{
    "info": {
        "author": "Anthony Underwood",
        "author_email": "au3@sanger.ac.uk",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python :: 3"
        ],
        "description": "# Card trick\nA software package that extracts information from the ontology relationships \nfrom The Comprehensive Antibiotic Resistance Database (CARD) \nhttps://card.mcmaster.ca/home\n\nOriginal code: https://gitlab.com/cgps/card_trick\n\nForked version code: https://gitlab.com/JFsanchezherrero/card_trick\n\nThis forked version retrieves all information for each entry available in CARD \nontology information.\n\n## Installation\nThis package requires Python3\n\n```\npip3 install card-trick\n```\n\n## Usage\nThere are two main modules: search and update\n\n```\nusage: card-trick [-h] [-v] {update,search} ...\n\npositional arguments:\n  {update,search}  The following commands are available. Type card_trick\n                   <COMMAND> -h for more help on a specific commands\n    update         Get latest CARD ontology\n    search         search CARD ontology\n\noptional arguments:\n  -h, --help       show this help message and exit\n  -v, --version    display the version number\n  --man            Additional information\n```\n\n### Download ontology database\n```\nusage: card-trick update [-h] [--path PATH] [-q QUIET]\n\noptional arguments:\n  -h, --help            show this help message and exit\n  --path PATH           Path to store CARD ontology.\n  -q QUIET, --quiet QUIET\n                        Do not print process information\n```\n\n\nThe update command `card-trick update` will download the latest version of the \ndatabase. If already exists in the path provided (or default) it would update it.\n\nDatabase in obo format is stored in your home directory in the .card-trick \ndirectory or in the directory stated using option --path \n\nObo format file would be parsed into a csv file for later analysis.\n\nAll information for each entry in CARD ontology database are stored in the \ncsv file.\n\n### Search ontology database\n```\nusage: card-trick search -i INPUT -t {ARO,gene,antibiotic,target,any} \n                         [-f {json,csv,tsv,all}] [-o OUTPUT_NAME] [-p PATH] [-b]\n                         [-i2 INPUT_2] [t2 {ARO,gene,antibiotic,target,any}] [-b2] [-q] [-h]\n\noptional arguments:\n  -h, --help            show this help message and exit\n\n  -i INPUT, --input INPUT \n                        Input term to search in CARD ontology. Provide a unique \n                        term o several using --batch option\n\n  -f {json,csv,tsv,all}, --format_output {json,csv,tsv,all}\n                        Output format. csv, tsv or json\n\n  -o OUTPUT_NAME, --output_name OUTPUT_NAME\n                        Output name.\n\n  -p PATH, --path PATH  \n                        Path containing CARD ontology. Default is user\u2019s home \n                        directory.\n\n  -t {ARO,gene,antibiotic,target,any}, --term {ARO,gene,antibiotic,target,any}\n                        The type of term provided to search.\n\n  -b, --batch           Provide this option if input is a file containing\n                        multiple terms, one per line.\n\n  -i2 INPUT_2, --input_2 INPUT_2\n                        Input term to search in results retrieved from first\n                        input. Provide a unique term o several using --batch\n                        option\n\n  -t2 {ARO,gene,antibiotic,target,any}, --term_2 {ARO,gene,antibiotic,target,any}\n                        The type of term provided to search for the second\n                        input. Default: any\n\n  -b2, --batch_2        Provide this option if input_2 is a file containing\n                        multiple terms, one per line.\n\n  -q, --quiet           Do not print process information\n\n```\n\nThe command  `card-trick search` will return matches as a dataframe and print \ninto a default tabular file. \n\nThere are several possibilities to search the dataframe. This module can search for:\n* gene entries\n* ARO terms\n* antibiotic to which a gene confers resistance \n* antibiotic to target a gene\n\nNo output is print to STDOUT as card-trick would retrieve all information from \nCARD ontology database and might be too much information.\n\nThere is a possibility to generate a batch search of multiple terms using option\nbatch.\n\nAlso, there is a possibility to link several searches: Use option --input_2, --term_2 or --batch_2\ne.g. CTX genes that have a resistance to ceftazidime\n\n\nExamples\n```\n## Different term options:\ncard-trick search -t antibiotic -i tigecycline\ncard-trick search -t target -i tigecycline\ncard-trick search -t gene -i ctx\ncard-trick search -t ARO -i ARO:3003032\ncard-trick search -t any -i ctx\n\n## Using path database provided\ncard-trick search -t gene -i ctx --path /folder/to/card_ontology\n\n## Batch example\ncard-trick search -t ARO --batch -i batch_entry_file.txt\n\n## Multiple search\ncard-trick search -t gene -i ctx --path /folder/to/card_ontology -i2 ceftazidime -t2 antibiotic\ncard-trick search -t gene -i ctx --path /folder/to/card_ontology --batch_2 -i2 file.txt -t2 any \n\n## Output\ncard-trick search -t ARO --batch -i batch_entry_file.txt -f tsv -o example_name\n\n```\n\n\n## Using in a python script or program\nHere is a simple code example to download, parse and search the database. \n\nIf the database is download and parsed as a csv, just load the information to a \npandas dataframe\n\n```\nimport card_trick\nimport pandas as pd\n\nCARD_folder=/path/to/your/database/ontology/card\n\n## uptade database in a path\naro_obo_file = card_trick.ontology_functions.update_ontology(CARD_folder, False)\n\n## get ontology and save it in csv\ncard_trick.ontology_functions.parse_ontology(aro_obo_file, False)\n\n## load information\ncsv_file = CARD_folder + '/aro.obo.csv'\ncard_ontology = pd.read_csv(csv_file, sep=',', index_col=0)\n\n## search for examples IDs\nAROS_identified = ('ARO:3000026', 'ARO:3004058')\nterm = 'ARO'\ninformation_ontology = card_trick_caller.get_info_CARD(AROS_identified, term, card_ontology)\n\n```\n\n\n",
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