如何从出租车获得王国，门，类，秩序，家庭，属和物种的分类特定ID？

I have a list of taxids that looks like this:

我有一个如下所示的出租车列表：

I am looking to get a file with taxonomic ids in order from the taxids above:

我希望从上面的出租车中获取一个带有分类标准的文件：

kingdom_id      phylum_id       class_id        order_id        family_id       genus_id        species_id

I am using the package "ete3". I use the tool ete-ncbiquery that tells you the lineage from the ids above. (I run it from my linux laptop with the command below)

我正在使用“ete3”包。我使用工具ete-ncbiquery来告诉你上面的id的谱系。（我使用下面的命令从我的linux笔记本电脑运行它）

ete3 ncbiquery --search 1204725 2162 13000163 420247 --info

The result looks like this:

结果如下：

# Taxid Sci.Name    Rank    Named Lineage   Taxid Lineage
2162    Methanobacterium formicicum species root,cellular organisms,Archaea,Euryarchaeota,Methanobacteria,Methanobacteriales,Methanobacteriaceae,Methanobacterium,Methanobacterium formicicum   1,131567,2157,28890,183925,2158,2159,2160,2162
1204725 Methanobacterium formicicum DSM 3637    no rank root,cellular organisms,Archaea,Euryarchaeota,Methanobacteria,Methanobacteriales,Methanobacteriaceae,Methanobacterium,Methanobacterium formicicum,Methanobacterium formicicum DSM 3637  1,131567,2157,28890,183925,2158,2159,2160,2162,1204725
420247  Methanobrevibacter smithii ATCC 35061   no rank root,cellular organisms,Archaea,Euryarchaeota,Methanobacteria,Methanobacteriales,Methanobacteriaceae,Methanobrevibacter,Methanobrevibacter smithii,Methanobrevibacter smithii ATCC 350611,131567,2157,28890,183925,2158,2159,2172,2173,420247

I have no idea which items (IDS) correspond to what I am looking for (if any)

我不知道哪些项目（IDS）对应于我要找的东西（如果有的话）

3 个解决方案

#1

The following code:

以下代码：

import csv
from ete3 import NCBITaxa

ncbi = NCBITaxa()

def get_desired_ranks(taxid, desired_ranks):
    lineage = ncbi.get_lineage(taxid)
    lineage2ranks = ncbi.get_rank(lineage)
    ranks2lineage = dict((rank, taxid) for (taxid, rank) in lineage2ranks.items())
    return {'{}_id'.format(rank): ranks2lineage.get(rank, '<not present>') for rank in desired_ranks}

def main(taxids, desired_ranks, path):
    with open(path, 'w') as csvfile:
        fieldnames = ['{}_id'.format(rank) for rank in desired_ranks]
        writer = csv.DictWriter(csvfile, delimiter='\t', fieldnames=fieldnames)
        writer.writeheader()
        for taxid in taxids:
            writer.writerow(get_desired_ranks(taxid, desired_ranks))

if __name__ == '__main__':
    taxids = [1204725, 2162,  1300163, 420247]
    desired_ranks = ['kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species']
    path = 'taxids.csv'
    main(taxids, desired_ranks, path)

Produces a file that looks like this:

生成一个如下所示的文件：

kingdom_id  phylum_id   class_id    order_id    family_id   genus_id    species_id
<not present>   28890   183925  2158    2159    2160    2162
<not present>   28890   183925  2158    2159    2160    2162
<not present>   28890   183925  2158    2159    2160    2162
<not present>   28890   183925  2158    2159    2172    2173

#2

With the Taxid Lineage numbers in your results, try using them in ete3's get_rank method. As an example:

使用结果中的Taxid Lineage数字，尝试在ete3的get_rank方法中使用它们。举个例子：

from ete3 import NCBITaxa
ncbi = NCBITaxa()

print ncbi.get_rank([9606, 9443])
# {9443: u'order', 9606: u'species'}

Presumably the resulting dictionary should contain the rank information of all IDs, including any intermediate "no rank" IDs that you may want to eliminate.

据推测，结果字典应包含所有ID的排名信息，包括您可能想要消除的任何中间“无排名”ID。

#3

You can also use the R packaage taxonomizr. The package takes a bit of time to download the necessary files, but after that its quite fast and easy.

您也可以使用R packaage taxonomizr。该软件包需要一些时间来下载必要的文件，但之后它非常快速和简单。

library("taxonomizr) getNamesAndNodes() taxaNodes <- read.nodes('nodes.dmp') taxaNames <- read.names('names.dmp') taxaID <- c("1204725", "2162", "1300163", "420247") getNamesAndNodes downloads the names.dmp and nodes.dmp file from ncbi.

library（“taxonomizr”）getNamesAndNodes（）taxaNodes < - read.nodes（'nodes.dmp'）taxaNames < - read.names（'names.dmp'）taxaID < - c（“1204725”，“2162”，“1300163” ，“420247”）getNamesAndNodes从ncbi下载names.dmp和nodes.dmp文件。

#1