NcbiTaxonomyTree {SMRUCC.genomics.Assembly.NCBI.Taxonomy} | .NET clr documentation |
Builds the following dictionnary from NCBI taxonomy nodes.dmp
and
names.dmp
files
{ Taxid : namedtuple('Node', ['name', 'rank', 'parent', 'children'] }
+https://www.biostars.org/p/13452/ +https://pythonhosted.org/ete2/tutorial/tutorial_ncbitaxonomy.html
>https://github.com/frallain/NCBItaxonomytree
The NCBI Taxonomy database Is a curated Set Of names And classifications For all Of the organisms that are
represented In GenBank (http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/).It can be accessed
viahttp://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgiOr it can be downloaded from
ftp://ftp.ncbi.nih.gov/pub/taxonomy/in the form of 2 files : nodes.dmp
for the structure of the tree
And names.dmp
for the names of the different nodes.
Here I make available my In-memory mapping Of the NCBI taxonomy : a Python 2.7 Class that maps the names.dmp
And nodes.dmp
files In a Python dictionnary which can be used To retrieve lineages, descendants, etc ...
# namespace SMRUCC.genomics.Assembly.NCBI.Taxonomy
export class NcbiTaxonomyTree {
# {taxid -> taxonomy_node}
Taxonomy: list;
}
Taxonomy
: list