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        "author": "Pauline Barbet, Arnaud Felten",
        "author_email": "pauline.barbet@anses.fr, arnaud.felten@anses.fr",
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        "classifiers": [
            "License :: OSI Approved :: GNU General Public License v2 (GPLv2)",
            "Operating System :: POSIX :: Linux",
            "Programming Language :: Python :: 3"
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        "description": "GENIAL : GENes Identification with Abricate for Lucky biologists\n================================================================\n\nAuthors : Barbet Pauline, Felten Arnaud\n\nAffiliation: [Food Safety Laboratory - ANSES Maisons Alfort (France)](https://www.anses.fr/en/content/laboratory-food-safety-maisons-alfort-and-boulogne-sur-mer)\n\nYou can find the latest version of the tool at [https://github.com/p-barbet/GENIAL](https://github.com/p-barbet/GENIAL)\n\n\nGENIAL\n======\n\nGENIAL aims to identify antimicrobial resistance and virulence genes from bacterial genomes matching them to a database gathering genes of interest using [ABRicate](https://github.com/tseemann/abricate).\n\n### Databases\n\nDefault databases available are ([Resfinder](https://cge.cbs.dtu.dk/services/ResFinder/), [CARD](https://card.mcmaster.ca/), [ARG-ANNOT](http://backup.mediterranee-infection.com/article.php?laref=282&titre=arg-annot), [NCBI](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA313047), [EcOH](https://github.com/katholt/srst2/tree/master/data), [PlasmidFinder](https://cge.cbs.dtu.dk/services/PlasmidFinder/), [Ecoli_VF](https://github.com/phac-nml/ecoli_vf) and [VFDB](http://www.mgc.ac.cn/VFs/))\n\nAs well as this databes, it's posible to use your own database.\n\nThe tool is divided into two scripts.\n\n### GENIALanalysis\n\nGENIALanalysis aims to run ABricate. It takes in input a tsv file containing genomes fasta files paths and IDs.If you want to use your own database you also need to provide a multifasta whith genes IDs as headers. Then the script run ABricate and produce in output one ABRicate result file per genome, corresponding to a tsv file including genes found in each sample.\n\n### GENIALresults\n\nGENIALresults aims to conditionning ABRicate results in the form of matrixes and heatmaps of presence/absence. It takes in input a temporary file produced by the Abricate analysis containing the genomes Abricate results paths and IDs. In the case of vfdb database a file containing the virulence factors names, their family and species is automticaly included in the script.\n\nThe output depending on the database used :\n\n* In any cases a matrix in tsv format and a heatmap in png format with all genes found are created\n\n\nOn top of that:\n\n* If you use one of the default databases [Resfinder](https://cge.cbs.dtu.dk/services/ResFinder/) or [VFDB](http://www.mgc.ac.cn/VFs/) news matrix and heatmap by gene type are produced with a correspondace table between the gene name, its family and its number in all genomes.\n\n* If you don't use one of the two previous databases or if you use your own database, only a corespondance table between the gene name and its number in all genomes is produced in addition.\n\n![](workflow.PNG?raw=true \"script workflow\")\n\n\nDependencies\n============\n\nThe script has been developed with python 3.6 (tested with 3.6.6)\n\n### External dependencies\n\n* [ABRicate](https://github.com/tseemann/abricate) tested with 0.8.7\n* [Pandas](https://pandas.pydata.org/) tested with 0.23.4\n* [seaborn](https://seaborn.pydata.org/installing.html) tested with 0.9.0\n\n\nParameters\n==========\n\n### Command line options\n\n\n|   Options   |                                                              Description                                                              |        Required        |      Default     |\n|:-----------:|:-------------------------------------------------------------------------------------------------------------------------------------:|:----------------------:|:----------------:|\n|      -f     |                                            tsv file with FASTA files paths ans strains IDs                                            |           Yes          |                  |\n|     -dbp    |                                   Path to ABRicate databases repertory. Implies -dbf and --privatedb                                  |   Yes if --privatedb   |                  |\n|     -dbf    |                           Multifasta containing the private database sequences. Implies -dbp and --privatedb                          |   Yes if --privatedb   |                  |\n|      -T     |                                                        Number of thread to use                                                        |           No           |         1        |\n|      -w     |                                                           Working directory                                                           |           No           |         .        |\n|      -r     |                                                         Results directory name                                                        |           No           | ABRicate_results |\n| --defaultdb |  default databases available : resfinder, card, argannot, acoh, ecoli_vf, plasmidfinder, vfdb or ncbi. Incompatible with --privatedb  | Yes if not --privatedb |                  |\n| --privatedb |                              Private database name. Implies -dbp and -dbf. Incompatible with --defaultdb                              | Yes if not --defaultdb |                  |\n|   --mincov  |                                                   Minimum proportion of gene covered                                                  |           No           |        80        |\n|   --minid   |                                             Minimum proportion of exact nucleotide matches                                            |           No           |        90        |\n|     --R     |                                          Remove genes present in all genomes from the matrix                                          |           No           |       False      |\n\nTest \n====\n\nAfter installing ABRicate and Pandas and seaborn you can test the script with the command line :\n\n## Default database\n\n\tpython AntiViruce.py -f input_file.tsv --defaultdb vfdb -r results_directory --minid 90 --mincov 80\n\n## Private database\n\n\tpython AntiViruce.py -f input_file.tsv  --privatedb private_db_name -T 10 -r results_directory --minid 90 --mincov 80 -dbp path_to_abricate_databases_repertory -dbf private_db_multifasta_path\n\n\n\n\n\n\n\n\n\n",
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