Step 1 - get taxonomic information

Given a species name or taxonomic ID, the query species lineage information is extracted with the help of the ete3 python toolkit and the NCBI taxonomy (Huerta-Cepas et al., 2016).

This information is needed alongside with the taxonomic classifications for all species used in the OrthoFinder comparison.

Note

The NCBI taxonomy database needs to be downloaded using the package ete3. A parsed version of it will be stored at your home directory: ~/.etetoolkit/taxa.sqlite.

oggmap provides a command line function to download or upgrade the NCBI taxonomy database (see Command line function - ncbitax).

How to get taxonomic information about your query species

Note

The oggmap submodule qlin helps to get taxonomic information for you with the qlin.get_qlin() function. The function will output the following list: - query name query_lineage[0] - query taxID query_lineage[1] - query lineage query_lineage[2] - query lineage dictionary query_lineage[3] - query lineage zip query_lineage[4] - query lineage names query_lineage[5] - reverse query lineage query_lineage[6] - query kingdom query_lineage[7]

Please download the notebooks from here or please click below to view the content.

• oggmap: Step 1 - get taxonomic information
  • Notebook file
  • Import libraries
  • Import oggmap python package submodules
  • Get query species taxonomic lineage information
  • Get query species lineage as a tree object