Metadata-Version: 1.1
Name: card-trick
Version: 0.1.2
Summary: Utility package to find gene <-> drug relationships within CARD
Home-page: UNKNOWN
Author: Anthony Underwood
Author-email: au3@sanger.ac.uk
License: MIT
Description: # Card trick
        A software package that extracts confers_resistance_to_drug relationships from 
        The Comprehensive Antibiotic Resistance Database (CARD) https://card.mcmaster.ca/home
        
        code: https://gitlab.com/cgps/card_trick
        
        ## Installation
        This package requires Python3
        ```
        pip3 install card-trick
        ```
        
        ## Usage
        usage: card-trick [-h] [-v] {update,search} ...
        
        positional arguments:
          {update,search}  The following commands are available. Type contig_tools
                           <COMMAND> -h for more help on a specific commands
            update         Get latest CARD ontology
            search         search CARD ontology
        
        optional arguments:
          -h, --help       show this help message and exit
          -v, --version    display the version number
        
        ### Update ontology database
        The software comes preloaded with version 3.0.0 of the database (October 2018 release).
        The update command `card-trick update` will download the latest version of the database and store it in your
        home directory in the .card-trick directory
        
        ### Search ontology database
        This will return matches to the STDOUT in either tsv (default) or json format. To write to a file just append `> OUTPUT_FILE` to the command
        
        Specify a full or partial gene name with the -g argument to search for antibiotics resistance to which is conferred by the specified gene e.g
        ```
        card-trick search -g ctx
        ```
        This will return the following output
        ```
        gene	antibiotics
        CTX-M-3	cefalotin,ceftazidime,ceftriaxone
        CTX-M-15	ceftazidime
        CTX-M-27	cefalotin,ceftazidime
        CTX-M-55	ceftazidime,ceftriaxone
        ```
        
        Specify a full or partial antibiotic name with the -a argument to search for genes who confer resistance to the specified antibiotic
        ```
        card-trick search -a tigecycline
        ```
        This will return the following output
        ```
        antibiotic	genes
        tigecycline	AcrAB-TolC,AdeABC,mepA,oqxAB,tet(A),tetX
        ```
        
        ## Using in a python script or program
        Examples
        ```
        import card_trick
        genes_conferring_resistance = card_trick.ontology_functions.search_antibiotics('tigecycline')
        antibiotics = card_trick.ontology_functions.search_genes('ctx-m-15')
        ```
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
