generate taxonomic groups from tax...-entries

[westram]

status quo:

• common arb databases contain "tax…"-entries defining taxonomy.
  format is e.g. domainName;phylumName;className;orderName;familyName,genusName
• arb has functions to generate such "tax…"-entries, e.g. using
  Search&Query/More functions/Modify fields of listed species
  with the predefined ACI script "store full taxonomy".

wanted feature:

• generate groups in from "tax…"-entries
  • this will only work (well) if tax-entries match the topology
  • (directly after creating tax-entries it should work perfect)
• choose location of group such that all member-species are contained
  • location may be root node ⇒ abort with error

proposed parameters:

• name of database fields containing taxonomic ranks
• characters used to separate
  • taxonomic ranks in the above field (default: ';')
  • combined group names, where multiple ranks fall onto one group instance (default: '_')
• group placement:
  • maximum percentage of outgroup members allowed (default: 0 = none)
  • maximum number of parts a group may be split into (default: 1; higher values allow to apply groups that are spread, as mentioned in #comment:1)
    • only allow monophyletic groups?
    • define minimum percentage of membership?

• action if any of these limitations reached:
  • skip +
    • log (should log whole content of tax-database-field) OR
    • write content of tax-field into custom field (e.g. "tax_notApplied")
  • insert group, optionally with customizable suffix (e.g. "—mismatches: ###")

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related: #832

[westram]

one problem are taxonomic groups, that are spread over the ,

Proposed naming convention:

Taxon
Taxon~1
Taxon~2

(located probably in different parent groups)

How is syntax of "tax.."-entries for members of such "spread groups"?