pmaf.pipe.specs

Pipe Specs (pmaf.pipe.specs)

This sub-package specs contain collection of simple classes that serve as specifications for data pipelines.

Specifications (Classes)

Primitive Specs

SpecIP(mediator, factor, **kwargs)	Identifiers -> Phylogeny.
SpecIS(mediator, factor, **kwargs)	Identifiers -> Sequence.
SpecTI(mediator, factor, **kwargs)	Taxonomy -> Identifier.
SpecIT(mediator, factor, **kwargs)	Identifiers -> Taxonomy.
SpecIA(mediator, factor, **kwargs)	Identifiers -> Accessions.

Composite Specs

SpecTP(*args, **kwargs)	Taxonomy - Phylogeny(reference tree)
SpecTS(*args, **kwargs)	Taxonomy -> Sequence.
SpecTSPBP(*args, branch_estimator, **kwargs)	Taxonomy -> Phylogeny/Topology + Sequence Alignments -> Branched Phylogeny.
SpecTSBP(*args, tree_builder, **kwargs)	Taxonomy -> Sequence Alignments -> Branched Phylogeny(de-novo)

Special Functions

ForgeSpec(name, *inters)

Function to forge a new spec from intermediate specs