net.maizegenetics.dna.snp

Class ExportUtils

net.maizegenetics.dna.snp.ExportUtils

public class ExportUtils

Exports Genotype Tables to various file formats.

Method Detail

writeGenotypeHDF5

public static java.lang.String writeGenotypeHDF5(GenotypeTable a,
                                                 java.lang.String newHDF5file)

writeGenotypeHDF5

public static java.lang.String writeGenotypeHDF5(GenotypeTable a,
                                                 java.lang.String newHDF5file,
                                                 boolean keepDepth)

writeGenotypeHDF5

public static java.lang.String writeGenotypeHDF5(GenotypeTable a,
                                                 java.lang.String newHDF5file,
                                                 TaxaList exportTaxa,
                                                 boolean keepDepth)

Exports a alignment into the Byte HDF5 format.

Parameters:

a - alignment to be exported

newHDF5file - filename for the new file (should end with "hmp.h5")

exportTaxa - subset of taxa (if null exports ALL taxa)

Returns:

org.jetbrains.dokka.NodeRenderContent@7faf2d2d:

writeToHapmap

public static java.lang.String writeToHapmap(GenotypeTable alignment,
                                             java.lang.String filename)

Write a GenotypeTable to HapMap format with standard settings - unphased single character, tab delimiter, and no progress tracking.

Parameters:

alignment - genotype table

filename - outfile name (will add ".hmp.txt" if needed)

Returns:

org.jetbrains.dokka.NodeRenderContent@3ab23ca0: name of the outfile with the appropriate suffix

writeToHapmap

public static java.lang.String writeToHapmap(GenotypeTable alignment,
                                             boolean diploid,
                                             java.lang.String filename,
                                             char delimChar,
                                             ProgressListener listener)

Write a GenotypeTable to HapMap format.

Parameters:

alignment - genotype table

diploid - true uses phased two letter encoding, false one letter unphased

filename - outfile name (will add ".hmp.txt" if needed)

delimChar - delimiter character normally tab

listener - progress listener, (null if unneeded)

Returns:

org.jetbrains.dokka.NodeRenderContent@7d411fb9: name of the outfile with the appropriate suffix

writeToHapmap

public static java.lang.String writeToHapmap(GenotypeTable alignment,
                                             boolean diploid,
                                             java.lang.String filename,
                                             char delimChar,
                                             boolean includeTaxaAnnotations,
                                             ProgressListener listener)

writeToVCF

public static java.lang.String writeToVCF(GenotypeTable gt,
                                          java.lang.String filename,
                                          boolean keepDepth)

Writes given alignment to a VCF file

Parameters:

gt -

filename -

Returns:

org.jetbrains.dokka.NodeRenderContent@452bb5b7:

writeToVCF

public static java.lang.String writeToVCF(GenotypeTable gt,
                                          java.lang.String filename,
                                          boolean keepDepth,
                                          ProgressListener listener)

writeToPlink

public static java.lang.String writeToPlink(GenotypeTable alignment,
                                            java.lang.String filename,
                                            char delimChar)

Writes given set of alignments to a set of Plink files

Parameters:

alignment -

filename -

delimChar -

saveDelimitedAlignment

public static java.lang.String saveDelimitedAlignment(GenotypeTable theAlignment,
                                                      java.lang.String delimit,
                                                      java.lang.String saveFile)

printSequential

public static void printSequential(GenotypeTable a,
                                   java.io.Writer out)

print alignment (in PHYLIP SEQUENTIAL format)

printInterleaved

public static void printInterleaved(GenotypeTable a,
                                    java.io.Writer out)

print alignment (in PHYLIP 3.4 INTERLEAVED format)

printCLUSTALW

public static void printCLUSTALW(GenotypeTable a,
                                 java.io.Writer out)

Print alignment (in CLUSTAL W format)

writeAlignmentToSerialGZ

public static java.lang.String writeAlignmentToSerialGZ(GenotypeTable sba,
                                                        java.lang.String outFile)

writeFasta

public static void writeFasta(GenotypeTable gt,
                              java.io.Writer out)

Simple method to export a GenotypeTable to a fasta file.

Parameters:

gt - Import GenotypeTable which we want to export.

out - FileWriter which will be used to export the FASTA file.

writeFastaNoGaps

public static void writeFastaNoGaps(GenotypeTable gt,
                                    java.io.Writer out)

Simple method to export a GenotypeTable to a fasta file while removing Gap characters.

Parameters:

gt - GenotypeTable which we want to export.

out - FileWriter which will be used to export the FASTA file.