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Eric Coissac
60b3753673
- 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.
25 lines
3.2 KiB
Plaintext
25 lines
3.2 KiB
Plaintext
>HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obitag_bestid":0.9797979797979798,"obitag_bestmatch":"AY227529","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9992 [Marmota]@genus"}
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ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
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gcctgaaactcaaaggacttggcggtgctttacatccct
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>HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obitag_bestid":0.9405940594059405,"obitag_bestmatch":"AF154263","obitag_match_count":9,"obitag_rank":"infraorder","obitag_similarity_method":"lcs","taxid":"taxon:35500 [Pecora]@infraorder"}
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ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
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agcttaaaactcaaaggacttggcggtgctttataccctt
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>HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obitag_bestid":1,"obitag_bestmatch":"AB245427","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9860 [Cervus elaphus]@species"}
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ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
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agcttaaaactcaaaggacttggcggtgctttataccctt
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>HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obitag_bestid":0.9494949494949495,"obitag_bestmatch":"AY227530","obitag_match_count":2,"obitag_rank":"tribe","obitag_similarity_method":"lcs","taxid":"taxon:337730 [Marmotini]@tribe"}
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ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
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gcttaaaactcaaaggacttggcggtgctttatatccct
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>HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obitag_bestid":0.9595959595959596,"obitag_bestmatch":"AC187326","obitag_match_count":1,"obitag_rank":"subspecies","obitag_similarity_method":"lcs","taxid":"taxon:9615 [Canis lupus familiaris]@subspecies"}
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ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
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gattaaacctcaaaggacttggcagtgctttatacccct
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>HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obitag_bestid":1,"obitag_bestmatch":"AJ885202","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
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ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
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agcttaaaactcaaaggacttggcggtgctttataccctt
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>HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obitag_bestid":1,"obitag_bestmatch":"AJ972683","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
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ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
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agcttaaaactcaaaggacttggcggtgctttataccctt
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>HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obitag_bestid":1,"obitag_bestmatch":"AB048590","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9611 [Canis]@genus"}
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ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
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gcttaaaactcaaaggacttggcggtgctttatatccct
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