从NCBI批量获取物种的分类信息

软件下载

从NCBI官方网站下载datasets和dataformat，chmod修改为可执行文件即可。

输入文件

直接用拉丁名即可。但是不能是Hordeum vulgare L.这种格式，不然会报错：

The taxonomy name 'Hordeum vulgare L.' is not exact. Try using one of the suggested taxids:
Hordeum vulgare (species, taxid: 4513)
Hordeum vulgare alphaendornavirus (species, taxid: 1774276, Hordeum vulgare endornavirus)
Hordeum vulgare subsp. vulgare (subspecies, taxid: 112509, Hordeum vulgare var. vulgare)
Hordeum vulgare var. distichon (varietas, taxid: 1288821, Hordeum vulgare var. distichum)
Hordeum vulgare var. coeleste (varietas, taxid: 2881371)
Hordeum vulgare subsp. spontaneum (subspecies, taxid: 77009)
Hordeum vulgare var. trifurcatum (varietas, taxid: 2821315)
Hordeum vulgare var. hexastichon (varietas, taxid: 1288822)
Hordeum vulgare f. agriocrithon (forma, taxid: 191506)
Hordeum vulgare dicistro-like virus 1 (species, taxid: 2872415)

No valid taxons provided for summary - exiting

输出文件

输出文件就是标准的tsv格式的：

Query   Taxid   Tax name        Authority       Rank    Basionym        Basionym authority      Curator common name     Has type material       Group name       Superkingdom name       Superkingdom taxid      Kingdom name    Kingdom taxid   Phylum name     Phylum taxid    Class name      Class taxid      Order name      Order taxid     Family name     Family taxid    Genus name      Genus taxid     Species name    Species taxid   Scientific name is formal
Oryza minuta    63629   Oryza minuta    J.Presl, 1830   SPECIES                         no      monocots        Eukaryota       2759    Viridiplantae    33090   Streptophyta    35493   Magnoliopsida   3398    Poales  38820   Poaceae 4479    Oryza   4527    Oryza minuta    63629   TRUE