src/nt_composition/{__main__.py, distance.py, make_nt_correlation}: add a parameter level to study exons but also genes

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

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/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

src/nt_composition/make_nt_correlation.py: creation of new functions to create the correlation between the frequency of nucleotides within an exon and either the mean frequency of every co-localized exons or the frequency of nucleotide of one

src/nt_composition/make_nt_correlation.py: creation of get_select_addition and modification of get_project_colocalisation to get the weight of the edges in the network if needed

src/nt_composition/make_nt_correlation.py: add the parameter ft_type when get_density_recap is called in create_all_frequency_figures

src/nt_composition/make_nt_correlation.py: creation of a get_dic_co_regulated_exon, deletion of get_all_exon_interacting_with_another and get_interacting_exon and modification of create_density_table to get all co-localized exon interacting with another more efficiently

src/nt_composition/make_nt_correlation.py: modification of get_project_colocalisation function to keep or not the co-localisation comming from the same gene. And deletion of remove_exonsrc/nt_composition/make_nt_correlation.pyin_the_same_gene function

src/nt_composition/get_projects_interaction.py: add a new parameter, same_gene to choose whether or not to keep the co-localised exons within the same gene + modification of get_interaction_by_project function to use this new parameter

src/nt_composition/make_nt_correlation.py src/nt_composition/__main__.py: Creation of a new parameter same_gene allowing to remove or keep the co-localisation within the same gene

src/nt_composition/make_nt_correlation.py src/nt_composition/__main__.py: Add the parameters ft_type to chose the kind of feature to analyse

src/nt_composition/config.py : Creation of a get_feature function to recover the feature of interest

src/nt_composition/make_nt_correlation.py: add a global weight parameters to combine projects co-localisations

src/nt_composition/config.py: Creation of get_interaction_file and get_weight_folder function + modification of get_density_file and get_density_recap function

src/nt_composition/make_nt_correlation.py: takes now a weight corresponding to the number of time an interaction must be seen to be taken into account

src/nt_composition/get_projects_interaction.py: takes now a weight corresponding to the number of time an interaction must be seen to be taken into account

src/nt_composition/make_nt_correlation.py: Modification of create_all_frequency_figure to make the density figure for all chIA-PET projets

src/nt_composition/make_nt_correlation.py: creation of a script that create density figures to see if regulated exons have the same composition as their co-localized exons