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
```
## 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')
```
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')
```
Project details
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
card-trick-0.1.2.tar.gz
(4.6 kB
view hashes)
Built Distribution
card_trick-0.1.2-py3-none-any.whl
(29.4 kB
view hashes)
Close
Hashes for card_trick-0.1.2-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 4e7e9d4f0894fa103434fdbcfac555c75b1418a0f4006490df9cf0ae878f79ee |
|
MD5 | d18ad778efb5644f5e7b8e2b14c47be4 |
|
BLAKE2b-256 | fdaf96b71900b45dbb9306f41f747632b77e311b3efcf67a24db39cf8802c83a |