Coverage report: 98%

Files Functions Classes

coverage.py v7.10.7, created at 2025-10-14 14:36 +0000

File function statements missing excluded coverage
binette/__init__.py (no function) 1 0 0 100%
binette/bin_manager.py Bin.__init__ 16 0 0 100%
binette/bin_manager.py Bin.contigs_key 1 0 0 100%
binette/bin_manager.py Bin.__eq__ 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.add_model 4 0 0 100%
binette/bin_manager.py Bin.checkm2_model 3 0 0 100%
binette/bin_manager.py Bin.contig_intersection 1 0 0 100%
binette/bin_manager.py Bin.contig_difference 1 0 0 100%
binette/bin_manager.py Bin.contig_union 1 0 0 100%
binette/bin_manager.py Bin.is_high_quality 3 0 0 100%
binette/bin_manager.py Bin.add_coding_density 4 1 0 75%
binette/bin_manager.py make_bins_from_bins_info 9 1 0 89%
binette/bin_manager.py get_bins_from_directory 9 0 0 100%
binette/bin_manager.py parse_bin_directories 5 0 0 100%
binette/bin_manager.py parse_contig2bin_tables 5 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 build_contig_index 5 0 0 100%
binette/bin_manager.py remove_bins_from_index 5 0 0 100%
binette/bin_manager.py select_best_bins 28 0 0 100%
binette/bin_manager.py get_contigs_in_bin_sets 11 0 0 100%
binette/bin_manager.py sum_contig_lengths 7 2 0 71%
binette/bin_manager.py create_intermediate_bins 65 6 0 91%
binette/bin_manager.py (no function) 45 0 0 100%
binette/bin_quality.py _initialize_keras_environment 10 2 0 80%
binette/bin_quality.py get_modelPostprocessing 5 0 0 100%
binette/bin_quality.py get_modelProcessing 5 0 0 100%
binette/bin_quality.py get_bins_metadata_df 31 0 0 100%
binette/bin_quality.py get_diamond_feature_per_bin_df 24 0 0 100%
binette/bin_quality.py calculate_KO_group 16 1 0 94%
binette/bin_quality.py calculate_module_completeness 14 1 0 93%
binette/bin_quality.py prepare_contig_sizes 5 0 0 100%
binette/bin_quality.py compute_N50 4 0 0 100%
binette/bin_quality.py add_bin_size_and_N50 7 0 0 100%
binette/bin_quality.py add_bin_coding_density 2 0 0 100%
binette/bin_quality.py add_bin_metrics 32 0 0 100%
binette/bin_quality.py add_bin_metrics._process_sequential 3 0 0 100%
binette/bin_quality.py add_bin_metrics.process_chunk 5 0 0 100%
binette/bin_quality.py chunks 2 0 0 100%
binette/bin_quality.py balanced_chunks 15 1 0 93%
binette/bin_quality.py assess_bins_quality 15 2 0 87%
binette/bin_quality.py _assess_bins_quality_batch 21 0 0 100%
binette/bin_quality.py (no function) 34 0 0 100%
binette/cds.py get_contig_from_cds_name 1 0 0 100%
binette/cds.py predict 8 0 0 100%
binette/cds.py get_contig_coding_len 6 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 5 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) 23 0 0 100%
binette/contig_manager.py parse_fasta_file 2 0 0 100%
binette/contig_manager.py make_contig_index 2 0 0 100%
binette/contig_manager.py apply_contig_index 1 0 0 100%
binette/contig_manager.py (no function) 6 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 12 0 0 100%
binette/diamond.py (no function) 13 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 25 1 0 96%
binette/io_manager.py write_bins_fasta.flush_buffer 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_contig2bin_table 9 0 0 100%
binette/io_manager.py write_original_bin_metrics 10 0 0 100%
binette/io_manager.py (no function) 16 0 0 100%
binette/main.py version_callback 5 1 0 80%
binette/main.py setup_logging 11 0 0 100%
binette/main.py verbose_callback 1 0 0 100%
binette/main.py quiet_callback 1 0 0 100%
binette/main.py preprocess_args 19 0 0 100%
binette/main.py parse_input_files 26 0 0 100%
binette/main.py manage_protein_alignement 21 2 0 90%
binette/main.py log_selected_bin_info 7 0 0 100%
binette/main.py binette 67 0 0 100%
binette/main.py main 2 0 0 100%
binette/main.py (no function) 26 0 0 100%
Total   993 22 0 98%

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