Index

_

__init__() (gratools.Graph.AsyncGfaDatabase method) (gratools.logger_config.ThreadedRichHandler method) (gratools.useful_function.CustomCommand method) (gratools.useful_function.CustomGroup method)

A

add_start_bases_first_segment (gratools.Graph.SubGraph attribute) AsyncBedWriter (class in gratools.Graph)

AsyncGfaDatabase (class in gratools.Graph) available_sample_names (gratools.Gratools.Gratools property)

B

bam_path (gratools.Graph.GFA attribute) (gratools.Graph.GratoolsBam attribute) (gratools.Graph.SubGraph attribute) (gratools.Gratools.Gratools attribute) bam_segments_file (gratools.Graph.GFA attribute) (gratools.Gratools.Gratools attribute) batch_insert_links() (gratools.Graph.AsyncGfaDatabase method) bed_path (gratools.Graph.GFA attribute) (gratools.Graph.SubGraph attribute) (gratools.Gratools.Gratools attribute)

build_fasta() (gratools.Graph.SubGraph method) build_fasta_flag (gratools.Graph.SubGraph attribute) (gratools.Gratools.Gratools attribute) build_segments() (gratools.Graph.GratoolsBam method) (gratools.Graph.SubGraph method) build_walks() (gratools.Graph.SubGraph method)

C

chromosome_query (gratools.Graph.SubGraph attribute) (gratools.Gratools.Gratools attribute) close() (gratools.Graph.AsyncGfaDatabase method) (gratools.logger_config.ThreadedRichHandler method) command() (gratools.useful_function.CustomGroup method) compute_intersection() (gratools.Graph.SubGraph method)

compute_statistics() (gratools.Graph.GFA method) concatenate_and_generate_subgfa_file() (gratools.Gratools.Gratools method) configure_logger() (in module gratools.logger_config) connect() (gratools.Graph.AsyncGfaDatabase method) create_indexes() (gratools.Graph.AsyncGfaDatabase method) CustomCommand (class in gratools.useful_function) CustomGroup (class in gratools.useful_function)

D

db_file_path (gratools.Graph.GFA attribute) db_links (gratools.Graph.GFA attribute) debug (gratools.Gratools.Gratools attribute) degrees (gratools.Graph.GFA attribute) depth_nodes_stat() (gratools.Graph.GratoolsBam method) dict_gfa_graph_object (gratools.Gratools.Gratools attribute) dict_samples_bed (gratools.Graph.GFA attribute) dict_samples_chrom (gratools.Graph.GFA attribute) (gratools.Gratools.Gratools attribute) dict_segments_samples (gratools.Graph.GFA attribute) (gratools.Graph.SubGraph attribute)

dict_segments_sequence (gratools.Graph.SubGraph attribute) dict_segments_size (gratools.Graph.GFA attribute) disable_progress_flag (gratools.Graph.GFA attribute) (gratools.Graph.GratoolsBam attribute) (gratools.Gratools.Gratools attribute) display_available_sample_names() (gratools.Gratools.Gratools method) display_chromosomes_summary() (gratools.Gratools.Gratools method) display_full_chromosome_fragment_data() (gratools.Gratools.Gratools method) display_gfa_statistics() (gratools.Gratools.Gratools method) display_or_save_segments_by_depth() (gratools.Gratools.Gratools method)

E

emit() (gratools.logger_config.ThreadedRichHandler method) enqueue() (gratools.Graph.AsyncBedWriter method)

enqueue_single_line() (gratools.Graph.AsyncBedWriter method) export_nodes_to_csv() (gratools.Graph.GratoolsBam method) export_to_bandage_csv() (gratools.Gratools.Gratools method)

F

filter_bed_with_awk() (gratools.Graph.SubGraph method) find_children_and_grandchildren() (gratools.Graph.AsyncGfaDatabase method)

find_specific_groups_sample_position() (gratools.Gratools.Gratools method) flatten() (in module gratools.Gratools) found_minigraph (gratools.Graph.GFA attribute)

G

generate_combined_fasta_file() (gratools.Gratools.Gratools method) get_chr_pos() (gratools.Graph.SubGraph method) get_chromosome_size() (gratools.Gratools.Gratools method) get_chromosomes_summary_by_sample_df() (gratools.Gratools.Gratools method) get_gfa_statistics_df() (gratools.Gratools.Gratools method) get_help() (gratools.useful_function.CustomCommand method) (gratools.useful_function.CustomGroup method) get_segments_and_positions_by_depth() (gratools.Graph.GratoolsBam method) get_segments_by_depth() (gratools.Gratools.Gratools method) get_specific_and_shared_segments() (gratools.Graph.GratoolsBam method) get_subgraph() (gratools.Gratools.Gratools method) GFA (class in gratools.Graph) gfa_link_list (gratools.Graph.SubGraph attribute) gfa_name (gratools.Graph.GFA attribute) (gratools.Graph.GratoolsBam attribute) (gratools.Gratools.Gratools attribute)

gfa_path (gratools.Graph.GFA attribute) (gratools.Gratools.Gratools attribute) gfa_segment_list (gratools.Graph.SubGraph attribute) gfa_walk_list (gratools.Graph.SubGraph attribute) Gratools (class in gratools.Gratools) gratools.Graph module gratools.Gratools module gratools.logger_config module gratools.main module gratools.useful_function module GratoolsBam (class in gratools.Graph) gzip_gfa (gratools.Gratools.Gratools attribute)

H

header_gfa (gratools.Graph.GFA attribute)

header_gfa_file (gratools.Graph.GFA attribute) (gratools.Gratools.Gratools attribute)

I

import_links (gratools.Graph.GFA attribute) (gratools.Gratools.Gratools attribute) import_path (gratools.Gratools.Gratools attribute) index_bam() (gratools.Graph.GratoolsBam method) input_genome_size (gratools.Graph.GFA attribute)

intersect_bed (gratools.Graph.SubGraph attribute) intersected_results_by_regions (gratools.Graph.SubGraph attribute) inverted_links_count (gratools.Graph.GFA attribute) invoke() (gratools.useful_function.CustomCommand method) isolated_segments (gratools.Graph.GFA attribute)

L

line_type_counts (gratools.Graph.GFA attribute) link_count (gratools.Graph.GFA attribute) LinkInfo (class in gratools.Graph)

logger (gratools.Graph.GFA attribute) (gratools.Graph.GratoolsBam attribute) (gratools.Graph.SubGraph attribute) (gratools.Gratools.Gratools attribute)

M

max_walk_rank (gratools.Graph.GFA attribute) merge (gratools.Graph.SubGraph attribute) (gratools.Gratools.Gratools attribute) meta (gratools.Gratools.Gratools attribute) module gratools.Graph gratools.Gratools gratools.logger_config gratools.main gratools.useful_function

N

negative_links_count (gratools.Graph.GFA attribute)

O

offset_first (gratools.Graph.SubGraph attribute) offset_last (gratools.Graph.SubGraph attribute) orient_key_seg_1 (gratools.Graph.LinkInfo attribute)

orient_key_seg_2 (gratools.Graph.LinkInfo attribute) orient_seg_1 (gratools.Graph.LinkInfo attribute) orient_seg_2 (gratools.Graph.LinkInfo attribute) outdir (gratools.Gratools.Gratools attribute)

P

pan_ratio() (gratools.Graph.GratoolsBam method) parse_gfa() (gratools.Graph.GFA method) processed_sample_names (gratools.Graph.GFA attribute)

progress (gratools.Graph.GFA attribute) (gratools.Graph.GratoolsBam attribute) progress_dict (gratools.Graph.SubGraph attribute)

Q

query_links_by_segment() (gratools.Graph.AsyncGfaDatabase method)

R

RE_ORIENTED_SEG_GT_LT (gratools.Graph.GFA attribute) RE_ORIENTED_SEG_PLUS_MINUS (gratools.Graph.GFA attribute) regions (gratools.Graph.SubGraph attribute) reverse_complement_string() (in module gratools.useful_function)

run() (gratools.Graph.GFA method) run_depth_nodes_statistics() (gratools.Gratools.Gratools method) run_get_specific_groups_sample_analysis() (gratools.Gratools.Gratools method) run_pan_ratio_analysis() (gratools.Gratools.Gratools method)

S

sample_name (gratools.Graph.SubGraph attribute) sample_name_query (gratools.Graph.SubGraph attribute) (gratools.Gratools.Gratools attribute) sample_reference (gratools.Graph.GFA attribute) samples_chrom_file_path (gratools.Graph.GFA attribute) samples_chrom_file_writer (gratools.Graph.GFA attribute) samples_chrom_path (gratools.Gratools.Gratools attribute) save_available_sample_names() (gratools.Gratools.Gratools method) save_chromosomes_summary_by_sample() (gratools.Gratools.Gratools method) save_full_chromosome_fragment_data() (gratools.Gratools.Gratools method) save_gfa_statistics() (gratools.Gratools.Gratools method) save_header() (gratools.Graph.GFA method) seg_id_1 (gratools.Graph.LinkInfo attribute) seg_id_2 (gratools.Graph.LinkInfo attribute) segment_count (gratools.Graph.GFA attribute) segment_id_first (gratools.Graph.SubGraph attribute) segment_id_first_query (gratools.Graph.SubGraph attribute) segment_id_first_strand (gratools.Graph.SubGraph attribute) segment_id_last (gratools.Graph.SubGraph attribute) segment_id_last_query (gratools.Graph.SubGraph attribute)

segment_id_last_strand (gratools.Graph.SubGraph attribute) segment_id_set (gratools.Graph.SubGraph attribute) self_links_count (gratools.Graph.GFA attribute) sequences_list (gratools.Graph.SubGraph attribute) shared_executor (gratools.Graph.GFA attribute) shutdown() (gratools.Graph.AsyncBedWriter method) sort_file_in_place() (gratools.Graph.GFA method) start() (gratools.Graph.AsyncBedWriter method) start_query (gratools.Graph.SubGraph attribute) (gratools.Gratools.Gratools attribute) stats_file (gratools.Graph.GFA attribute) stats_gfa_file (gratools.Gratools.Gratools attribute) stop_processing() (gratools.logger_config.ThreadedRichHandler method) stop_query (gratools.Graph.SubGraph attribute) (gratools.Gratools.Gratools attribute) sub_graph_query (gratools.Gratools.Gratools attribute) SubGraph (class in gratools.Graph) suffix (gratools.Graph.GratoolsBam attribute) (gratools.Gratools.Gratools attribute) sum_rank0_length (gratools.Graph.GFA attribute)

T

tag() (gratools.Graph.GratoolsBam method) tag_bam() (gratools.Graph.GFA method) tagging (gratools.Graph.GratoolsBam attribute) task_id (gratools.Graph.SubGraph attribute) test_query_links() (gratools.Graph.AsyncGfaDatabase method)

ThreadedRichHandler (class in gratools.logger_config) threads (gratools.Graph.GFA attribute) (gratools.Graph.GratoolsBam attribute) (gratools.Gratools.Gratools attribute) total_segment_length (gratools.Graph.GFA attribute)

U

update_logger_file_suffix() (in module gratools.logger_config)

V

validate_percentage_or_int() (in module gratools.useful_function)

version (gratools.Graph.GFA attribute)

W

walks_count (gratools.Graph.GFA attribute) walks_info (gratools.Graph.GFA attribute) works_path (gratools.Graph.GFA attribute) (gratools.Graph.GratoolsBam attribute) (gratools.Graph.SubGraph attribute) (gratools.Gratools.Gratools attribute)