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 -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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