taxonkit reformat 如何显示kingdom 信息

[zhaolei6116]

reformat 格式选择如下

Output format can be formated by flag --format, available placeholders:

{k}: superkingdom
{p}: phylum
{c}: class
{o}: order
{f}: family
{g}: genus
{s}: species
{t}: subspecies/strain

{S}: subspecies
{T}: strain

• [ ] {k}:superkingdom 如何改为 {k}: kingdom？ 我希望结果是 kingdom 而不是 superlingdom 如何做呢

[shenwei356]

先说答案：（目前）不支持。

NCBI taxonomy 似乎只有一些病毒和真核里面有kingdom，都不包含细菌。

$ taxonkit list -I "" --ids 1 \
    | taxonkit lineage -n -r \
    | csvtk grep -Ht -f 4 -p kingdom -l \
    | csvtk pretty -Ht
2732396   Viruses;Riboviria;Orthornavirae                     Orthornavirae    kingdom
2732397   Viruses;Riboviria;Pararnavirae                      Pararnavirae     kingdom
2731360   Viruses;Duplodnaviria;Heunggongvirae                Heunggongvirae   kingdom
2732090   Viruses;Monodnaviria;Loebvirae                      Loebvirae        kingdom
2732091   Viruses;Monodnaviria;Sangervirae                    Sangervirae      kingdom
2732092   Viruses;Monodnaviria;Shotokuvirae                   Shotokuvirae     kingdom
2732093   Viruses;Monodnaviria;Trapavirae                     Trapavirae       kingdom
2732005   Viruses;Varidnaviria;Bamfordvirae                   Bamfordvirae     kingdom
2732006   Viruses;Varidnaviria;Helvetiavirae                  Helvetiavirae    kingdom
2840023   Viruses;Adnaviria;Zilligvirae                       Zilligvirae      kingdom
33090     cellular organisms;Eukaryota;Viridiplantae          Viridiplantae    kingdom
4751      cellular organisms;Eukaryota;Opisthokonta;Fungi     Fungi            kingdom
33208     cellular organisms;Eukaryota;Opisthokonta;Metazoa   Metazoa          kingdom

我们一般都是看superkingdom，对应平常说的“界门纲目科属种”的“界”。

$ taxonkit list -I "" --ids 1 \
    | taxonkit lineage -n -r \
    | csvtk grep -Ht -f 4 -p superkingdom -l \
    | csvtk pretty -Ht
10239   Viruses                        Viruses     superkingdom
2       cellular organisms;Bacteria    Bacteria    superkingdom
2157    cellular organisms;Archaea     Archaea     superkingdom
2759    cellular organisms;Eukaryota   Eukaryota   superkingdom

[zhaolei6116]

OK thank you 我研究真菌， Fungi 正好对应的是kingdom。

[shenwei356]

Just added it ({K})

    {k}: superkingdom
    {K}: kingdom
    {p}: phylum

• taxonkit_windows_amd64.exe.tar.gz
• taxonkit_darwin_amd64.tar.gz
• taxonkit_linux_amd64.tar.gz

$ echo 5207 | ./taxonkit reformat -I 1 -f "{k};{K};{p};{c};{o};{f};{g};{s}" 
5207    Eukaryota;Fungi;Basidiomycota;Tremellomycetes;Tremellales;Cryptococcaceae;Cryptococcus;Cryptococcus neoformans

[zhaolei6116]

Wow 👍👍👍， thank you, It's been an amazing journey， 这是一段神奇的经历，谢谢。