codon_usage_by_gene_presence-ALL-Wilcoxon-V3.1.pl

Program will make histograms and boxplots for the distribution of values of each column of several
The list of must be in the file
its format must be:
lines beginning with # are not considered
first line not starting with # must have a single file containing the codon usages in all genomes format like in file average-b.txt
following lines (not starting with #) must have three fields separated by tabs:
First field : name of the gene
Second field: first file, has data for genomes with the gene
Third field : second file, has data for genomes withOUT the gen

All data files need to be in the same format. Data divided be tab separated columns
First line starts with "#" and indicates the name of each field

corresponds to the gene that has been analyzed. Will be used in plots names
Results files will be constructed based on the and the names of each column and
A file with all plots will be saved to a file that additionally contains
Results will be saved in . It must end with "/"

Additionally, the program adds an histogram. For that, the (size of bins), as well as the minimum value to count () and the number of bins to include () must also be added to the command line. If is set to zero, please use 0.0 instead of 0.

This script requires the following modules
Statistics::Descriptive
Statistics::Test::WilcoxonRankSum
This script do not suppose normal distribution as it uses Wilcoxon Rank Sum test. P value is set to 0.00005. If a different value is required, please change the variable $pvalue accordingly.

Usage: perl codon_usage_by_gene_presence-ALL-Wilcoxon-V3.1.pl