README_totalCUB

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Total Codon and Pairing Count Per Sample  Calculator
TotalCUB.py
Created by: Matt Hodgman
Emails: matthodg@byu.edu


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Purpose: for each sample, calculate the total number of times each codon or codon pair appears. 


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ARGUMENT OPTIONS:

	-h	--help			show this help message and exit
	-i 	INPUT			Input FastA File
	-o	OUTPUT			Output file name
	-k	KEYFILE			Sample to Population Key CSV File
	-c	--cotRNAPairing		indicates to use amino acid dict instead of codon dict


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REQUIREMENTS:

TotalCUB.py uses Python version 3.7

Python libraries that must be installed include:
1. csv
2. argparse
3. pandas

If any of those libraries is not currently in your Python Path, use the following command:
pip install --user [library_name]
to install the library to your path.


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Input Files:
This program requires one or more CSV files generated from CodonCounter.py or CodonPairingCounter.py.

Output Files:
An output file name must be supplied as an argument. The output file will be written to the same directory as TotalCUB.py or a passed directory, if provided. The resulting file will be a single CSV with a column for every amino acid or codon and a row for each sample. Each subsequent cell will contain the total number of times that the codon or amino acid occrs in the sample.


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USAGE:

The -i argument is required, followed by the input FastA file. The -o argument is required to name the output file.

Example usage:
python3 TotalCUB.py -i identical_codon_pairing_files/* -o total_identical_pairing.csv


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