Index

Symbols

--build_fasta gratools-extract_sub_graph command line option --chr gratools-extract_sub_graph command line option gratools-get_fasta command line option --end gratools-extract_sub_graph command line option gratools-get_fasta command line option --filter_len gratools-segments_info command line option gratools-specific_and_shared_segments command line option --full gratools-show_chr command line option --gfa gratools-extract_sub_graph command line option gratools-get_fasta command line option gratools-segments_info command line option gratools-show_chr command line option gratools-show_samples command line option gratools-specific_and_shared_segments command line option --log-path gratools-extract_sub_graph command line option gratools-get_fasta command line option gratools-segments_info command line option gratools-show_chr command line option gratools-show_samples command line option gratools-specific_and_shared_segments command line option --no-build_fasta gratools-extract_sub_graph command line option --no-full gratools-show_chr command line option --sample gratools-extract_sub_graph command line option gratools-get_fasta command line option --sample_list_a_path gratools-specific_and_shared_segments command line option --sample_list_b_path gratools-specific_and_shared_segments command line option --samples_list gratools-extract_sub_graph command line option gratools-get_fasta command line option --shared_samples_min gratools-segments_info command line option --specific_samples_max gratools-segments_info command line option --start gratools-extract_sub_graph command line option gratools-get_fasta command line option --threads gratools-extract_sub_graph command line option gratools-get_fasta command line option gratools-segments_info command line option gratools-show_chr command line option gratools-show_samples command line option gratools-specific_and_shared_segments command line option --verbosity gratools-extract_sub_graph command line option gratools-get_fasta command line option gratools-segments_info command line option gratools-show_chr command line option gratools-show_samples command line option gratools-specific_and_shared_segments command line option

--version gratools command line option -c gratools-extract_sub_graph command line option gratools-get_fasta command line option -e gratools-extract_sub_graph command line option gratools-get_fasta command line option -f gratools-segments_info command line option gratools-specific_and_shared_segments command line option -g gratools-extract_sub_graph command line option gratools-get_fasta command line option gratools-segments_info command line option gratools-show_chr command line option gratools-show_samples command line option gratools-specific_and_shared_segments command line option -l gratools-extract_sub_graph command line option, [1] gratools-get_fasta command line option, [1] gratools-segments_info command line option gratools-show_chr command line option gratools-show_samples command line option gratools-specific_and_shared_segments command line option -s gratools-extract_sub_graph command line option gratools-get_fasta command line option gratools-specific_and_shared_segments command line option -sh gratools-segments_info command line option -sn gratools-extract_sub_graph command line option gratools-get_fasta command line option -sp gratools-segments_info command line option gratools-specific_and_shared_segments command line option -t gratools-extract_sub_graph command line option gratools-get_fasta command line option gratools-segments_info command line option gratools-show_chr command line option gratools-show_samples command line option gratools-specific_and_shared_segments command line option -v gratools command line option -vv gratools-extract_sub_graph command line option gratools-get_fasta command line option gratools-segments_info command line option gratools-show_chr command line option gratools-show_samples command line option gratools-specific_and_shared_segments command line option

A

apply_common_options() (in module gratools.main)

available_colors (in module gratools.logger_config)

B

bam_path (gratools.Graph.GFA attribute), [1] (gratools.Gratools.Gratools attribute), [1] bam_segments_file (gratools.Graph.GFA attribute), [1] (gratools.Gratools.Gratools attribute), [1] bed_path (gratools.Graph.GFA attribute), [1] (gratools.Gratools.Gratools attribute), [1]

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

C

chromosome (gratools.Graph.SubGraph attribute) (gratools.Gratools.Gratools attribute) ColoredFormatter (class in gratools.logger_config) common_options (in module gratools.main) compute_intersection() (gratools.Graph.SubGraph method)

concat_generate_sub_graph() (gratools.Gratools.Gratools method) configure_logger() (in module gratools.logger_config) configure_logging() (in module gratools.main) CONTEXT_SETTINGS (in module gratools.main) converter() (gratools.logger_config.ColoredFormatter method)

D

default_msec_format (gratools.logger_config.ColoredFormatter attribute) default_time_format (gratools.logger_config.ColoredFormatter attribute) description_tools (in module gratools.main) dict_link_SA_SB (gratools.Graph.GFA attribute) dict_samples_chrom (gratools.Graph.GFA attribute) (gratools.Gratools.Gratools attribute)

dict_segments_samples (gratools.Graph.GFA attribute) dict_segments_size (gratools.Graph.GFA attribute) display_chromosome_names() (gratools.Gratools.Gratools method) display_full_chromosome_data() (gratools.Gratools.Gratools method) display_sample_names() (gratools.Gratools.Gratools method)

E

extract_sub_graph (in module gratools.main)

extract_sub_graph() (gratools.Gratools.Gratools method)

F

flatten() (in module gratools.Gratools) format() (gratools.logger_config.ColoredFormatter method) formatException() (gratools.logger_config.ColoredFormatter method)

formatMessage() (gratools.logger_config.ColoredFormatter method) formatStack() (gratools.logger_config.ColoredFormatter method) formatTime() (gratools.logger_config.ColoredFormatter method)

G

generate_fasta() (gratools.Gratools.Gratools method) get_chr_pos() (gratools.Graph.SubGraph method) get_chromosome_data (gratools.Gratools.Gratools attribute) get_chromosome_size() (gratools.Gratools.Gratools method) get_chromosomes_by_sample (gratools.Gratools.Gratools attribute) get_fasta (in module gratools.main) get_sample_names (gratools.Gratools.Gratools attribute) GFA (class in gratools.Graph) gfa_name (gratools.Graph.GFA attribute), [1] (gratools.Gratools.Gratools attribute), [1] gfa_path (gratools.Graph.GFA attribute) (gratools.Gratools.Gratools attribute) Gratools (class in gratools.Gratools) gratools command line option --version -v gratools-extract_sub_graph command line option --build_fasta --chr --end --gfa --log-path --no-build_fasta --sample --samples_list --start --threads --verbosity -c -e -g -l, [1] -s -sn -t -vv gratools-get_fasta command line option --chr --end --gfa --log-path --sample --samples_list --start --threads --verbosity -c -e -g -l, [1] -s -sn -t -vv gratools-segments_info command line option --filter_len --gfa --log-path --shared_samples_min --specific_samples_max --threads --verbosity -f -g -l -sh -sp -t -vv

gratools-show_chr command line option --full --gfa --log-path --no-full --threads --verbosity -g -l -t -vv gratools-show_samples command line option --gfa --log-path --threads --verbosity -g -l -t -vv gratools-specific_and_shared_segments command line option --filter_len --gfa --log-path --sample_list_a_path --sample_list_b_path --threads --verbosity -f -g -l -s -sp -t -vv gratools.Graph module gratools.Gratools module gratools.logger_config module gratools.main module GratoolsBam (class in gratools.Graph) gzip_gfa (gratools.Gratools.Gratools attribute)

H

header_gfa (gratools.Graph.GFA attribute)

human_sort_key() (in module gratools.Graph)

I

index_bam() (gratools.Graph.GratoolsBam method)

intersect_bed (gratools.Graph.SubGraph attribute)

L

LinkInfo (class in gratools.Graph)

LOG_COLORS (in module gratools.logger_config) LOG_LEVELS (in module gratools.main)

M

main_command (in module gratools.main) module gratools.Graph gratools.Gratools gratools.logger_config gratools.main

P

parallelize_samples() (gratools.Gratools.Gratools method) parse_gfa() (gratools.Graph.GFA method)

process_sample() (gratools.Gratools.Gratools method) progress (gratools.Graph.SubGraph attribute)

S

sample_name (gratools.Graph.SubGraph attribute) (gratools.Gratools.Gratools attribute) sample_reference (gratools.Graph.GFA attribute), [1] samples_chrom_path (gratools.Gratools.Gratools attribute), [1] save_header() (gratools.Graph.GFA method) save_samples_bed() (gratools.Graph.GFA method) save_samples_chrom() (gratools.Graph.GFA method) segment_id_first (gratools.Graph.SubGraph attribute) segment_id_last (gratools.Graph.SubGraph attribute) segments_info (in module gratools.main) segments_info() (gratools.Graph.GratoolsBam method) (gratools.Gratools.Gratools method)

show_chr (in module gratools.main) show_samples (in module gratools.main) specific_and_shared_segments (in module gratools.main) specific_and_shared_segments() (gratools.Graph.GratoolsBam method) (gratools.Gratools.Gratools method) start (gratools.Graph.SubGraph attribute) (gratools.Gratools.Gratools attribute) stop (gratools.Graph.SubGraph attribute) (gratools.Gratools.Gratools attribute) SubGraph (class in gratools.Graph) suffix (gratools.Gratools.Gratools attribute)

T

tag() (gratools.Graph.GratoolsBam method) tag_bam() (gratools.Graph.GFA method)

task_id (gratools.Graph.SubGraph attribute) threads (gratools.Graph.GratoolsBam attribute) (gratools.Gratools.Gratools attribute)

U

update_logger_file_paths() (in module gratools.logger_config)

usesTime() (gratools.logger_config.ColoredFormatter method)

V

version (gratools.Graph.GFA attribute), [1]

W

works_path (gratools.Graph.GFA attribute), [1] (gratools.Gratools.Gratools attribute), [1]