Structure improvements
-
Allow different ploidy in outgroup (typically if there is only one outgroup sequence). Statistics requiring a consistent ploidy in the outgroup should be silently skipped.
- All the architecture is designed to enforce a constant ploidy so allowing varying ploidy within the ingroup is likely to cause nasty side-effects for little benefit.
-
Specify outgroup with
struct_from_iterable(e.g. using a special markup instead of the population label). -
Ploidy option withstruct_from_iterable. -
Add new function:
struct_from_mapping- Signature:
struct_from_mapping(indivs, ploidy=1[, pop[, clusters[, otg]]]) - Example1:
struct = struct_from_mapping(['A', 'B', 'C', 'D'], ploidy=2, {'pop1': ['A', 'B'], {'pop2': ['C', 'D']}) - Example2:
struct = struct_from_mapping('AABBCCDDE', {'pop1': ['A', 'B'], {'pop2': ['C', 'D']}, outgroup=['E'])
- Signature:
Edited by Stéphane De Mita