CHIKV_DMS

Deep mutational scanning repository for Thomas (Tem) Morrison Lab

This repository contains code to run analysis for deep mutational scanning projects related to analysis for CHIKV.

Table of Contents

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• CHIKV_DMS
  • Table of Contents
    • Introduction and Overview
    • Software Requirements and Dependencies
    • Installation
    • General Usage

• script: plot_mutational_frequency_and_qc_stats.py

Introduction and Overview

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The repository contains code for analyzing deep mutational scanning projects, particularly related to CHIKV.

Software Requirements and Dependencies

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For script plot_mutational_frequency_and_qc_stats.py:

• python >= v3.9
• pandas
• numpy
• matplotlib
• logomaker

Installation

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There is no installation required, please just clone the repository:

git clone https://github.com/tbrunetti/CHIKV_DMS.git

Then cd into the code directory where all scripts will be present:

cd code  

General Usage

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For using the logo_plot_standalone.py script, general use is as follows:

python3 logo_plot_standalone.py --input wtDNA_filtered_df1_dedup.csv --sampleName wtDNA --annotConfig ../ref/annotations_config.csv --codonStartPos 9 

For all possible arguments available, you can run the following:

python3 logo_plot_standalone.py --help

,which will show the following options and their defaults:

usage: logo_plot_standalone.py [-h] --input INPUT [--sampleName SAMPLENAME] [--annotConfig ANNOTCONFIG] [--codonStartPos CODONSTARTPOS] [--codonEndPos CODONENDPOS]
                               [--aaSpacing AASPACING] [--minAnnotLabel MINANNOTLABEL]

Generates logo plot for predefined input matrix

options:
  -h, --help            show this help message and exit  
  --input INPUT         Path to input csv matrix containing data to plot (default: None)  
  --sampleName SAMPLENAME  
                        string indicating the name to give to sample (default: sample_1)  
  --annotConfig ANNOTCONFIG  
                        Path to csv containing annotations. Example file located in ref folder of github repo (default: None)  
  --codonStartPos CODONSTARTPOS  
                        The position of which codon position you want to start at (must be present in your csv matrix provided to --input; default is to plot every position in
                        your matrix) (default: None)  
  --codonEndPos CODONENDPOS  
                        The position of which codon position you want to end at (must be present in your csv matrix provided to --input; default is to plot every position in your
                        matrix) (default: None)  
  --aaSpacing AASPACING  
                        the number of amino acids to show per line on the logo plot (default: 65)  
  --minAnnotLabel MINANNOTLABEL  
                        the minimum length of consecutive amino acids under an annotation bar; anything smaller (non-inclusive) than this value will not have text written in the
                        bar, to help prevent text from overflowing into margins (default: 7)