gratools list_samples๏
Quickly identify all unique samples integrated into your pangenome graph.
The list_samples command scans the GFA file (specifically the Walk or Path lines) to extract the unique names of all samples. This is a crucial step to ensure you have the correct sample identifiers for subsequent queries like get_subgraph or get_fasta.
Options๏
๐ ๏ธ View Command Line Options
$ gratools list_samples
Welcome to GraTools version: '0.1.0.dev134'
@author: GraTools team's
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Please cite our gitlab: https://forge.ird.fr/diade/gratools.git\
Usage: gratools list_samples [OPTIONS]
Aliases: samples
Lists all unique sample names found in the walks (W lines) of the GFA file
after its importation by GraTools. This command thus relies on the pre-
existing GraTools import for the specified GFA file.
For more details, see the full documentation:
https://gratools.readthedocs.io/en/latest/commands/list_samples.html
List Samples Options:
-g, --gfa PATH
Path to the input GFA file (e.g., myGraph.gfa or myGraph.gfa.gz).
[required]
-o, --outdir DIRECTORY
Output directory for GraTools results. If not specified, results are
typically placed in a subdirectory within the GFA file's parent directory
(e.g., 'GraTools-output_<gfa_name>').
--save / --no-save
Save the list of the embedded sample names to a text file in the GraTools
output directory. [default: no-save]
Logging Options:
-vv, --verbosity [DEBUG|INFO|ERROR]
Set the logging verbosity level. [default: INFO]
-l, --log-path DIRECTORY
Directory where the log files will be saved. If not specified, logs will be
placed in the main output directory (or in a default GraTools log
location).
Performance Options:
-t, --threads INTEGER
Number of threads to be used for parallelizable operations. [default: 1]
Other options:
-h, --help
Show this message and exit.
Usage Example๏
Display a clean summary table of all individuals present in the graph.
$ gratools list_samples --gfa Og_cactus.gfa.gz
Output Summary:
โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ Summary โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ
Total samples in GFA: 5
Available Samples in GFA:
Og_cactus
โญโโโโโโโโโโโโโโฎ
โ Sample Name โ
โโโโโโโโโโโโโโโค
โ CG14 โ
โ Og20 โ
โ Og103 โ
โ Og182 โ
โ Tog5681 โ
โฐโโโโโโโโโโโโโโฏ
GFA files often use specific prefixes or internal IDs for samples. Since commands like get_subgraph or get_fasta require an exact match for the --sample-query argument, always use list_samples first to confirm the exact spelling and case-sensitivity of your sample names.
๐ Quick Links
Command Import: gratools import
Next Step (Chromosomes): gratools list_chr
Graph Stats: gratools stats