In this document I will explain how to use the software contained in this project.

The easiest way to run the project is to execute the script named 'main.py'. The defaults that are provided are sufficient to run the project with the inputs provided. Each accompanying script can be run on its own as well. main.py does not allow for the intermediate files or folders to be renamed by the user. Currently the user cannot select the point that analysis begins at through main.py, but this functionality will be added later.

./main.py -h usage: main.py [-h] [-i FILE] [-I FOLDER] [-o FOLDER] [-f FILE] [-n INT] [-m INT] [-g INT] [-e FLOAT]

The purpose of this script is to run the full software suite that we have developed to study operons using as few inputs as possible. This will facilitate the ease of use as much as possible.

optional arguments: -h, --help show this help message and exit -i FILE, --infile FILE Input file for the operon query step of the pipeline. -I FOLDER, --infolder FOLDER Folder containing all genbank files for use by the program. -o FOLDER, --outfolder FOLDER Folder where results will be stored. -f FILE, --filter FILE File restrictiong which accession numbers this script will process. If no file is provided, filtering is not performed. -n INT, --num_proc INT Number of processors that you want this script to run on. The default is every CPU that the system has. -m INT, --min_genes INT Minum number of genes that an operon must contain before it can be considered for further analysis. The default is 5 because that is what we are currently using in the study. -g INT, --max_gap INT Size in nucleotides of the maximum gap allowed between genes to be considered neighboring. The default is 500. -e FLOAT, --eval FLOAT eval for the BLAST search.