src/find_interaction_cluster/nt_and_community.py: modifications to add the control used for each community in every figure

src/find_interaction_cluster/colocalisation_n_ppi_analysis.py: removing the duplicates in final file

src/find_interaction_cluster/colocalisation_n_ppi_analysis.py: comparison of string scores between couples of genes that are in the same community (at dna level)

src/find_interaction_cluster/nt_and_community.py: fix create_and_save_ctrl_dataframe by deleting outfile parameter

src/find_interaction_cluster/nt_and_community.py: add functions for barplot creation and refactoring of get_stat_nt_communities functions

src/find_interaction_cluster/nt_and_community.py: change in output folder from sf_community_enrichment to community_enrichment

src/find_interaction_cluster/*.py: replace list parameters weights and global_weights by int paramet weight and global_weight

src/find_interaction_cluster/create_ppi_files.py: fix filter_most_overllaping_ppi to correct community size and nb_com-ppi columns

src/find_interaction_cluster/create_ppi_files.py: modification to call the new functions created in src/find_interaction_cluster/radomization_test_ppi.py

src/find_interaction_cluster/radomization_test_ppi.py: add 3 functions to check if the number communities that are enriched in common genes between dna and protein level is also enriched

src/find_interaction_cluster/create_ppi_files.py: scripts that check if communities of genes interacting at DNA level are more similar at protein level than randomly expected

creation of a file linking protein and the fasterDB gene id encoding them from a file containing ensembl! id for genes and their protein in hg19

modification of get_community_file function to be able to chose the subfolder in which we want to create file

src/find_interaction_cluster/ppi_scripts/*.py: scripts to create a file containing string ppi file with fasterdb gene id

src/nt_composition/make_nt_correlation.py: add a distance parameter into get_project_colocalisation function to recover only interaction far from at least 10kb

src/db_utils/*.py: modifications to add a column region in cin_gene_frequency to have the frequency of feature inside the entire genes, their introns and exons

src/nt_composition/make_nt_correlation.py: modification of get_project_colocalisation function by adding a parameter level

src/find_interaction_cluster/nt_and_community.py: add a script allowing to create a control community to see if the communities are different from the rest of the genes/exons not in a community

db_utils/interactions/features_interactions.py: removal of completely overlapping anchors, genes and exons

db_utils/interactions/features_interactions.py: replace distance (null) with 0 for exons that have different IDs, but identical coordinates

db_utils/interactions/config_interactions.py: modifications to allow to add the distance between genes or exons in pairwise interactions

db_utils/db_creation.py: modifications to add the distance information in the tables cin_gene_interaction and cin_exon_interaction