GraTools is a powerful tool for analyzing and handling pangenome graphs quickly, whatever the model and therefore the size and the complexity of the GFA file.
It allows users to extract sequences or subgraphs, convert graphs into FASTA sequences, and identify shared and specific nodes across samples. Additionally, it provides essential statistics for chromosomes and samples data. With multi-threading support and flexible logging capabilities, Gratools is an efficient solution for pangenome graph analysis.
GraTools has been developed by IRD and CIRAD, as part of a collaboration between the PANEEC/DIADE and PHIM research teams.
Documentation
Install GraTools
GraTools can be installed like any standard Python package. For a quick start, please refer to the quick start guide in the official documentation.
Using GraTools
Gratools is composed of multiple commands that can be used with the following syntax:
gratools [command] [options]To view the list of available commands and their descriptions, simply run:
gratoolsThis will display all the commands supported by Gratools.
For example, to list the chromosomes per sample in a GFA file
gratools show_chr --gfa graph.gfa --fullFor more details, refer to the For more details, refer to the Quick Start section or the full command manual in the official documentation. or the full command manual in the official documentation.
Test GraTools with a GFA file
wget http://itrop.ird.fr/GraTools/data-gratools.tar.gz
tar -zxvf data-gratools.tar.gzDiscovering GraSuite
GraTools is one of the tools in GraSuite, a comprehensive ecosystem of tools for working with GFA pangenome graphs — from creation to analysis and visualization.
Citation
Maintainer
Sébastien RAVEL (PHIM, CIRAD), sebastien.ravel@cirad.fr
Christine TRANCHANT (DIADE, IRD), christine.tranchant@ird.fr
Thanks
Cécile Triay for the logo.
the i-trop plateform, especially Ndomassi Tando, for the support.
License
Licensed under GLPLv3.
Intellectual property belongs to IRD , CIRAD and previously cited authors.
2 maintainers
Metadata
2 maintainers
Release files for GraTools 1.1.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| gratools-1.1.0.tar.gz | 415.7 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| gratools-1.1.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 558.0 kB
Release files / gratools-1.1.0.tar.gz
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| Download URL | gratools-1.1.0-py3-none-any.whl |
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| Size | 142.3 kB |
| Tags | Python 3 |
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