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

features_interactions.py: modifications to add the distance between genes or exons in pairwise interactions

src/find_interaction_cluster/nt_and_community.py: creation of a script to check if the nucleotide frequency is not randomly distributed amongs communities of exons

src/find_interaction_cluster/sf_and_communities.py: creation of expand_dataframe, glmm_maker and glmm_statistics to see if the regulation of exons by a splicing factor between communities is not random

src/find_interaction_cluster/sf_and_communities.py: fix get_stat4communities to keep the same community names

move get_community from src/find_interaction_cluster/community_finder.py to src/find_interaction_cluster/config.py

src/nt_composition/__main__.py: addition of parameter community_size to limit nt frequency analysis to only exons located in large community of co-regulated exons. This parameter can be set to -1 for using the old behavior

src/nt_composition/make_nt_correlation.py: major modification corresponding to the addition of the parameter community_size to limit nt frequency analysis to only exons located in large community of co-regulated exons. This parameter can be set to -1 for using the old behavior

src/nt_composition/distance.py: modification of create_all_distance_figures to only concider good ChIA-PET projects + modification of compute_controls_distances, add_in_dic, create_distance_table to create a table saying how many interaction are located in control and test groups

src/nt_composition/config.py: add the parameter community_size in get_weight_folder, get_density_file and get_density_recap functions. This parameter corresponds to the minimum size of community for which we want to concider the exons it contains. None if we don't want this filter