wendellor.py

It reads configuration file and execute the pipeline:
organism.py -> downloader.py -> unifier.py -> muscle -> tabajara

Usage

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

usage: wendellor.py [-h] conf

wendellor - main script to run scripts using config file

positional arguments:
  conf        Configuration filepath

optional arguments:
  -h, --help  show this help message and exit

Read configuration file and execute scripts

wendellor.py just receives the config filepath paramater:

wendellor.py conf_examples/example_both_discrimination.conf

Configuration file

Functions

This script have the following functions

run_muscle_and_tabajara()

Method used to run muscle and tabajara

Parameters	Type	Description
organism	str	Organism name
discriminate	str	Discrimination parameter from unifier ['yes', 'no', 'both']
muscle_parameters	str	Muscle parameters
tabajara_parameters	str	Tabajara parameters
output	str	Output dir
muscle_filepath	str	Muscle executable filepath
tabajara_filepath	str	Tabajara executable filepath