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obitools4/obitests/obitools/obiconvert/taxonomy.csv
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Eric Coissac 60b3753673 feat(obiconvert): add --raw-taxid option and refactor taxID formatting 
- Add new `--tax-id` mode (`obiconvert --raw-taxid`) to output bare numeric taxIDs instead of full-format strings.
- Introduce `TaxNode.FullString()` to always return the complete "code:id [name]@rank" format, regardless of global `UseRawTaxids()` setting.
- Update `.String(taxonomyCode)` to respect the global flag, returning bare ID when `--raw-taxid` is active.
- Extract raw taxID from full-format strings in taxonomy methods when needed (e.g., fallback without loaded DB).
- Add comprehensive test suite covering:
a) `--raw-taxid` execution and idempotency
b) full-format taxID output with `--taxonomy`
c interaction of both flags
d format validation
- Add test data: new reference files `out_ecotag.fasta`, taxonomy.csv, and updated shell script.
2026-04-30 16:57:38 +02:00

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1taxidparenttaxonomic_rankscientific_name
2taxon:1 [root]@no ranktaxon:1 [root]@no rankno rankroot
3taxon:131567 [cellular organisms]@cellular roottaxon:1 [root]@no rankcellular rootcellular organisms
4taxon:2759 [Eukaryota]@domaintaxon:131567 [cellular organisms]@cellular rootdomainEukaryota
5taxon:33154 [Opisthokonta]@cladetaxon:2759 [Eukaryota]@domaincladeOpisthokonta
6taxon:33208 [Metazoa]@kingdomtaxon:33154 [Opisthokonta]@cladekingdomMetazoa
7taxon:6072 [Eumetazoa]@cladetaxon:33208 [Metazoa]@kingdomcladeEumetazoa
8taxon:33213 [Bilateria]@cladetaxon:6072 [Eumetazoa]@cladecladeBilateria
9taxon:33511 [Deuterostomia]@cladetaxon:33213 [Bilateria]@cladecladeDeuterostomia
10taxon:7711 [Chordata]@phylumtaxon:33511 [Deuterostomia]@cladephylumChordata
11taxon:89593 [Craniata]@subphylumtaxon:7711 [Chordata]@phylumsubphylumCraniata
12taxon:7742 [Vertebrata]@cladetaxon:89593 [Craniata]@subphylumcladeVertebrata
13taxon:7776 [Gnathostomata]@cladetaxon:7742 [Vertebrata]@cladecladeGnathostomata
14taxon:117570 [Teleostomi]@cladetaxon:7776 [Gnathostomata]@cladecladeTeleostomi
15taxon:117571 [Euteleostomi]@cladetaxon:117570 [Teleostomi]@cladecladeEuteleostomi
16taxon:8287 [Sarcopterygii]@superclasstaxon:117571 [Euteleostomi]@cladesuperclassSarcopterygii
17taxon:1338369 [Dipnotetrapodomorpha]@cladetaxon:8287 [Sarcopterygii]@superclasscladeDipnotetrapodomorpha
18taxon:32523 [Tetrapoda]@cladetaxon:1338369 [Dipnotetrapodomorpha]@cladecladeTetrapoda
19taxon:32524 [Amniota]@cladetaxon:32523 [Tetrapoda]@cladecladeAmniota
20taxon:40674 [Mammalia]@classtaxon:32524 [Amniota]@cladeclassMammalia
21taxon:32525 [Theria]@cladetaxon:40674 [Mammalia]@classcladeTheria
22taxon:9347 [Eutheria]@cladetaxon:32525 [Theria]@cladecladeEutheria
23taxon:1437010 [Boreoeutheria]@cladetaxon:9347 [Eutheria]@cladecladeBoreoeutheria
24taxon:314146 [Euarchontoglires]@superordertaxon:1437010 [Boreoeutheria]@cladesuperorderEuarchontoglires
25taxon:314145 [Laurasiatheria]@superordertaxon:1437010 [Boreoeutheria]@cladesuperorderLaurasiatheria
26taxon:33554 [Carnivora]@ordertaxon:314145 [Laurasiatheria]@superorderorderCarnivora
27taxon:91561 [Artiodactyla]@ordertaxon:314145 [Laurasiatheria]@superorderorderArtiodactyla
28taxon:314147 [Glires]@cladetaxon:314146 [Euarchontoglires]@superordercladeGlires
29taxon:9845 [Ruminantia]@subordertaxon:91561 [Artiodactyla]@ordersuborderRuminantia
30taxon:35500 [Pecora]@infraordertaxon:9845 [Ruminantia]@suborderinfraorderPecora
31taxon:9989 [Rodentia]@ordertaxon:314147 [Glires]@cladeorderRodentia
32taxon:379584 [Caniformia]@subordertaxon:33554 [Carnivora]@ordersuborderCaniformia
33taxon:9608 [Canidae]@familytaxon:379584 [Caniformia]@suborderfamilyCanidae
34taxon:9850 [Cervidae]@familytaxon:35500 [Pecora]@infraorderfamilyCervidae
35taxon:9881 [Odocoileinae]@subfamilytaxon:9850 [Cervidae]@familysubfamilyOdocoileinae
36taxon:33553 [Sciuromorpha]@subordertaxon:9989 [Rodentia]@ordersuborderSciuromorpha
37taxon:55153 [Sciuridae]@familytaxon:33553 [Sciuromorpha]@suborderfamilySciuridae
38taxon:34878 [Cervinae]@subfamilytaxon:9850 [Cervidae]@familysubfamilyCervinae
39taxon:9611 [Canis]@genustaxon:9608 [Canidae]@familygenusCanis
40taxon:9857 [Capreolus]@genustaxon:9881 [Odocoileinae]@subfamilygenusCapreolus
41taxon:9612 [Canis lupus]@speciestaxon:9611 [Canis]@genusspeciesCanis lupus
42taxon:337726 [Xerinae]@subfamilytaxon:55153 [Sciuridae]@familysubfamilyXerinae
43taxon:9859 [Cervus]@genustaxon:34878 [Cervinae]@subfamilygenusCervus
44taxon:337730 [Marmotini]@tribetaxon:337726 [Xerinae]@subfamilytribeMarmotini
45taxon:9992 [Marmota]@genustaxon:337730 [Marmotini]@tribegenusMarmota
46taxon:9860 [Cervus elaphus]@speciestaxon:9859 [Cervus]@genusspeciesCervus elaphus
47taxon:9615 [Canis lupus familiaris]@subspeciestaxon:9612 [Canis lupus]@speciessubspeciesCanis lupus familiaris
48taxon:9858 [Capreolus capreolus]@speciestaxon:9857 [Capreolus]@genusspeciesCapreolus capreolus
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