net.maizegenetics.pangenome.db_loading

Class TestPHGStuff

java.lang.Object

net.maizegenetics.pangenome.db_loading.TestPHGStuff

public class TestPHGStuff
extends Object

Author:

lcj34

Constructor Summary

Constructors

Constructor and Description
TestPHGStuff()

Method Summary

Modifier and Type	Method and Description
static int	calcLevenshtein(String seq1, String seq2, int maxEditDistance)
static void	checkChrom2DupAnchor(String refGenome)
static void	compareRefToReAssembledChrom(String refGenome, String reAssembledChromFasta, String chrom, String coordinatesFile, String outputFile)
static void	countNsInFasta()
static void	createFindProteomeFile()
static void	freqChartHaplotypeCollapse(String inputFile, String outputDir)
static void	freqHaplotypeCollapse(String inputFile, String outputDir)
static void	getDataFromAssembly(String assemblyFile, String outputFile)
static void	getGenomeSequenceValues()
static void	main(String[] args)
static void	printTrimTables(String origData, String trimData, String outputFile)
static void	sortListCreatehash()
static void	splitW22GenomeGetChrom10()
static void	testChrMatch()
static void	testChromLength(String genome)
static void	testMafftfromJava()
static void	testObjectAssignment()
static void	testPythonLD(String seq1, String seq2, String mode, String task)
static void	testSortedRange()

Methods inherited from class java.lang.Object

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

Constructor Detail

TestPHGStuff

public TestPHGStuff()

Method Detail

checkChrom2DupAnchor

public static void checkChrom2DupAnchor(String refGenome)

calcLevenshtein

public static int calcLevenshtein(String seq1,
                                  String seq2,
                                  int maxEditDistance)

testPythonLD

public static void testPythonLD(String seq1,
                                String seq2,
                                String mode,
                                String task)

printTrimTables

public static void printTrimTables(String origData,
                                   String trimData,
                                   String outputFile)

freqChartHaplotypeCollapse

public static void freqChartHaplotypeCollapse(String inputFile,
                                              String outputDir)

freqHaplotypeCollapse

public static void freqHaplotypeCollapse(String inputFile,
                                         String outputDir)

testMafftfromJava

public static void testMafftfromJava()

testObjectAssignment

public static void testObjectAssignment()

testChrMatch

public static void testChrMatch()

getDataFromAssembly

public static void getDataFromAssembly(String assemblyFile,
                                       String outputFile)

testChromLength

public static void testChromLength(String genome)

getGenomeSequenceValues

public static void getGenomeSequenceValues()

compareRefToReAssembledChrom

public static void compareRefToReAssembledChrom(String refGenome,
                                                String reAssembledChromFasta,
                                                String chrom,
                                                String coordinatesFile,
                                                String outputFile)

createFindProteomeFile

public static void createFindProteomeFile()

sortListCreatehash

public static void sortListCreatehash()

testSortedRange

public static void testSortedRange()

splitW22GenomeGetChrom10

public static void splitW22GenomeGetChrom10()

countNsInFasta

public static void countNsInFasta()

main

public static void main(String[] args)