Package ubic.gemma.core.loader.genome.gene.ncbi

Class NcbiGeneLoader

java.lang.Object
ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader
public class NcbiGeneLoader extends Object
Load or update information about genes from the NCBI Gene database.
Author:
jsantos, paul

  • Constructor Details

    • NcbiGeneLoader

      public NcbiGeneLoader()

    • NcbiGeneLoader

      public NcbiGeneLoader(Persister persisterHelper)

  • Method Details

    • getLoadedGeneCount

      public int getLoadedGeneCount()
      Returns:
      the loadedGeneCount

    • isLoaderDone

      public boolean isLoaderDone()

    • load

      public void load(boolean filterTaxa)
      download the gene_info and gene2accession files, then call load
      Parameters:
      filterTaxa - filter taxa

    • load

      public void load(String geneInfoFile, String gene2AccFile, String geneHistoryFile, String geneEnsemblFile, boolean filterTaxa)
      Parameters:
      geneInfoFile - the gene_info file
      gene2AccFile - the gene2accession file
      geneHistoryFile - history file
      geneEnsemblFile - mapping file
      filterTaxa - should we filter out taxa we're not supporting

    • load

      public void load(String geneInfoFile, String gene2AccFile, String geneHistoryFile, String geneEnsemblFile, Taxon t)

    • load

      public void load(Taxon t)

    • setPersisterHelper

      public void setPersisterHelper(Persister persisterHelper)
      Parameters:
      persisterHelper - the persisterHelper to set

    • setTaxonService

      public void setTaxonService(TaxonService bean)

    • updateTaxaWithGenesUsable

      public void updateTaxaWithGenesUsable(Collection<Taxon> taxaGenesLoaded)
      Method to update taxon to indicate that genes have been loaded for that taxon are are usable. If there is a parent taxon for this species and it has genes loaded against it then use that parent's taxons genes rather than the species found in NCBI. Set the flag genesUSable to false for that child taxon that was found in ncbi.
      Parameters:
      taxaGenesLoaded - List of taxa that have had genes loaded into GEMMA from NCBI.

    • setSkipDownload

      public void setSkipDownload(boolean skipDownload)
      Set to true to avoid downloading the files, if copies already exist (not recommended if you want an update!)
      Parameters:
      skipDownload - skip download

    • setStartingNcbiId

      public void setStartingNcbiId(Integer startNcbiid)
      Indicate
      Parameters:
      startNcbiid - start ncbi id