Package org.monarchinitiative.lirical.io

Class LiricalDataResolver

java.lang.Object
org.monarchinitiative.lirical.io.LiricalDataResolver
public class LiricalDataResolver extends Object
A convenience class for accessing resources from LIRICAL data directory.

The resource files include:

  • HPO in JSON format (hp.json)
  • HPO annotations (phenotype.hpoa)
  • HGNC complete set - a table with gene identifiers, symbols, and other metadata (hgnc_complete_set.txt)
  • MIM to medgene mapping file (mim2gene_medgen)
  • Orpha to gene mapping file (en_product6.xml). Optional
  • Jannovar caches (hg(19|38)_(ucsc|refseq).ser)

The resolver checks if all non-optional files are present and will raise an exception otherwise.

  • Method Details

    • of

      public static LiricalDataResolver of(Path dataDirectory) throws LiricalDataException
      Throws:
      LiricalDataException

    • dataDirectory

      public Path dataDirectory()

    • hpoJson

      public Path hpoJson()

    • orpha2gene

      public Path orpha2gene()

    • hgncCompleteSet

      public Path hgncCompleteSet()

    • mim2geneMedgen

      public Path mim2geneMedgen()

    • phenotypeAnnotations

      public Path phenotypeAnnotations()

    • hg19UcscTxDatabase

      public Path hg19UcscTxDatabase()

    • hg19RefseqTxDatabase

      public Path hg19RefseqTxDatabase()

    • hg19RefseqCuratedTxDatabase

      public Path hg19RefseqCuratedTxDatabase()

    • hg19EnsemblTxDatabase

      public Path hg19EnsemblTxDatabase()

    • hg38UcscTxDatabase

      public Path hg38UcscTxDatabase()

    • hg38RefseqTxDatabase

      public Path hg38RefseqTxDatabase()

    • hg38RefseqCuratedTxDatabase

      public Path hg38RefseqCuratedTxDatabase()

    • hg38EnsemblTxDatabase

      public Path hg38EnsemblTxDatabase()

    • transcriptCacheFor

      public Path transcriptCacheFor(GenomeBuild genomeBuild, TranscriptDatabase txDb)