net.maizegenetics.taxa

Class TaxaListIOUtils

net.maizegenetics.taxa.TaxaListIOUtils

public class TaxaListIOUtils

Utilities for reading and writing IdGroup and PedigreeIdGroups.

Method Detail

getMapOfTaxonByAnnotation

public static com.google.common.collect.Multimap<java.lang.String,net.maizegenetics.taxa.Taxon> getMapOfTaxonByAnnotation(TaxaList taxaList,
                                                                                                                          java.lang.String annotation)

Create a Multimap of all the taxa associated with a particular annotation value.

Parameters:

taxaList - input taxa list with annotation associated with

annotation - annotation key used to create the multimap, the values of these keys become the key of the resulting Multimap

Returns:

org.jetbrains.dokka.NodeRenderContent@3cc388a8: Map of AnnotationValues -> Taxon

getUniqueMapOfTaxonByAnnotation

public static java.util.Optional<java.util.Map> getUniqueMapOfTaxonByAnnotation(TaxaList taxaList,
                                                                                java.lang.String annotation)

Create a Map of all the taxa associated with a particular annotation value. If there would be a duplicate mapping, then an Optional.empty() is returned.

Parameters:

taxaList - input taxa list with annotation associated with

annotation - annotation key used to create the map, the values of these keys become the key of the resulting map

Returns:

org.jetbrains.dokka.NodeRenderContent@7c4b881e: Map of AnnotationValues -> Taxon

subsetTaxaListByAnnotation

public static TaxaList subsetTaxaListByAnnotation(TaxaList baseTaxaList,
                                                  java.lang.String annotation,
                                                  java.lang.String annoValue)

Returns a subsetted taxa list based on annotation value. For example, return all taxa where GermType=Inbred.

Parameters:

baseTaxaList - base annotated taxa list

annotation - annotation name (key)

annoValue - annotation value being tested for

Returns:

org.jetbrains.dokka.NodeRenderContent@762e7125: TaxaList equal to the annotation value

retainSpecificAnnotations

public static TaxaList retainSpecificAnnotations(TaxaList baseTaxaList,
                                                 java.lang.String[] annotationsToKeep)

Creates a new taxa list with the taxa only retaining annotations within a specified list. All taxa are retained, only the annotations are changed.

Parameters:

baseTaxaList -

annotationsToKeep - the retained keys annotation

Returns:

org.jetbrains.dokka.NodeRenderContent@58041e97: new TaxaList with a subset of the annotations

removeSpecificAnnotations

public static TaxaList removeSpecificAnnotations(TaxaList baseTaxaList,
                                                 java.lang.String[] annotationsToRemove)

Creates a new taxa list with the taxa retaining annotations EXCEPT those specified by the list. All taxa are retained, only the annotations are changed.

Parameters:

baseTaxaList -

annotationsToRemove - the retained keys annotation

Returns:

org.jetbrains.dokka.NodeRenderContent@78a24bf7: new TaxaList with a subset of the annotations

allAnnotationKeys

public static java.util.Set<java.lang.String> allAnnotationKeys(TaxaList baseTaxaList)

Provides the set of all annotation key found in any of taxa

Parameters:

baseTaxaList -

Returns:

org.jetbrains.dokka.NodeRenderContent@58892785:

exportAnnotatedTaxaListTable

public static void exportAnnotatedTaxaListTable(TaxaList taxa,
                                                java.lang.String filename)

importAnnotatedTaxaList

public static TaxaList importAnnotatedTaxaList(java.lang.String filename)

readTaxaAnnotationFile

public static TaxaList readTaxaAnnotationFile(java.lang.String fileName,
                                              java.lang.String taxaNameField,
                                              java.util.Map<java.lang.String,java.lang.String> filters,
                                              boolean mergeSameNames)

Returns an annotated TaxaList from a text annotation file in matrix format. This is a tab delimited file. First row in the file with the field taxaNameField is the header row. taxaNameField indicated the taxon name, all other fields are user defined. The fields become the keys for the taxa annotation. Quantitative fields should be tagged with "#" sign, e.g. <#INBREEDF>. Multiple values are supported per key, and additional values can be either described with an additional column or ";" to delimit values with the same key.

Filters are a map of filters to be applied. Key are the fields, and value are what are tested for equality. Only taxa rows true for filters are retained.

<#InbreedF>

B73 Inbred Goodman282 0.98 ISU;IBMFounder

MO17 Inbred Goodman282 0.98 UMC;IBMFounder

Produces:

B73

MO17

The standardized keys are described in the class Taxon, and these constant fields are all upper case.

Parameters:

fileName - with complete path

taxaNameField - field name with the taxon name

filters - Map of filter to determine which rows to retain as the file is processed.

Returns:

org.jetbrains.dokka.NodeRenderContent@5d2bc2e8: TaxaList with annotations

See Also:

class Taxon

readTaxaAnnotationFileAL

public static java.util.ArrayList<net.maizegenetics.taxa.Taxon> readTaxaAnnotationFileAL(java.lang.String fileName,
                                                                                         java.lang.String taxaNameField,
                                                                                         java.util.Map<java.lang.String,java.lang.String> filters)

readTaxaAnnotationFile

public static TaxaList readTaxaAnnotationFile(java.lang.String fileName,
                                              java.lang.String taxaNameField)

Returns an annotated TaxaList from a text annotation file in matrix format. This is a tab delimited file. First row in the file with the field taxaNameField is the header row. taxaNameField indicated the taxon name, all other fields are user defined. The fields become the keys for the taxa annotation. Quantitative fields should be tagged with "#" sign, e.g. <#INBREEDF>. Multiple values are supported per key, and additional values can be either described with an additional column or ";" to delimit values with the same key.

<#InbreedF>

B73 Inbred Goodman282 0.98 ISU;IBMFounder

MO17 Inbred Goodman282 0.98 UMC;IBMFounder

Produces:

B73

MO17

The standardized keys are described in the class Taxon, and these constant fields are all upper case.

Parameters:

fileName - with complete path

taxaNameField - field name with the taxon name

Returns:

org.jetbrains.dokka.NodeRenderContent@25238f7c: TaxaList with annotations

See Also:

class Taxon

doesTaxonHaveAllAnnotations

public static boolean doesTaxonHaveAllAnnotations(Taxon taxon,
                                                  java.util.Map<java.lang.String,java.lang.String> filters)

Tests whether a taxon has annotation values in the map

Parameters:

taxon -

filters -

Returns:

org.jetbrains.dokka.NodeRenderContent@4f3485dc: true if all present, false is otherwise

parseVCFHeadersIntoMap

public static com.google.common.collect.SetMultimap<java.lang.String,java.lang.String> parseVCFHeadersIntoMap(java.lang.String s)

Parses a VCF header with the taxa names and annotations into a multimap. The taxa name is return as the "ID" key, as used by the VCF format.

Parameters:

s -

Returns:

org.jetbrains.dokka.NodeRenderContent@5e1026b0:

readTissueAnnotationFile

public static java.util.List<java.lang.String> readTissueAnnotationFile(java.lang.String fileName,
                                                                        java.lang.String tissueNameField)

This method takes a key file and creates a SortedSet that contains a set of the tissue values. The set will be null if no tissues are present

Parameters:

fileName - - name of Keyfile containing Tissue header

tissueNameField - - field name

Returns:

org.jetbrains.dokka.NodeRenderContent@5daf9318: