Coverage report: 98%

Files Functions Classes

coverage.py v7.6.1, created at 2025-01-06 19:22 +0000

File function statements missing excluded coverage
binette/__init__.py (no function) 1 0 0 100%
binette/bin_manager.py Bin.__init__ 12 0 0 100%
binette/bin_manager.py Bin.__eq__ 1 0 0 100%
binette/bin_manager.py Bin.__hash__ 1 0 0 100%
binette/bin_manager.py Bin.__str__ 1 0 0 100%
binette/bin_manager.py Bin.overlaps_with 1 0 0 100%
binette/bin_manager.py Bin.add_length 3 0 0 100%
binette/bin_manager.py Bin.add_N50 3 0 0 100%
binette/bin_manager.py Bin.add_quality 3 0 0 100%
binette/bin_manager.py Bin.intersection 5 0 0 100%
binette/bin_manager.py Bin.difference 5 0 0 100%
binette/bin_manager.py Bin.union 5 0 0 100%
binette/bin_manager.py Bin.is_complete_enough 3 1 0 67%
binette/bin_manager.py Bin.is_high_quality 3 1 0 67%
binette/bin_manager.py get_bins_from_directory 9 0 0 100%
binette/bin_manager.py parse_bin_directories 9 1 0 89%
binette/bin_manager.py parse_contig2bin_tables 9 0 0 100%
binette/bin_manager.py get_bins_from_contig2bin_table 14 0 0 100%
binette/bin_manager.py from_bins_to_bin_graph 5 0 0 100%
binette/bin_manager.py get_all_possible_combinations 1 0 0 100%
binette/bin_manager.py get_intersection_bins 10 1 0 90%
binette/bin_manager.py get_difference_bins 11 1 0 91%
binette/bin_manager.py get_union_bins 12 1 0 92%
binette/bin_manager.py select_best_bins 11 0 0 100%
binette/bin_manager.py group_identical_bins 4 0 0 100%
binette/bin_manager.py dereplicate_bin_sets 9 0 0 100%
binette/bin_manager.py get_contigs_in_bin_sets 11 0 0 100%
binette/bin_manager.py get_contigs_in_bins 1 0 0 100%
binette/bin_manager.py rename_bin_contigs 3 0 0 100%
binette/bin_manager.py create_intermediate_bins 19 0 0 100%
binette/bin_manager.py (no function) 38 0 0 100%
binette/bin_quality.py get_bins_metadata_df 15 0 0 100%
binette/bin_quality.py get_diamond_feature_per_bin_df 23 0 0 100%
binette/bin_quality.py compute_N50 9 0 0 100%
binette/bin_quality.py add_bin_size_and_N50 5 0 0 100%
binette/bin_quality.py add_bin_metrics 11 0 0 100%
binette/bin_quality.py chunks 2 0 0 100%
binette/bin_quality.py assess_bins_quality_by_chunk 6 0 0 100%
binette/bin_quality.py assess_bins_quality 24 0 0 100%
binette/bin_quality.py (no function) 20 0 0 100%
binette/cds.py get_contig_from_cds_name 1 0 0 100%
binette/cds.py predict 10 0 0 100%
binette/cds.py predict_genes 1 0 0 100%
binette/cds.py write_faa 4 0 0 100%
binette/cds.py is_nucleic_acid 4 0 0 100%
binette/cds.py parse_faa_file 11 0 0 100%
binette/cds.py get_aa_composition 4 0 0 100%
binette/cds.py get_contig_cds_metadata_flat 6 0 0 100%
binette/cds.py get_contig_cds_metadata 12 0 0 100%
binette/cds.py filter_faa_file 17 0 0 100%
binette/cds.py (no function) 20 0 0 100%
binette/contig_manager.py parse_fasta_file 2 0 0 100%
binette/contig_manager.py make_contig_index 3 0 0 100%
binette/contig_manager.py apply_contig_index 1 0 0 100%
binette/contig_manager.py (no function) 5 0 0 100%
binette/diamond.py get_checkm2_db 13 0 0 100%
binette/diamond.py check_tool_exists 2 0 0 100%
binette/diamond.py run 10 0 0 100%
binette/diamond.py get_contig_to_kegg_id 9 0 0 100%
binette/diamond.py (no function) 12 0 0 100%
binette/io_manager.py get_paths_common_prefix_suffix 26 1 0 96%
binette/io_manager.py infer_bin_set_names_from_input_paths 17 0 0 100%
binette/io_manager.py write_bin_info 13 0 0 100%
binette/io_manager.py write_bins_fasta 6 0 0 100%
binette/io_manager.py check_contig_consistency 5 0 0 100%
binette/io_manager.py check_resume_file 10 0 0 100%
binette/io_manager.py write_original_bin_metrics 10 0 0 100%
binette/io_manager.py (no function) 14 0 0 100%
binette/main.py init_logging 8 1 0 88%
binette/main.py UniqueStore.__call__ 3 0 0 100%
binette/main.py is_valid_file 4 0 0 100%
binette/main.py parse_arguments 21 0 0 100%
binette/main.py parse_input_files 20 0 0 100%
binette/main.py manage_protein_alignement 19 2 0 89%
binette/main.py select_bins_and_write_them 19 0 0 100%
binette/main.py log_selected_bin_info 7 0 0 100%
binette/main.py main 42 4 0 90%
binette/main.py (no function) 18 0 0 100%
Total   747 14 0 98%

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