GraTools: A Pangenome GFA Toolkit๏
๐ CLI Overview๏
The gratools command-line interface is organized into logical subcommands. You can access the global help or specific command help at any time.
๐ ๏ธ View Available Subcommands (CLI Output)
$ gratools
Welcome to GraTools version: '1.1.0'
@author: GraTools team's
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Please cite our gitlab: https://forge.ird.fr/diade/gratools.git\
Usage: gratools [OPTIONS] COMMAND [ARGS]...
A toolkit for analyzing, manipulating, and extracting information from
pangenome graphs in GFA format.
Options:
-v, --version Show the version and exit.
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-h, --help Show this message and exit.
GFA Content Information:
list_samples (samples)
List the samples embedded in the imported GFA file.
list_chr (chr)
List the embedded chromosomes and their fragments if relevant from the
imported GFA file.
stats
Compute and display various statistics for a GFA file.
GFA Data Extraction:
get_subgraph (subgraph)
Extracts a subgraph from a GFA file based on a query region.
get_fasta (fasta)
Extracts sequences for a specific genomic region in FASTA format.
to_bandage
Generates a CSV file for the Bandage graph visualizer.
GFA Analysis:
pan_ratio (ratio)
Compute and display the ratio of core and dispensable segments.
depth_nodes_stat (dns)
Display various statistics about segment depth (number of embedded
samples).
specific_groups_sample (groups)
Identify segments shared by or specific to defined sample groups.
get_segments_by_depth (depth)
List segments within a specified depth range (number of encompassing
samples).
Other commands:
import
Pre-processes a GFA file for faster GraTools operations.
shell_completion
Generates shell completion scripts (Bash, Zsh, Fish).
๐ Command Reference๏
Explore the detailed documentation for each subcommand, including options, logic, and examples.
Core Operations๏
gratools import
Pre-processes a GFA file to create optimized import files. This is the mandatory first step for high-performance analysis.
gratools stats
Calculates and displays a wide range of metrics about graph size, connectivity, and complexity.
GFA Content Information๏
gratools list_samples
Quickly lists all unique sample names found in the GFA walk lines.
gratools list_chr
Lists all chromosomes and contigs per sample in short or full formats.
GFA Data Extraction๏
gratools get_subgraph
Extracts a valid subgraph in GFA format based on a specific genomic region and sample list.
gratools get_fasta
Extracts sequences in FASTA format for a specific region across multiple samples.
GFA Pangenome Analysis๏
If you are new to GraTools, we recommend starting with the ๐ Quick Start Guide to understand the typical workflow and see common use cases.