NcbiTaxonomyTree {SMRUCC.genomics.Assembly.NCBI.Taxonomy}

.NET clr documentation

NcbiTaxonomyTree

Description

Builds the following dictionnary from NCBI taxonomy nodes.dmp and names.dmp files

 { Taxid   : namedtuple('Node', ['name', 'rank', 'parent', 'children'] }

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NCBItaxonomytree

> https://github.com/frallain/NCBI_taxonomy_tree 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 via http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi Or 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 ...

Declare

            
# namespace SMRUCC.genomics.Assembly.NCBI.Taxonomy
export class NcbiTaxonomyTree {
   # {taxid -> taxonomy_node}
   Taxonomy: list;
}

        

.NET clr type reference tree

1. use by property member Taxonomy: list

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