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Utility package to find gene - drug relationships within CARD

Project 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

Specify a full aro term to search for antibiotics assosiated directly with that term

card-trick search --aro_name ARO:3003032

This wil return the following output

aro antibiotics
ARO:3003032 acriflavine,amikacin,chloramphenicol,ciprofloxacin,erythromycin,gentamicin C,meropenem,norfloxacin,ofloxacin,tetracycline,tobramycin

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')
antibiotics = card_trick.ontology_functions.search_aros('ARO:3003032')

Project details


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