|
Descripción
|
Program will make histograms and boxplots for the distribution of values of each column of several <data-files>
The list of <data-files> must be in the file <data-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
<gene_name> corresponds to the gene that has been analyzed. Will be used in plots names
Results files will be constructed based on the <results_base_name> and the names of each column and <gene_name>
A file with all plots will be saved to a file that additionally contains <summary_file_base_name>
Results will be saved in <Results_directory>. It must end with "/"
Additionally, the program adds an histogram. For that, the <Range> (size of bins), as well as the minimum value to count (<Beginning>) and the number of bins to include (<Steps>) must also be added to the command line. If <Beginning> is set to zero, please use 0.0 instead of 0.
This script requires the following modules
Statistics::Descriptive
Statistics::Ttest
Please consider that this script uses T-test to define statistical confidence of differences. This suppose a normal distribution of data. If your data is not normally distributed, please use codon_usage_by_gene_presence-ALL-Wilcoxon-V3.1.pl instead. 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-V3.1.pl <data-file> <results_base_name> <summary_file_base_name> <Results_directory> <Range> <Beginning> <Steps> |
.png)
