID, TreeMap(OTU, count)) OTU counts by sample

Throws:

Exception - if any of the input file names are missing "_"otuCount"_"

isOtuFile

public static boolean isOtuFile(File file)

Check the file name and contents to determine if file is an OTU count file.

Parameters:

file - File

Returns:

boolean TRUE if file is an OTU count file