dataset_to_database.py

Convert an existing PhyloFisher database to the new SQLite database format. This is required for version 2.0+ of PhyloFisher.

dataset_to_database.py [OPTIONS]

Required arguments:

• -i, --input <db_dir> Path to directory containing an existing PhyloFisher v1 database.

Optional arguments:

• -o, --output Path to user-defined output directory.
  • Default: ./dataset_to_database_<M.D.Y>

dataset_to_database.py output:

• a directory called ./dataset_to_database_<M.D.Y> with:
  • phylofisher.db - an SQLite database file containing metadata, sequence data, taxonomic data, and gene data.
  • orthomcl/ - a directory containing the orthomcl files:
    • orthomcl.diamonddb.dmnd - a diamond database of OrthoMCL.
    • gene_og - a tsv file detailing the names of the 240 genes and their corresponding OrthoMCL orthogroup number(s).
    • bacterial - abbreviated names of bacterial species present in OrthoMCL.
  • proteomes - a directory containing the proteomes of the taxa in the database.
  • nucleotides - a directory containing the CDSs of the taxa in the database.
  • profiles - a directory containing hmm profiles of the genes in the database.