GraTools
Quick Start Guide
Install GraTools
Install the lastest GraTools release (Recommended)
Install the development version from github
Verify the installation
Command List and Help
Using GraTools
stats
list_samples
list_chr
extract_subgraph
get_fasta
core_dispensable_ratio
get_segments_by_depth
depth_nodes_stat
specific_groups_sample
Typical Workflow
Testing GraTools
Troubleshooting
Further Assistance
Advanced Usage
GraTools: A Pangenome GFA Toolkit
Available Subcommands
Command Reference
gratools index
Options
Usage Examples
What
index
Does
gratools stats
Options
Usage Examples
Stats Explained
Graph Overview
Segment Statistics
Link Statistics
Path (Walk) Statistics
Segment Sharing & Depth
Graph Structure
gratools list_samples
Options
Usage Examples
gratools list_chr
Options
Usage Examples
gratools extract_subgraph
Options
Usage Examples
Extracting a subgraph for a specific region
Extracting a subgraph for a specific region and generate a FASTA file from the subgraph
Extracting a subgraph for a list of samples provided in a file
Illustrated Example
The
–merge-dist
Option Explained
gratools get_fasta
Options
Usage Examples
Extracting a sequence for a specific sample and region
Extracting sequences for all samples included in the graph
Extracting sequences for a list of samples provided in a file
Illustrated Example
gratools core_dispensable_ratio
Options
Usage Examples
Displays the ratio of core and dispensable segments
Illustrated Example
gratools get_segments_by_depth
Options
Usage Examples
List segments shared by a number of individuals and save to a file
List core segments (by percentage) and display them in the terminal
Illustrated Example
gratools depth_nodes_stat
Options
Usage Examples
Display statistics about the node depth
gratools specific_groups_sample
Options
Complete Usage Example
Illustrated Example
gratools shell_completion
Introduction
Options
Setup Instructions
How to Use Shell Completion
GraTools for developers
gratools Package
Functions
configure_logger
update_logger_file_suffix
validate_percentage_or_int
Classes
AsyncGfaDatabase
SubGraph
GFA
GratoolsBam
ThreadedRichHandler
CustomCommand
CustomGroup
GraTools
Index
Edit on GitLab
Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
_
__call__() (gratools.CustomCommand method)
(gratools.CustomGroup method)
A
acquire() (gratools.ThreadedRichHandler method)
add_command() (gratools.CustomGroup method)
add_multiple_commands() (gratools.CustomGroup method)
add_section() (gratools.CustomGroup method)
add_start_bases_first_segment (gratools.SubGraph attribute)
addFilter() (gratools.ThreadedRichHandler method)
allow_extra_args (gratools.CustomCommand attribute)
(gratools.CustomGroup attribute)
allow_interspersed_args (gratools.CustomCommand attribute)
(gratools.CustomGroup attribute)
AsyncGfaDatabase (class in gratools)
B
bam_path (gratools.GFA attribute)
bam_segments_file (gratools.GFA attribute)
batch_insert_links() (gratools.AsyncGfaDatabase method)
bed_path (gratools.GFA attribute)
build_fasta() (gratools.SubGraph method)
build_fasta_flag (gratools.SubGraph attribute)
build_segments() (gratools.GratoolsBam method)
(gratools.SubGraph method)
build_walks() (gratools.SubGraph method)
C
chromosome_query (gratools.SubGraph attribute)
close() (gratools.AsyncGfaDatabase method)
(gratools.ThreadedRichHandler method)
collect_usage_pieces() (gratools.CustomCommand method)
(gratools.CustomGroup method)
command() (gratools.CustomGroup method)
command_class (gratools.CustomGroup attribute)
compute_intersection() (gratools.SubGraph method)
compute_statistics() (gratools.GFA method)
configure_logger() (in module gratools)
connect() (gratools.AsyncGfaDatabase method)
core_dispensable_ratio() (gratools.GratoolsBam method)
create_indexes() (gratools.AsyncGfaDatabase method)
createLock() (gratools.ThreadedRichHandler method)
CustomCommand (class in gratools)
CustomGroup (class in gratools)
D
db_file_path (gratools.GFA attribute)
db_links (gratools.GFA attribute)
depth_nodes_stat() (gratools.GratoolsBam method)
E
emit() (gratools.ThreadedRichHandler method)
export_nodes_to_csv() (gratools.GratoolsBam method)
F
filter() (gratools.ThreadedRichHandler method)
filter_bed_with_awk() (gratools.SubGraph method)
find_children_and_grandchildren() (gratools.AsyncGfaDatabase method)
flush() (gratools.ThreadedRichHandler method)
format() (gratools.ThreadedRichHandler method)
format_aliases() (gratools.CustomCommand method)
(gratools.CustomGroup method)
format_commands() (gratools.CustomGroup method)
format_constraints() (gratools.CustomCommand method)
(gratools.CustomGroup method)
format_epilog() (gratools.CustomCommand method)
(gratools.CustomGroup method)
format_help() (gratools.CustomCommand method)
(gratools.CustomGroup method)
format_help_text() (gratools.CustomCommand method)
(gratools.CustomGroup method)
format_options() (gratools.CustomCommand method)
(gratools.CustomGroup method)
format_params() (gratools.CustomCommand method)
(gratools.CustomGroup method)
format_subcommand_aliases() (gratools.CustomGroup static method)
format_subcommand_name() (gratools.CustomGroup method)
format_usage() (gratools.CustomCommand method)
(gratools.CustomGroup method)
found_minigraph (gratools.GFA attribute)
G
get_argument_help_record() (gratools.CustomCommand method)
(gratools.CustomGroup method)
get_arguments_help_section() (gratools.CustomCommand method)
(gratools.CustomGroup method)
get_chr_pos() (gratools.SubGraph method)
get_command() (gratools.CustomGroup method)
get_default_option_group() (gratools.CustomCommand method)
(gratools.CustomGroup method)
get_help() (gratools.CustomCommand method)
(gratools.CustomGroup method)
get_help_option() (gratools.CustomCommand method)
(gratools.CustomGroup method)
get_help_option_names() (gratools.CustomCommand method)
(gratools.CustomGroup method)
get_level_text() (gratools.ThreadedRichHandler method)
get_name() (gratools.ThreadedRichHandler method)
get_normalized_epilog() (gratools.CustomCommand method)
(gratools.CustomGroup method)
get_param_by_name() (gratools.CustomCommand method)
(gratools.CustomGroup method)
get_params() (gratools.CustomCommand method)
(gratools.CustomGroup method)
get_params_by_name() (gratools.CustomCommand method)
(gratools.CustomGroup method)
get_segments_and_positions_by_depth() (gratools.GratoolsBam method)
get_short_help_str() (gratools.CustomCommand method)
(gratools.CustomGroup method)
get_specific_and_shared_segments() (gratools.GratoolsBam method)
get_ungrouped_options() (gratools.CustomCommand method)
(gratools.CustomGroup method)
get_usage() (gratools.CustomCommand method)
(gratools.CustomGroup method)
GFA (class in gratools)
gfa_name (gratools.GFA attribute)
(gratools.GratoolsBam attribute)
gratools
module
,
[1]
gratools.Graph
module
gratools.Gratools
module
gratools.logger_config
module
gratools.main
module
gratools.useful_function
module
GratoolsBam (class in gratools)
group() (gratools.CustomGroup method)
group_class (gratools.CustomGroup attribute)
H
handle() (gratools.ThreadedRichHandler method)
handle_bad_command_name() (gratools.CustomGroup method)
handleError() (gratools.ThreadedRichHandler method)
header_gfa_file (gratools.GFA attribute)
I
ignore_unknown_options (gratools.CustomCommand attribute)
(gratools.CustomGroup attribute)
index_bam() (gratools.GratoolsBam method)
index_links (gratools.GFA attribute)
input_genome_size (gratools.GFA attribute)
intersect_bed (gratools.SubGraph attribute)
intersected_results_by_regions (gratools.SubGraph attribute)
inverted_links_count (gratools.GFA attribute)
invoke() (gratools.CustomCommand method)
(gratools.CustomGroup method)
K
KEYWORDS (gratools.ThreadedRichHandler attribute)
L
link_count (gratools.GFA attribute)
list_commands() (gratools.CustomGroup method)
list_sections() (gratools.CustomGroup method)
M
main() (gratools.CustomCommand method)
(gratools.CustomGroup method)
make_commands_help_section() (gratools.CustomGroup method)
make_context() (gratools.CustomCommand method)
(gratools.CustomGroup method)
make_option_group_help_section() (gratools.CustomCommand method)
(gratools.CustomGroup method)
make_parser() (gratools.CustomCommand method)
(gratools.CustomGroup method)
max_walk_rank (gratools.GFA attribute)
merge (gratools.SubGraph attribute)
module
gratools
,
[1]
gratools.Graph
gratools.Gratools
gratools.logger_config
gratools.main
gratools.useful_function
must_align_option_groups() (gratools.CustomCommand method)
(gratools.CustomGroup method)
must_align_sections() (gratools.CustomGroup method)
must_show_constraints() (gratools.CustomCommand method)
(gratools.CustomGroup method)
must_show_subcommand_aliases() (gratools.CustomGroup method)
N
name (gratools.ThreadedRichHandler attribute)
negative_links_count (gratools.GFA attribute)
O
offset_first (gratools.SubGraph attribute)
offset_last (gratools.SubGraph attribute)
P
parse_args() (gratools.CustomCommand method)
(gratools.CustomGroup method)
parse_gfa() (gratools.GFA method)
progress (gratools.GFA attribute)
progress_dict (gratools.SubGraph attribute)
Q
query_links_by_segment() (gratools.AsyncGfaDatabase method)
R
regions (gratools.SubGraph attribute)
release() (gratools.ThreadedRichHandler method)
removeFilter() (gratools.ThreadedRichHandler method)
render() (gratools.ThreadedRichHandler method)
render_message() (gratools.ThreadedRichHandler method)
resolve_command() (gratools.CustomGroup method)
resolve_command_name() (gratools.CustomGroup method)
result_callback() (gratools.CustomGroup method)
run() (gratools.GFA method)
S
sample_name (gratools.SubGraph attribute)
sample_name_query (gratools.SubGraph attribute)
sample_reference (gratools.GFA attribute)
save_header() (gratools.GFA method)
save_samples_chrom() (gratools.GFA method)
section() (gratools.CustomGroup method)
segment_count (gratools.GFA attribute)
segment_id_first (gratools.SubGraph attribute)
segment_id_first_query (gratools.SubGraph attribute)
segment_id_first_strand (gratools.SubGraph attribute)
segment_id_last (gratools.SubGraph attribute)
segment_id_last_query (gratools.SubGraph attribute)
segment_id_last_strand (gratools.SubGraph attribute)
self_links_count (gratools.GFA attribute)
set_name() (gratools.ThreadedRichHandler method)
setFormatter() (gratools.ThreadedRichHandler method)
setLevel() (gratools.ThreadedRichHandler method)
shared_executor (gratools.GFA attribute)
shell_complete() (gratools.CustomCommand method)
(gratools.CustomGroup method)
SHOW_SUBCOMMAND_ALIASES (gratools.CustomGroup attribute)
start_query (gratools.SubGraph attribute)
stats_file (gratools.GFA attribute)
stop_processing() (gratools.ThreadedRichHandler method)
stop_query (gratools.SubGraph attribute)
SubGraph (class in gratools)
suffix (gratools.GratoolsBam attribute)
sum_rank0_length (gratools.GFA attribute)
T
tag() (gratools.GratoolsBam method)
tag_bam() (gratools.GFA method)
tagging (gratools.GratoolsBam attribute)
task_id (gratools.SubGraph attribute)
test_query_links() (gratools.AsyncGfaDatabase method)
ThreadedRichHandler (class in gratools)
threads (gratools.GFA attribute)
(gratools.GratoolsBam attribute)
to_info_dict() (gratools.CustomCommand method)
(gratools.CustomGroup method)
total_segment_length (gratools.GFA attribute)
U
update_logger_file_suffix() (in module gratools)
V
validate_percentage_or_int() (in module gratools)
version (gratools.GFA attribute)
W
walks_count (gratools.GFA attribute)
works_path (gratools.GFA attribute)
(gratools.GratoolsBam attribute)
(gratools.SubGraph attribute)