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add a new example
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shenwei356 committed Jul 7, 2019
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Expand Up @@ -90,6 +90,26 @@ Example 2 (*E.coli* with taxid `562`)
1637691 2015-05-01 REUSE_DEL Escherichia sp. MAR species cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia sp. MAR 131567;2;1224;1236;91347;543;561;1637691
1637691 2015-11-01 MERGE 562 Escherichia sp. MAR species cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia sp. MAR 131567;2;1224;1236;91347;543;561;1637691

Example 3 (All subspecies and strain in *Akkermansia muciniphila* 239935)

# species in Akkermansia
$ taxonkit list --show-rank --show-name --ids 239935
239935 [species] Akkermansia muciniphila
349741 [no rank] Akkermansia muciniphila ATCC BAA-835

# check them all
$ pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f taxid -P <(taxonkit list --indent "" --ids 239935) \
| csvtk pretty
taxid version change change-value name rank lineage lineage-taxids
239935 2014-08-01 NEW Akkermansia muciniphila species cellular organisms;Bacteria;Chlamydiae/Verrucomicrobia group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Verrucomicrobiaceae;Akkermansia;Akkermansia muciniphila 131567;2;51290;74201;203494;48461;203557;239934;239935
239935 2015-05-01 CHANGE_LIN_TAX Akkermansia muciniphila species cellular organisms;Bacteria;Chlamydiae/Verrucomicrobia group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila 131567;2;51290;74201;203494;48461;1647988;239934;239935
239935 2016-03-01 CHANGE_LIN_TAX Akkermansia muciniphila species cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila 131567;2;1783257;74201;203494;48461;1647988;239934;239935
239935 2016-05-01 ABSORB 1834199 Akkermansia muciniphila species cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila 131567;2;1783257;74201;203494;48461;1647988;239934;239935
349741 2014-08-01 NEW Akkermansia muciniphila ATCC BAA-835 no rank cellular organisms;Bacteria;Chlamydiae/Verrucomicrobia group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Verrucomicrobiaceae;Akkermansia;Akkermansia muciniphila;Akkermansia muciniphila ATCC BAA-835 131567;2;51290;74201;203494;48461;203557;239934;239935;349741
349741 2015-05-01 CHANGE_LIN_TAX Akkermansia muciniphila ATCC BAA-835 no rank cellular organisms;Bacteria;Chlamydiae/Verrucomicrobia group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila;Akkermansia muciniphila ATCC BAA-835 131567;2;51290;74201;203494;48461;1647988;239934;239935;349741
349741 2016-03-01 CHANGE_LIN_TAX Akkermansia muciniphila ATCC BAA-835 no rank cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila;Akkermansia muciniphila ATCC BAA-835 131567;2;1783257;74201;203494;48461;1647988;239934;239935;349741

## Results

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