plot-codonusage-vs-GC-V3-High_expression-vs-all-genes.pl

Program will take data on files and and make plots comparing codon usage with frequency of nucleotides in genomes. First line in each file has to be commented and indicate the column titles. This line must use the same titles as given by previous scripts so that the program can recognize them. Also, both files must use the same names for fields. Each file should contain the columns presenting the usage of each codon as well as columns presenting the content of each nucleotide. In linux, you can use the paste command to construct this file pasting the average codon file and the GC content files produced by the following scripts:
Codon_statistics-V2.pl
AGCT_count_V2.pl
For example:
paste average-b.txt genomic_AGCT.tab > usage-genomic_AGCT.tab
Results files will use the to construct result files in
This program calculate linear regression using perl “Statistics::LineFit” module and uses GnuPlot to construct plots. Both must 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

Usage: perl plot-codonusage-vs-GC-V3-High_expression-vs-all-genes.pl