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Created with Raphaël 2.2.023Apr23Mar19225Feb22179852127Jan25222120191815131275417Dec1627Nov2625242320191716629Oct28272625Sep24177Aug415Jul1063130Jun2625231918171210910Apr9627Mar26111096543src/find_interaction_cluster/clip_figures/communities_similarities.py: removing print in is_overlapping method of partition classsrc/find_interaction_cluster/clip_figures/clip_analyser_fake_community.py: fix test in create_compo_figuressrc/figures_utils/exons_interactions.py: fix test in get_info_from_database functionsrc/db_utils/projects_metadata/get_fill_metadata.py: fix importrequirements.txt: updatesrc/find_interaction_cluster/clip_figures/clip_compo_analyser.py: modification to create on the component (nt, dnt, aa) enrichment for each factors analysedtests/files/exons.bed: header removedsrc/download_encode_eclip/merge_eclip.py: add a parameter level in create_merged_files function to filter within genes (without first and last exons) or within exons (extended by 200 nt at each side)src/download_encode_eclip/create_gene_bed.py: add a parameter level in create_gene_bed to choose ti create a bed containing genes without their first and last exons or a bed file containing exons (extended by 200 nt at both side) without the first and the last exonssrc/download_encode_eclip/config.py: add variable output_exontests/files/expression.txt: add an expression test filesrc/find_interaction_cluster/clip_figures/clip_compo_launcher.py: add a parameter expression_filesrc/find_interaction_cluster/clip_figures/clip_compo_analyser.py: changes to be able to use an expression file to filter out unexpressed genessrc/find_interaction_cluster/clip_figures/clip_launcher_4_many_communities.py: changes in select_community_file, create_figure function and creation of load_clip_folder_param function: allow to create community figure showing enrichement for gene/exon regulated (in splicing) by a splicing factorsrc/find_interaction_cluster/clip_figures/clip_analyser.py: add new functions get_ctrl_exon get_regulation_table and modification of create_table function to be able to make community figure based on exon/gene regulated in splicing by a splicing factorsrc/download_encode_eclip/merge_eclip.py: modification of merge_files function to filter onily the peaks with a score of 1000 and inside a gene (first and last exons not included)"src/download_encode_eclip/config.py: add a new variable 'output_gene'src/download_encode_eclip/create_gene_bed.py: script to create a bed file of human geneswithout the first and the last exonssrc/find_interaction_cluster/clip_figures/clip_compo_analyser.py: fix middle community analysissrc/find_interaction_cluster/clip_figures/clip_analyser_fake_community.py: script to create fake community based on the peak density of each genessrc/hic_TAD_caller/create_TAD_HiC_files/calling_tads.py: avoid merging adjacent TAD togethersrc/find_interaction_cluster/clip_figures/communities_similarities.py: Create the adjusted rand index heatmap of the differnts communitiessrc/find_interaction_cluster/clip_figures/clip_compo_analyser.py: the differents violins (enriched, imoverished) are now order in the figure with custom colorssrc/find_interaction_cluster/clip_figures/clip_analyser.py: fix bedtools intersect functionsrc/find_interaction_cluster/clip_figures/clip_compo_analyser.py: chnages and creation of new functionssrc/find_interaction_cluster/clip_figures/clip_compo_launcher.py: pep8 changessrc/find_interaction_cluster/clip_figures/clip_launcher_4_many_communities.py: chnage tiles in merge_figures function + pep8 changessrc/find_interaction_cluster/clip_figures/config.py: add arrowhead communitiessrc/download_encode_eclip/merge_eclip.py: modification of merge_files function to remove the heading chr in the first bed columnsrc/hic_TAD_caller/create_TAD_HiC_files/calling_tads.py: Add a step that merges the TADs before the liftoversrc/hic_TAD_caller/create_TAD_HiC_files/calling_tads.py: change in liftover and check_n_save_bed functionsrc/find_interaction_cluster/clip_figures/config.py: add communities and communities_name variablesrc/find_interaction_cluster/clip_figures/clip_launcher_4_many_communities.py: add pointsize argument in mantage commandsrc/find_interaction_cluster/tad_to_communities/config.py: Add target_gene and target_exon valuessrc/find_interaction_cluster/tad_to_communities/tad_to_communities.py: creation of functions targeted_tad_to_communities removing_chr and targeted_bedtools_intersect to convert custom TAD to communitiessrc/find_interaction_cluster/config.py: fix merge problem by re-creating function get_communities_basefilesrc/hic_TAD_caller/create_TAD_HiC_files/__main__.py: creation of a function launcher with a parameter resolutionsrc/hic_TAD_caller/create_TAD_HiC_files/calling_tads.py: add a parameter resolutionMerge branch 'master' into devsrc/find_interaction_cluster/clip_figures/clip_launcher_4_many_communities.py: create for each clip the community figures obtained using many community files