如何从taxid获取分类级别名称？

Question

这个问题涉及： How to get taxonomic specific ids for kingdom, phylum, class, order, family, genus and species from taxid?

这里给出的解决方案是可行的，但是我希望为定义的列组提供每个分类ID的名称。我在ete3上找到了这个可以做的工作：

names = ncbi.get_taxid_translator(lineage)
print [names[taxid] for taxid in lineage]

但作为python程序员，我未能将其整合到上面链接中给出的代码中。以下是我尝试过的：

^{pr2}$

非常感谢您能提供的任何帮助。在

Answer 1

我没有足够的声誉来评论马克西米利安·彼得斯的回答。我尝试了他的代码，它成功了，但是信息没有按desired_ranks = ['kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species']的顺序显示。在

要获取右栏中的信息以及超级王国信息，请使用：

import csv
from ete3 import NCBITaxa

ncbi = NCBITaxa()

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

if __name__ == '__main__':
    taxids = [1204725, 2162,  1300163, 420247]
    desired_ranks = ['superkingdom', 'kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species']
    results = list()
    for taxid in taxids:
        results.append(list())
        results[-1].append(str(taxid))
        ranks = get_desired_ranks(taxid, desired_ranks)
        for key, rank in ranks.items():
            if rank != '<not present>':
                results[-1].append(list(ncbi.get_taxid_translator([rank]).values())[0])
            else:
                results[-1].append(rank)

    #generate the header
    header = ['Original_query_taxid']
    header.extend(desired_ranks)
    print('\t'.join(header))

    #print the results
    for result in results:
        print('\t'.join([result[i] for i in [0, 2, 5, 7, 4, 6, 3, 8, 1]]))

输出：

^{pr2}$

此输出与NCBI信息匹配，例如https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1204725。在

Answer 2

让我们让你的taxids保持原样。在

taxids = [1204725, 2162,  1300163, 420247]

然后为每个taxid调用get_desired_ranks。在

^{pr2}$

现在为ranks和{}中的每个key（rank）调用ncbi.get_taxid_translator输出：

for taxid in taxids:
    print(ncbi.get_taxid_translator([taxid]))
    ranks = get_desired_ranks(taxid, desired_ranks)
    for key, rank in ranks.items():
        if rank != '<not present>':
            print(ncbi.get_taxid_translator([rank]))

输出

{1204725: 'Methanobacterium formicicum DSM 3637'}
{183925: 'Methanobacteria'}
{2159: 'Methanobacteriaceae'}
{2160: 'Methanobacterium'}
{28890: 'Euryarchaeota'}
{2162: 'Methanobacterium formicicum'}
{2158: 'Methanobacteriales'}
{2162: 'Methanobacterium formicicum'}
[...]      
{420247: 'Methanobrevibacter smithii ATCC 35061'}
{183925: 'Methanobacteria'}
{2159: 'Methanobacteriaceae'}
{2172: 'Methanobrevibacter'}
{28890: 'Euryarchaeota'}
{2173: 'Methanobrevibacter smithii'}
{2158: 'Methanobacteriales'}

改进输出的完整代码

import csv
from ete3 import NCBITaxa

ncbi = NCBITaxa()

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

if __name__ == '__main__':
    taxids = [1204725, 2162,  1300163, 420247]
    desired_ranks = ['kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species']
    for taxid in taxids:
        print(list(ncbi.get_taxid_translator([taxid]).values())[0])
        ranks = get_desired_ranks(taxid, desired_ranks)
        for key, rank in ranks.items():
            if rank != '<not present>':
                print(key + ': ' + list(ncbi.get_taxid_translator([rank]).values())[0])
        print('=' * 60)

---

如果您想要一个用制表符分隔的输出，可以用\t连接字符串，或者只将所有结果添加到list和{}中，并使用\t。在

在下面的代码片段中，结果存储在一个名为list的results中，其中包含另一个存储字段（原始ID、kingdom等）的列表。在每个循环中，结果被添加到最后一个条目（results[-1]）。在

if __name__ == '__main__':
    taxids = [1204725, 2162,  1300163, 420247]
    desired_ranks = ['kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species']
    results = list()
    for taxid in taxids:
        results.append(list())
        results[-1].append(str(taxid))
        ranks = get_desired_ranks(taxid, desired_ranks)
        for key, rank in ranks.items():
            if rank != '<not present>':
                results[-1].append(list(ncbi.get_taxid_translator([rank]).values())[0])
            else:
                results[-1].append(rank)

    #generate the header
    header = ['Original_query_taxid']
    header.extend(desired_ranks)
    print('\t'.join(header))

    #print the results
    for result in results:
        print('\t'.join(result))

输出

Original_query_taxid    kingdom phylum  class   order   family  genus   species
1204725 Methanobacterium formicicum     Methanobacteriaceae     Euryarchaeota
Methanobacteria Methanobacteriales      Methanobacterium        <not present>
2162    Methanobacterium formicicum     Methanobacteriaceae     Euryarchaeota
Methanobacteria Methanobacteriales      Methanobacterium        <not present>
1300163 Methanobacterium formicicum     Methanobacteriaceae     Euryarchaeota
Methanobacteria Methanobacteriales      Methanobacterium        <not present>
420247  Methanobrevibacter smithii      Methanobacteriaceae     Euryarchaeota
Methanobacteria Methanobacteriales      Methanobrevibacter      <not present>