Algorithm to smooth contiguous gene cluster predictions into single regions.
- class gecco.refine.ClusterRefiner(object)[source]¶
A post-processor to extract contiguous clusters from CRF predictions.
- __init__(threshold: float = 0.8, criterion: str = 'gecco', n_cds: int = 5, n_biopfams: int = 5, average_threshold: float = 0.6, edge_distance: int = 0) None [source]¶
Create a new
float) – The probability threshold to use to consider a protein to be part of a gene cluster.
str) – The criterion to use when checking for cluster validity.
int) – The minimum number of genes a gene cluster must contain to be considered valid. If
gecco, then this is the minimum number of annotated CDS.
int) – The minimum number of biosynthetic Pfam domains a gene cluster must contain to be considered valid (only when the criterion is
int) – The average probability threshold to use to consider a gene cluster valid (only when the criterion is
int) – The minimum distance from the edge the gene cluster must be located (it may start at an edge, but must span for longer than
edge_distance), in number of annotated genes (only when the criterion is
- iter_clusters(genes: List[gecco.model.Gene]) Iterator[gecco.model.Cluster] [source]¶
Find all clusters in a table of CRF predictions.
Gene) – A list of genes with probability annotations estimated by
gecco.model.Cluster– Valid clusters found in the input with respect to the postprocessing criterion given at initialisation.