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.
The repository contains code for analyzing deep mutational scanning projects, particularly related to CHIKV.
For script plot_mutational_frequency_and_qc_stats.py:
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
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)
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