Skip to main content

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

## 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')
```


Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for card-trick, version 0.1.1
Filename, size File type Python version Upload date Hashes
Filename, size card_trick-0.1.1-py3-none-any.whl (29.4 kB) File type Wheel Python version py3 Upload date Hashes View
Filename, size card-trick-0.1.1.tar.gz (4.6 kB) File type Source Python version None Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring DigiCert DigiCert EV certificate Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page