Index Symbols | A | B | C | D | F | G | H | M | P | R | S | T | V Symbols --download-example-data proksee-batch command line option --input proksee-batch command line option --output proksee-batch command line option --version proksee-batch command line option A add_bed_features_and_tracks() (in module proksee_batch.parse_additional_features) add_blast_features_and_tracks() (in module proksee_batch.parse_additional_features) add_gff_features_and_tracks() (in module proksee_batch.parse_additional_features) add_vcf_features_and_tracks() (in module proksee_batch.parse_additional_features) B BedFeatureDict (class in proksee_batch.parse_additional_features) BedMetaDict (class in proksee_batch.parse_additional_features) BlastFeatureDict (class in proksee_batch.parse_additional_features) BlastMetaDict (class in proksee_batch.parse_additional_features) C check_vcf_ref_vs_alt_genotypes() (in module proksee_batch.validate_input_data) check_vcf_seq_ids() (in module proksee_batch.validate_input_data) D download_example_genbank_files() (in module proksee_batch.download_example_input) download_example_input() (in module proksee_batch.download_example_input) download_file() (in module proksee_batch.download_example_input) download_genbank_file() (in module proksee_batch.download_example_input) F fasta_to_cgview_json() (in module proksee_batch.seq_file_to_cgview_json) FeatureDecorationDict (class in proksee_batch.parse_additional_features) G genbank_to_cgview_json() (in module proksee_batch.seq_file_to_cgview_json) generate_js_data() (in module proksee_batch.__main__) generate_report_html() (in module proksee_batch.generate_report_html) get_data_files() (in module proksee_batch.validate_input_data) get_description_from_metadata() (in module proksee_batch.__main__) get_feature_locations_and_scores_from_bed_features() (in module proksee_batch.parse_additional_features) get_feature_locations_and_scores_from_blast_features() (in module proksee_batch.parse_additional_features) get_feature_locations_and_scores_from_gff_features() (in module proksee_batch.parse_additional_features) get_feature_locations_and_scores_from_vcf_features() (in module proksee_batch.parse_additional_features) get_stats_from_seq_file() (in module proksee_batch.get_stats_from_seq_file) GffFeatureDict (class in proksee_batch.parse_additional_features) GffMetaDict (class in proksee_batch.parse_additional_features) H handle_error_exit() (in module proksee_batch.__main__) (in module proksee_batch.validate_input_data) M merge_cgview_json_with_template() (in module proksee_batch.merge_cgview_json_with_template) module proksee_batch proksee_batch.__main__ proksee_batch.download_example_input proksee_batch.generate_report_html proksee_batch.get_stats_from_seq_file proksee_batch.merge_cgview_json_with_template proksee_batch.parse_additional_features proksee_batch.seq_file_to_cgview_json proksee_batch.validate_input_data P parse_bed_files() (in module proksee_batch.parse_additional_features) parse_blast_files() (in module proksee_batch.parse_additional_features) parse_gff_files() (in module proksee_batch.parse_additional_features) parse_vcf_files() (in module proksee_batch.parse_additional_features) proksee-batch command line option --download-example-data --input --output --version proksee_batch module proksee_batch.__main__ module proksee_batch.download_example_input module proksee_batch.generate_report_html module proksee_batch.get_stats_from_seq_file module proksee_batch.merge_cgview_json_with_template module proksee_batch.parse_additional_features module proksee_batch.seq_file_to_cgview_json module proksee_batch.validate_input_data module R remove_problematic_characters_from_contig_name() (in module proksee_batch.seq_file_to_cgview_json) S seq_to_json_contig() (in module proksee_batch.seq_file_to_cgview_json) T TrackDict (class in proksee_batch.parse_additional_features) V validate_input_directory_contents() (in module proksee_batch.validate_input_data) VcfFeatureDict (class in proksee_batch.parse_additional_features) VcfMetaDict (class in proksee_batch.parse_additional_features)