如何从滑行中获取分类学等级名称? [英] How can I get taxonomic rank names from taxid?
问题描述
This question is related to: How to get taxonomic specific ids for kingdom, phylum, class, order, family, genus and species from taxid?
那里给出的解决方案是可行的，但是我想为定义等级的每个分类ID提供名称.我已经在ete3上找到了它，它可以完成这项工作:
The solution given there works but I would like to have the names for each taxonomic ids for defined ranks. I have found this on ete3 which can do the job:
names = ncbi.get_taxid_translator(lineage)
print [names[taxid] for taxid in lineage]
但不是Python程序员，我无法将其合并到以上链接中给出的代码中.这是我尝试过的:
but not being python programmer, I am failing to incorporate this into the code given in the link above. Here is what I have tried:
import csv
from ete3 import NCBITaxa
ncbi = NCBITaxa()
def get_desired_ranks(taxid, desired_ranks):
lineage = ncbi.get_lineage(taxid)
print lineage
#[1, 131567, 2157, 28890, 183925, 2158, 2159, 2160, 2162, 1204725]
names = ncbi.get_taxid_translator(lineage)
print names
#{1: u'root', 2157: u'Archaea', 2158: u'Methanobacteriales', 2159: u'Methanobacteriaceae', 2160: u'Methanobacterium', 2162: u'Methanobacterium formicicum', 183925: u'Methanobacteria', 28890: u'Euryarchaeota', 131567: u'cellular organisms', 1204725: u'Methanobacterium formicicum DSM 3637'}
lineage2ranks = ncbi.get_rank(names)
print lineage2ranks
#{1: u'no rank', 2157: u'superkingdom', 2158: u'order', 2159: u'family', 2160: u'genus', 2162: u'species', 183925: u'class', 28890: u'phylum', 131567: u'no rank', 1204725: u'no rank'}
ranks2lineage = dict((rank,taxid) for (taxid, rank) in lineage2ranks.items())
print ranks2lineage
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)
非常感谢您能提供的任何帮助.
Many thanks for any help you could provide.
推荐答案
让您的taxids保持原样.
taxids = [1204725, 2162, 1300163, 420247]
然后为每个单独的taxid调用get_desired_ranks.
Then call get_desired_ranks for each individual taxid.
for taxid in taxids:
ranks = get_desired_ranks(taxid, desired_ranks)
现在分别对ranks和print中的每个key(等级)调用ncbi.get_taxid_translator:
Now call ncbi.get_taxid_translator for each key (rank) in ranks and print the output:
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'}
完整代码，输出得到改善
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)
如果要使用制表符分隔的输出，可以使用\t连接字符串，或仅使用\t将所有结果添加到list和join.
If you want to have a tab-separated output you can concatenate the strings with \t or just add all results to a list and join with \t.
在下面的代码片段中，结果存储在名为results的list中，其中包含另一个存储您的字段(原始ID，王国等)的列表.在每个循环中，结果将添加到最后一个条目(results[-1]).
In the snippet below, the results are stored in a list called results which contains another list which stores your fields (original ID, kingdom, etc.). In each loop the results are added to the last entry (results[-1]).
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>
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