buildNuccoreExtension.glue

  # Feline lentivirus project extension
  project lentivirus

    # Import nuccore sequences
    import source sources/virus/extension/feline/ncbi-nuccore-feline

    # Link nuccore sequences to isolate data
    run script glue/build/extension/feline/linkIsolateNuccoreSeqsFeline.js

    # Extract data from the XML files
    delete module genbankXmlPopulatorFeline
    create module -f modules/build/extension/feline/genbankXmlPopulatorFeline.xml
    module genbankXmlPopulatorFeline populate -w "source.name = 'ncbi-nuccore-feline'"

    # Import previously computed genotypes
    delete module sideDataImporterFelineGenotypes
    create module -f modules/build/extension/feline/sideDataImporterFelineGenotypes.xml
    module sideDataImporterFelineGenotypes
        populate -f tabular/extension/feline/fiv-nuccore-genotypes.tsv
        exit

    # Genotype nuccore sequences
    #run script glue/build/extension/feline/doRaxmlGenotyping.js

    # Add nuccore sequences to feline lentivirus alignment tree
    run file glue/build/extension/feline/extendAlignmentTreeFiv.glue

    # Record feature presence in constrained alignments
    run file glue/build/extension/feline/recordFeaturePresenceFeline.glue

    exit