net.maizegenetics.dna.snp

Class ImportUtils

java.lang.Object

net.maizegenetics.dna.snp.ImportUtils

public class ImportUtils
extends Object

Methods for importing GenotypeTables from various file formats.

Author:

Terry Casstevens, Ed Buckler

Field Summary

Fields

Modifier and Type	Field and Description
static int	NUM_HAPMAP_NON_TAXA_HEADERS

Method Summary

Modifier and Type	Method and Description
static GenotypeTable	read(String filename) This utility attempts to identify the file format(i.e.
static DataSet	readDataSet(String filename) This utility attempts to identify the file format(i.e.
static GenotypeTable	readFasta(String filename)
static GenotypeTable	readFromHapmap(String filename) Read GenotypeTable from HapMap file
static GenotypeTable	readFromHapmap(String filename, ProgressListener listener) Read GenotypeTable from HapMap file
static GenotypeTable	readFromHapmap(String filename, ProgressListener listener, boolean sortPositions) Read GenotypeTable from HapMap file
static GenotypeTable	readFromPLink(String pedFilename, String mapFilename, ProgressListener listener)
static GenotypeTable	readFromPLink(String pedFilename, String mapFilename, ProgressListener listener, boolean sortPositions)
static GenotypeTable	readFromVCF(String filename)
static GenotypeTable	readFromVCF(String filename, ProgressListener listener)
static GenotypeTable	readFromVCF(String filename, ProgressListener listener, boolean keepDepth)
static GenotypeTable	readFromVCF(String filename, ProgressListener listener, boolean keepDepth, boolean sortPositions)
static GenotypeTable	readGuessFormat(String fileName) Deprecated. Use ImportUtils.read()

Methods inherited from class java.lang.Object

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

Field Detail

NUM_HAPMAP_NON_TAXA_HEADERS

public static final int NUM_HAPMAP_NON_TAXA_HEADERS

See Also:

Constant Field Values

Method Detail

read

public static GenotypeTable read(String filename)

This utility attempts to identify the file format(i.e. Hapmap, VCF, HDF5, Fasta, PLINK, Phylip, Numerical Genotype) of the given file and loads it as a Genotype Table.

Parameters:

filename -

Returns:

readDataSet

public static DataSet readDataSet(String filename)

This utility attempts to identify the file format(i.e. Hapmap, VCF, HDF5, Fasta, PLINK, Phylip, Numerical Genotype) of the given file and loads it as a DataSet.

Parameters:

filename -

Returns:

readGuessFormat

public static GenotypeTable readGuessFormat(String fileName)

Deprecated. Use ImportUtils.read()

readFromVCF

public static GenotypeTable readFromVCF(String filename,
                                        ProgressListener listener,
                                        boolean keepDepth,
                                        boolean sortPositions)

readFromVCF

public static GenotypeTable readFromVCF(String filename,
                                        ProgressListener listener,
                                        boolean keepDepth)

readFromVCF

public static GenotypeTable readFromVCF(String filename,
                                        ProgressListener listener)

readFromVCF

public static GenotypeTable readFromVCF(String filename)

readFromHapmap

public static GenotypeTable readFromHapmap(String filename)

Read GenotypeTable from HapMap file

Parameters:

filename - input HapMap file name

Returns:

a genotype table

readFromHapmap

public static GenotypeTable readFromHapmap(String filename,
                                           ProgressListener listener)

Read GenotypeTable from HapMap file

Parameters:

filename - input HapMap file name

listener - progress listener to track reading rate

Returns:

a genotype table

readFromHapmap

public static GenotypeTable readFromHapmap(String filename,
                                           ProgressListener listener,
                                           boolean sortPositions)

Read GenotypeTable from HapMap file

Parameters:

filename - input HapMap file name

listener - progress listener to track reading rate

sortPositions - whether to sort positions

Returns:

readFromPLink

public static GenotypeTable readFromPLink(String pedFilename,
                                          String mapFilename,
                                          ProgressListener listener)

readFromPLink

public static GenotypeTable readFromPLink(String pedFilename,
                                          String mapFilename,
                                          ProgressListener listener,
                                          boolean sortPositions)

readFasta

public static GenotypeTable readFasta(String filename)
                               throws FileNotFoundException,
                                      IOException

Throws:

FileNotFoundException

IOException