chikvExtensionProject.glue

project chikv

  delete source ncbi-curated

  # Define extension modules
  run file glue/chikvExtensionModules.glue

  # NCBI refseqs - taxa in the reference phylogeny
  import source sources/ncbi-curated
  import source sources/ncbi-curated-short

  # Link sequence table entries to isolate table
  run script glue/chikvLoadIsolateDataCurated.js 
  run script glue/chikvLoadIsolateDataCuratedShort.js 

  # Populate refseq + outgroup metadata from GenBank XML
  module chikvGenbankXmlPopulator populate -w "source.name = 'ncbi-curated'"
  module chikvGenbankXmlPopulator populate -w "source.name = 'ncbi-curated-short'"

  # Import genotype data
  run file glue/chikvLoadGenotypesCurated.glue

  # Import genotype data
  run file glue/chikvAlignmentTreeCurated.glue

  # Compute multiple sequence alignments with curated sequences included
  run file glue/chikvComputeAlignments.glue

  # Record feature presence in multiple sequence alignments
  run file glue/chikvRecordFeaturePresence.glue

  # Validate
  validate

  exit