organism.py

Find taxonomic ID using NCBI Taxonomy Database
It performs a search using taxonomic ID or organism name and feed Organism object with descendants

Usage

You can run this script from command line passing args or using a configuration file

Command line

You can read help message running organism.py -h:

usage: organism.py [-h] [--taxon TAXON] [--log LOG] [--groups GROUPS]
                   [--output_file OUTPUT_FILE] [--conf CONF]

Organism - Find taxonomic ID using taxonomony sqlite database

optional arguments:
  -h, --help            show this help message and exit
  --taxon TAXON         Organism name or taxonomic ID
  --log LOG             Log output
  --groups GROUPS       Groups descendants from taxon parameter to be
                        considered
  --output_file OUTPUT_FILE
                        Output filepath
  --conf CONF           Configuration file

Search for organism names or taxonomic IDs related from taxon parameter and
put into a file

An command example:

organism.py --taxon 1980416 --groups all --output_file test
organism.py --taxon Peribunyaviridae --groups all --output_file test

Config file

You can use a configuration file with this content:

[Organism]                                                                      
taxon = 1980416
log = organism.log
groups = all
output_file = ids.txt 

In first line, you're setting between "[]" the section, organism script use "Organism" section to get parameters. After that, everything is parameter = value (until it finds another section), they're the same parameters from help message without "--" before the keys.
Run script using:

organism.py --conf example.conf

Organism

It is just a class used as a model/transfer object used to represent a oragnism from NCBI Taxonomy having the following properties:

Property	Type	Description
tax_id	int	Taxonomic ID
name	str	Organism name
descendants	list	List of Organisms

Functions

This script have the following functions

get_organism()

This method create request for NCBI Taxonomy and return a Organism

Parameters	Type	Description
taxon	str	int

read_taxonomy_page()

This method reads taxonomy response page and return a Organism object filled

Parameters	Type	Description
content	str	Response content from request