The files located in this repository are the foundation of calculating and interpreting the RSCU values for the paper (insert here)
Below is a descripution of each file and its purpose (Each file is explained in sequential order to determine which files need to be ran first):
codonTable_script.sh - This shell script uses emboss to create codontables for each coding sequence from the CDS yeast files and appends it to a single file of all its codon tables.
csv_conversion.sh - This is another shell script that just converts the codon tables into a csv file for further analysis (RSCU_analysis.py).
RSCU_analysis.py - This python file is a script used to calculate the RSCU values for every coding sequence in every species. This accounts certain yeast species codon reassignments (CUG-Ser1 clade, CUG-Ser2 clade, and CUG-Ala clade). The files required for this script are the codon table csv files and the 1154yeasts_21outrgoups_info_20220408.csv profile to calculate the genome wide RSCU values.
RSCU_stats.R - This is an R script that calculates the average RSCU values of a codon throughout the CDS of a yeast species, requires the output files from RSCU_analysis.py
RSCU_stats_editor.sh - Shell script that formats the RSCU_stats.R output files in a more convetional way for processing
RSCU_matrix_generator.R - These files take the outputs of the RSCU_stats_editor.sh script that converts all the yeast species average RSCU files into one matrix file
transcript_assembly.sh - Shell script for trancriptome assembly, annotation, and extracting of CDS from replicates