如何根据物种拉丁名找到其在NCBI Taxonomy所处的位置

2020-03-03 14:27:40 浏览数 (3)
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
代码语言：javascript复制
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

代码语言：javascript复制
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
代码语言：javascript复制
Lumnitzera littorea
Punica granatum
Heimia myrtifolia
Sonneratia alba
Epilobium ulleungensis

代码

代码语言：javascript复制
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
网站 bi dos pip windows10

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