FEV_KEGG.Evolution.Comparison module

FEV_KEGG.Evolution.Comparison.getOrthologsWithinEnzymes(enzymes: Iterable[FEV_KEGG.Graph.Elements.Enzyme], eValue: float = 1e-15) → Dict[FEV_KEGG.Graph.Elements.Enzyme, Set[FEV_KEGG.Graph.Elements.Enzyme]][source]

Get orthologs within enzymes.

Parameters:
  • enzymes (Iterable[Enzyme]) – Enzymes among which to search for orthology.
  • eValue (float, optional) – Statistical expectation value (E-value), below which a sequence alignment is considered significant.
Returns:

Dictionary of every enzyme in enzymes which has at least one ortholog in enzymes, pointing to a set of all its orthologs.
Return type:

Dict[Enzyme, Set[Enzyme]]
Raises:
  • ImpossiblyOrthologousError – If any gene ID in geneIDs is from comparisonOrganism.
  • ValueError – If any organism does not exist.
  • URLError – If connection to KEGG fails.

Warning

This operation has a worst-case complexity class of O(n(n+1)/2)! To make matters worse, each step involves at least one, if not several, network operations with KEGG SSDB/GENE, which are inherently slow. The best-case complexity class is still O(n-1).

FEV_KEGG.Evolution.Comparison.getOrthologsWithinGeneIDs(geneIDs: Iterable[FEV_KEGG.Graph.Elements.GeneID], eValue: float = 1e-15) → Dict[FEV_KEGG.Graph.Elements.GeneID, Set[FEV_KEGG.Graph.Elements.GeneID]][source]

Get orthologs within geneIDs.

Parameters:
  • geneIDs (Iterable[GeneID]) – Gene IDs among which to search for orthology.
  • eValue (float, optional) – Statistical expectation value (E-value), below which a sequence alignment is considered significant.
Returns:

Dictionary of every gene in geneIDs which has at least one ortholog in geneIDs, pointing to a set of all its orthologs.
Return type:

Dict[GeneID, Set[GeneID]]
Raises:
  • ValueError – If any organism does not exist.
  • URLError – If connection to KEGG fails.

Warning

This operation has a worst-case complexity class of O(n(n+1)/2)! To make matters worse, each step involves at least one, if not several, network operations with KEGG SSDB/GENE, which are inherently slow. The best-case complexity class is O(n-1).