plot-codonusage-vs-tRNAgenes-V3.pl

Program will take data on file and make plots comparing codon usage with the number of tRNA genes with complementary anticodons. First line in the data file has to be commented and have the column titles. This line must use the same titles as given by previous scripts so that this program recognize them. Each file should contain the columns presenting the usage of each codon as well as columns presenting the number of tRNA genes. In Linux, you can use the paste command to construct this file pasting the average codon file and the tRNA genes content files produced by the following scripts:
Codon_statistics-V2.pl
count_trnascan.pl
For example:
paste average-b.txt tRNA_genes.tab > usage-tRNAs.tab
Results files will use the to construct result files in
This program calculate linear regression using perl “Statistics::LineFit” module and produces plots using GnuPlot. Both should be installed. After finishing, the program will unite all pdf files of the folder in and add to that file name a ".pdf" extension
Additionally it will make a text file with the same name, but finishing in ".tab", that contains the slope, intercept and R² for each codon. Some additional plots are made based on this file

Usage: perl plot-codonusage-vs-tRNAgenes-V3.pl