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

src/fig_utils/stat_annot.py: new parameter min_pval that allow to define the minimum p-value to display on the figure

src/find_interaction_cluster/community_finder.py: add multiple_stat_launcher function that is written in sf_and_communities.py file

src/find_interaction_cluster/community_finder.py: fix get_communities function and add some loggin ddebug display in community_finder

src/find_interaction_cluster/sf_and_communities.py: script allowing to check if exons regulated by the sample splicing factor are co-localized

src/find_interaction_cluster/install_hipMCL.py: display logging message when tring to download and install hipmcl

src/find_interaction_cluster/__main__.py: launch installation of hipMCL before searching for communities

src/find_interaction_cluster/config.py: creation of three new variables get_hip_folder, get_hipmcl_prog and hip_zip

src/nt_composition/__main__.py: modification of launcher function to either launch create_all_frequency_figures or create_all_distance_figures based on input parameters

src/nt_composition/config.py: modification of get_density_file by adding a new parameter king to distinguish between density and distance figure

src/nt_composition/distance.py: script to check whether the co-localised exons have a nucleotide distance lower than randomly expected