a-lud / etetools

A helper tool for wrangling output from CodeML via ETE3 evol

EteTools

This is a simple tool I've written to parse output from ETE3 evol and write summary CSV files. The tools uses BioPython to interface with the CodeML output files. Calculation of the LRT statistic has been based off the method used in the ETE3 evol software.

Required python modules

The tools requires the following non-standard python libraries.

• Pandas
• SciPy
• BioPython

How to use

EteTools has been designed to be used in a custom Nextflow pipeline, but can work on any output directory generated by ete evol. The tool parses the CodeML output file in each model directory to get key information. It then uses this information to:

• Perform LRT statistics for all valid comparisons (comparisons the same as those from ETE3 evol)
• Create concatenated summary tables for each model type
• Report the sites under selection (BEB >= 0.99)

For usage examples, simply call the help page:

usage: eteTools.py [-h] [-m [MODELS ...]] /path/to/input /path/to/outdir

    # -------------------------------------------------------- #
    #                ETE3 Evol output-to-table                 #
    # -------------------------------------------------------- #

    This is a simple script that parses the output of ETE3 evol
    and returns a series of informative tables. This tool
    provides a little more flexibility than just using the std-
    out from the ETE3 evol tool.

    ------------------------------------------------------------


positional arguments:
  /path/to/input        Directory path to ETE3 evol results
  /path/to/outdir       Pipeline output directory

options:
  -h, --help            show this help message and exit

    Code written by Alastair J. Ludington
    University of Adelaide
    2022

Nextflow pipeline

I've implemented this tool in my nextflow pipeline that can be found here