Opened 4 years ago
Last modified 2 years ago
#832 _started task
emphasize group name conventions
Reported by: | westram | Owned by: | westram |
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Priority: | major | Milestone: | |
Component: | ARB_NTREE | Version: | SVN |
Keywords: | Cc: |
Description (last modified by westram)
The following conventions for names of taxonomic groups are/shallBe used in arb databases.
Some characters are problematic
character | problem | implemented behavior |
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used for groups combining multiple taxonomic ranks |
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used when a taxon is "spread" across the
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used by taxonomy() ACI-command. |
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| used in "tax…" entries to separate groups |
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used as prefix for keeled groups |
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Needed fixes:
- extend ACI command taxonomy to accept a 3rd parameter to specify the separator to use, e.g. taxonomy(100,";")
- predefined ACIs for generating tax entries shall
- use new taxonomy parameter to directly create ';'-separated tax-entries
- translate _ → ;
- remove enumerated suffixes
- review parts of arb which auto-generate group names
- make sure their defaults follow the above conventions:
- group name modifications performed by Move groups.. (see also predefined config "report2name")
group names generated by Cluster detectionfixed by [19283]
- group names generated/assumed by predefined configs in Search taxonomic groups
do not notify about violation of group naming convention for each of e.g. 100 generated groups.
Instead collect all and maybe show the first three warnings or so.implemented with [19277].
- make sure their defaults follow the above conventions:
- implement #833 (generate taxonomic groups from tax…-entries)
Change History (11)
comment:1 Changed 4 years ago by westram
- Description modified (diff)
comment:2 Changed 4 years ago by westram
- Description modified (diff)
comment:3 Changed 4 years ago by westram
- Description modified (diff)
comment:4 Changed 4 years ago by westram
- Description modified (diff)
comment:5 Changed 2 years ago by westram
- Owner changed from devel to westram
- Priority changed from normal to major
- Status changed from new to _started
comment:6 Changed 2 years ago by westram
- Description modified (diff)
comment:7 Changed 2 years ago by westram
- Description modified (diff)
comment:8 Changed 2 years ago by westram
- Description modified (diff)
comment:9 Changed 2 years ago by westram
comment:10 Changed 2 years ago by westram
- Description modified (diff)
comment:11 Changed 2 years ago by westram
- Description modified (diff)
arb now complains about "unwanted" group names using the following messages: