Browse all GraTools commands organized by category.
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$ gratools
Welcome to GraTools version: '1.2.0.dev19'
@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.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-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).
GFA Content
Explore samples, chromosomes, and graph statistics.
Data Extraction
Extract subgraphs and FASTA sequences.
GFA Analysis
Core/dispensable, depth, and group comparisons.
Other
Import and shell completion.
GFA Content Informationο
Compute and display various statistics for a GFA file.
List all unique samples embedded in the GFA file.
List chromosomes and fragments per sample.
GFA Data Extractionο
Extract a subgraph from a GFA file based on a query region.
Extract sequences for a specific genomic region in FASTA format.
GFA Analysisο
Compute the ratio of core and dispensable segments.
Display statistics about segment depth across samples.
Identify segments shared by or specific to sample groups.
List segments within a specified depth range.
Other Commandsο
Pre-process a GFA file for faster GraTools operations. Run this first.
Generate shell completion scripts for Bash, Zsh, and Fish.
Start with the π¦ Installation to understand the typical workflow, or explore the 1 β Graph Description for real-world biological examples.