Expects an ENVO CURIE from the environmental material hierarchy,
Environment broad scale context
Expects an ENVO CURIE from the biome hierarchy
Environment local scale context
Expects an ENVO CURIE from the astronomical body part, or layer, hierarchies
*Note that the system will only search for terms from one of the three major GO hierarchies (biological process, cellular component, or molecular function ) at a time.
NCBI Taxonomy ontology term
Expects a NCBITaxon CURIE from the Bacteria or Archaea lineages
Query for subclasses of input quality argument
Experts a BFO, ENVO or PMO quality CURIE
See Appendix section for list of qualities
-ql str [str ...], --quality_list
Query for a list of input quality arguments
Experts BFO, ENVO or PMO quality CURIE see list in Appendix section for list
E.g., ENVO:09200014 ENVO:3100031
Output file path to write tsv file of go term counts
Typical use would be `output/custom_file_name`
E.g., "Amazon Plume Metagenomes"
*The list of available projects are as follows: "Amazon Plume Metagenomes", "Amazon River Metagenomes", "BATS Chisholm", "HOT 224-283", "HOT 144-166", or "Tara Oceans".
File path to input sparql query file with query for
basic metadata universal across samples
Default is: base_metadata.rq
Only needs to be run once but should be run at first to get metadata table
-dmin int, --depth_minimum int
Filter samples by depth with minimum value cutoff
-dmax int, --depth_maximum
Filter samples by depth with maximum value cutoff