Eric Coissac
8c7017a99d
- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5" - Update version.txt from 4.29 → .30 (automated by Makefile)
1.3 KiB
Taxonomic Annotation Workers in obiseq
This Go package provides functional workers for annotating biological sequences with taxonomic information using a hierarchical taxonomy (e.g., from NCBI or UNITE). Each worker is implemented as a SeqWorker—a function that processes one sequence and returns an updated slice of sequences.
-
MakeSetTaxonAtRankWorker(taxonomy, rank):
Assigns a taxonomic label at a specific rank (e.g.,"genus","family"). Validates that the requestedrankexists in the taxonomy before proceeding. -
MakeSetSpeciesWorker(taxonomy):
Annotates each sequence with its inferred species name using the provided taxonomy. -
MakeSetGenusWorker(taxonomy):
Adds genus-level taxonomic assignment to sequences. -
MakeSetFamilyWorker(taxonomy):
Adds family-level taxonomic assignment. -
MakeSetPathWorker(taxonomy):
Populates the full taxonomic path (e.g.,"Eukaryota;Metazoa;Chordata;...") for each sequence.
All workers rely on methods of BioSequence (e.g., .SetSpecies(), .SetPath()), which internally use the obitax.Taxonomy object to resolve taxonomic IDs or names. Errors are logged via logrus; invalid ranks cause a fatal exit.
These utilities support modular, pipeline-friendly taxonomic annotation—ideal for high-throughput metabarcoding workflows.