HOW TO RUN:

• 1: ./make
• 2: ./neighborhood_comparer

full --> default execution
-e --execution_mode full
-n --neighborhoods_filename "File containing the genomic neighborhoods"
-s --prot_sim_filename "File containing pairs of proteins and their similarities"
-f --formatted_prot_filename "File already formatted as the input for the homology detection method"
-p --protein_comparing "Method for comparing proteins (default: nc)"
-t --prot_stringency "Minimum similarity required to treat two proteins as a related pair (default 0)"
-r --neigh_stringency "Minimum threshold to display the similarity between two neighborhoods (default 0)"
-g --neigh_comparing "Method for comparing genomic neighborhoods (default: porthodom method)"
-o --output "Where the neighborhood similarities should be written (outputs do stdout if the filename is - or if not used)" -a --pairings_filename "Where the chosen pairings between proteins in the neighborhoods should be written (if not specified, does not generate a pairings file)"

partial --> Already has the similarities between the proteins.
-e --execution_mode partial
-n --neighborhoods_filename
-s --prot_sim_filename
-l --normalize_prot_sim" "Indicates that the protein similarities file should be normalized" -t --prot_stringency
-r --neigh_stringency "Minimum threshold to display the similarity between two neighborhoods" -g --neigh_comparing
-o --output
-a --pairings_filename "Where the chosen pairings between proteins in the neighborhoods should be written"

Help option: -h --help
protein scoring methods: nc. neighborhood scoring methods: porthodom, porthodomO2.

Output format: "accession1 cds_begin1 cds_end1 accession2 cds_begin2 cds_end2 score"
Pairings format: ">accession1 cds_begin1 cds_end1 accession2 cds_begin2 cds_end2 prot1 prot2 sim"

NOTE: the number of unique proteins in the prot_sim_filename or in the formatted_prot_filename can't be bigger than the number of unique proteins in the neighborhoods_filename.

To add a new neighborhood scoring method: include the file containing the scoring function in genome_grouping.h, add a new "if else" clause at the genome_clustering function in the genome_grouping.cpp file comparing the genomic neighborhoods using the new scoring function. Add new files to Makefile.