org.opencb.cellbase.lib.builders

Class GeneParserUtils

java.lang.Object

org.opencb.cellbase.lib.builders.GeneParserUtils

public class GeneParserUtils
extends Object

Created by imedina on 12/11/15.

Constructor Summary

Constructors

Constructor and Description
GeneParserUtils()

Method Summary

Modifier and Type	Method and Description
static Map<String,List<org.opencb.biodata.models.core.Constraint>>	getConstraints(Path gnomadFile)
static Map<String,List<org.opencb.biodata.models.variant.avro.GeneTraitAssociation>>	getGeneDiseaseAssociationMap(Path hpoFilePath, Path disgenetFilePath)
static Map<String,List<org.opencb.biodata.models.variant.avro.GeneDrugInteraction>>	getGeneDrugMap(Path geneDrugFile)
static Map<String,List<org.opencb.biodata.models.variant.avro.Expression>>	getGeneExpressionMap(String species, Path geneExpressionFile)
static Map<String,SortedSet<org.opencb.biodata.formats.feature.gff.Gff2>>	getTfbsMap(Path tfbsFile)
static Map<String,ArrayList<org.opencb.biodata.models.core.Xref>>	getXrefMap(Path xrefsFile, Path uniprotIdMappingFile)

Methods inherited from class java.lang.Object

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

Constructor Detail

GeneParserUtils

public GeneParserUtils()

Method Detail

getTfbsMap

public static Map<String,SortedSet<org.opencb.biodata.formats.feature.gff.Gff2>> getTfbsMap(Path tfbsFile)
                                                                                     throws IOException,
                                                                                            NoSuchMethodException,
                                                                                            org.opencb.biodata.formats.io.FileFormatException

Throws:

IOException

NoSuchMethodException

org.opencb.biodata.formats.io.FileFormatException

getXrefMap

public static Map<String,ArrayList<org.opencb.biodata.models.core.Xref>> getXrefMap(Path xrefsFile,
                                                                                    Path uniprotIdMappingFile)
                                                                             throws IOException

Throws:

IOException

getGeneDrugMap

public static Map<String,List<org.opencb.biodata.models.variant.avro.GeneDrugInteraction>> getGeneDrugMap(Path geneDrugFile)
                                                                                                   throws IOException

Throws:

IOException

getGeneExpressionMap

public static Map<String,List<org.opencb.biodata.models.variant.avro.Expression>> getGeneExpressionMap(String species,
                                                                                                       Path geneExpressionFile)
                                                                                                throws IOException

Throws:

IOException

getGeneDiseaseAssociationMap

public static Map<String,List<org.opencb.biodata.models.variant.avro.GeneTraitAssociation>> getGeneDiseaseAssociationMap(Path hpoFilePath,
                                                                                                                         Path disgenetFilePath)
                                                                                                                  throws IOException

Throws:

IOException

getConstraints

public static Map<String,List<org.opencb.biodata.models.core.Constraint>> getConstraints(Path gnomadFile)
                                                                                  throws IOException

Throws:

IOException