org.opencb.cellbase.lib.builders

Class GeneParser

java.lang.Object

org.opencb.cellbase.lib.builders.CellBaseParser

org.opencb.cellbase.lib.builders.GeneParser

public class GeneParser
extends CellBaseParser

Field Summary

Fields inherited from class org.opencb.cellbase.lib.builders.CellBaseParser

logger, serializer

Constructor Summary

Constructors

Constructor and Description
GeneParser(Path gtfFile, Path geneDescriptionFile, Path xrefsFile, Path uniprotIdMappingFile, Path tfbsFile, Path geneExpressionFile, Path geneDrugFile, Path hpoFile, Path disgenetFile, Path gnomadFile, Path genomeSequenceFilePath, SpeciesConfiguration speciesConfiguration, boolean flexibleGTFParsing, CellBaseSerializer serializer)
GeneParser(Path geneDirectoryPath, Path genomeSequenceFastaFile, SpeciesConfiguration speciesConfiguration, boolean flexibleGTFParsing, CellBaseSerializer serializer)
GeneParser(Path geneDirectoryPath, Path genomeSequenceFastaFile, SpeciesConfiguration speciesConfiguration, CellBaseSerializer serializer)

Method Summary

Modifier and Type	Method and Description
void	parse()
protected int	processExons(org.opencb.biodata.models.core.Transcript transcript, org.opencb.biodata.models.core.Exon exon, int cdna, int cds, org.opencb.biodata.formats.feature.gtf.Gtf gtf)

Methods inherited from class org.opencb.cellbase.lib.builders.CellBaseParser

disconnect

Methods inherited from class java.lang.Object

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

Constructor Detail

GeneParser

public GeneParser(Path geneDirectoryPath,
                  Path genomeSequenceFastaFile,
                  SpeciesConfiguration speciesConfiguration,
                  CellBaseSerializer serializer)

GeneParser

public GeneParser(Path geneDirectoryPath,
                  Path genomeSequenceFastaFile,
                  SpeciesConfiguration speciesConfiguration,
                  boolean flexibleGTFParsing,
                  CellBaseSerializer serializer)

GeneParser

public GeneParser(Path gtfFile,
                  Path geneDescriptionFile,
                  Path xrefsFile,
                  Path uniprotIdMappingFile,
                  Path tfbsFile,
                  Path geneExpressionFile,
                  Path geneDrugFile,
                  Path hpoFile,
                  Path disgenetFile,
                  Path gnomadFile,
                  Path genomeSequenceFilePath,
                  SpeciesConfiguration speciesConfiguration,
                  boolean flexibleGTFParsing,
                  CellBaseSerializer serializer)

Method Detail

parse

public void parse()
           throws Exception

Specified by:

parse in class CellBaseParser

Throws:

Exception

processExons

protected int processExons(org.opencb.biodata.models.core.Transcript transcript,
                           org.opencb.biodata.models.core.Exon exon,
                           int cdna,
                           int cds,
                           org.opencb.biodata.formats.feature.gtf.Gtf gtf)