DaCA-utils is a collection of utility scripts written in python to convert output of metabarcoding pipelines according to Darwin Core Archive standards for upload to GBIF or OBIS. DaCA-utils is under development and not yet operational.
DaCA-combine merges annotated sequence data with metadata to produce an occurrence and a dna extension table that can be uploaded to GBIF.
Usage:
python DaCA-combine.py -dna <asv_input.csv> -metai <metadata_input.csv> -occ <occurrence_output.csv> -dnaex <dna_extension_output.csv> -metao <metadata_output.csv>
DaCA-uuid generates persistent identifiers (unique universal IDs) for a given list of objects in a csv file (e.g. individual samples in rows).
Usage:
python DaCA-uuid.py -i <input.csv> -o <output.csv>
DaCA-aphia retrieves AphiaIDs, lsids, and taxonomic information (kingdom, phylum, class, order, family, genus, binomen, and author and year of first description) from WoRMS for a given list of species names (binomen) in a csv file.
Usage:
python DaCA-aphia.py -i <input.csv> -s <name of column containing species names (binomen)> -o <output.csv>