如何根据物种拉丁名找到其在NCBI Taxonomy所处的位置

用户7010445

发布于 2020-03-03 06:27:40

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代码可运行

文章被收录于专栏：小明的数据分析笔记本小明的数据分析笔记本

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代码可运行

问题描述：

我想知道某个物种在NCBI的分类系统里被归为哪个目、哪个科、哪个属？单个物种可以手动NCBI网站检索，如果物种数非常多如何实现？

之前读 ete3 的帮助文档的时候看到过类似的功能http://etetoolkit.org/docs/latest/tutorial/tutorial_ncbitaxonomy.html。最近可能会用到这个功能，记录自己使用的代码 (首先是安装ete3：自己windows10电脑安装了Anaconda3，直接在DOS窗口下使用命令pip install ete3即可安装)

单个物种 以石榴（Punica granatum）为例

from ete3 import NCBITaxa
ncbi = NCBITaxa
name2taxid = ncbi.get_name_translator(["Punica granatum"])
for a,b in name2taxid.items():
    lineage = ncbi.get_lineage(b[0])
    names = ncbi.get_taxid_translator(lineage)
    for taxid in lineage:
        print(names[taxid])

输出结果

root
cellular organisms
Eukaryota
Viridiplantae
Streptophyta
Streptophytina
Embryophyta
Tracheophyta
Euphyllophyta
Spermatophyta
Magnoliophyta
Mesangiospermae
eudicotyledons
Gunneridae
Pentapetalae
rosids
malvids
Myrtales
Lythraceae
Punica
Punica granatum

多个物种将物种拉丁名放到文本文件里，每行一个

Lumnitzera littorea
Punica granatum
Heimia myrtifolia
Sonneratia alba
Epilobium ulleungensis

代码

import sys
from ete3 import NCBITaxa
input_file = sys.argv[1]
output_file = sys.argv[2]
ncbi = NCBITaxa()
fw = open(output_file,"w")
with open(input_file,"r") as fr:
    for line in fr:
        species_name = line.strip()
        name2taxid = ncbi.get_name_translator([species_name])
        for a,b in name2taxid.items():
            lineage = ncbi.get_lineage(b[0])
            names = ncbi.get_taxid_translator(lineage)
            i = 1
            for taxid in lineage:   
                if i < len(lineage):
                    fw.write(names[taxid]+",")
                    i = i + 1
                else:
                    fw.write(names[taxid]+"\n")
        print(species_name + ":","OK")


fw.close()
#使用方法
python .\get_species_placement_in_NCBI.py .\Organism_name.txt placement.txt
#输出结果
root,cellular organisms,Eukaryota,Viridiplantae,Streptophyta,Streptophytina,Embryophyta,Tracheophyta,Euphyllophyta,Spermatophyta,Magnoliophyta,Mesangiospermae,eudicotyledons,Gunneridae,Pentapetalae,rosids,malvids,Myrtales,Combretaceae,Lumnitzera,Lumnitzera littorea
root,cellular organisms,Eukaryota,Viridiplantae,Streptophyta,Streptophytina,Embryophyta,Tracheophyta,Euphyllophyta,Spermatophyta,Magnoliophyta,Mesangiospermae,eudicotyledons,Gunneridae,Pentapetalae,rosids,malvids,Myrtales,Lythraceae,Punica,Punica granatum
root,cellular organisms,Eukaryota,Viridiplantae,Streptophyta,Streptophytina,Embryophyta,Tracheophyta,Euphyllophyta,Spermatophyta,Magnoliophyta,Mesangiospermae,eudicotyledons,Gunneridae,Pentapetalae,rosids,malvids,Myrtales,Lythraceae,Heimia,Heimia myrtifolia
root,cellular organisms,Eukaryota,Viridiplantae,Streptophyta,Streptophytina,Embryophyta,Tracheophyta,Euphyllophyta,Spermatophyta,Magnoliophyta,Mesangiospermae,eudicotyledons,Gunneridae,Pentapetalae,rosids,malvids,Myrtales,Lythraceae,Sonneratia,Sonneratia alba
root,cellular organisms,Eukaryota,Viridiplantae,Streptophyta,Streptophytina,Embryophyta,Tracheophyta,Euphyllophyta,Spermatophyta,Magnoliophyta,Mesangiospermae,eudicotyledons,Gunneridae,Pentapetalae,rosids,malvids,Myrtales,Onagraceae,Onagroideae,Epilobieae,Epilobium,Epilobium ulleungensis