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card-trick-0.2.1
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مشاهده بیشتر
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مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
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مشاهده بیشترتوضیحات
Utility package to find gene - drug relationships within CARD
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | card-trick-0.2.1 |
| نام | card-trick |
| نسخه کتابخانه | 0.2.1 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Anthony Underwood |
| ایمیل نویسنده | au3@sanger.ac.uk |
| آدرس صفحه اصلی | - |
| آدرس اینترنتی | https://pypi.org/project/card-trick/ |
| مجوز | MIT |
# Card trick
A software package that extracts information from the ontology relationships
from The Comprehensive Antibiotic Resistance Database (CARD)
https://card.mcmaster.ca/home
Original code: https://gitlab.com/cgps/card_trick
Forked version code: https://gitlab.com/JFsanchezherrero/card_trick
This forked version retrieves all information for each entry available in CARD
ontology information.
## Installation
This package requires Python3
```
pip3 install card-trick
```
## Usage
There are two main modules: search and update
```
usage: card-trick [-h] [-v] {update,search} ...
positional arguments:
{update,search} The following commands are available. Type card_trick
<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
--man Additional information
```
### Download ontology database
```
usage: card-trick update [-h] [--path PATH] [-q QUIET]
optional arguments:
-h, --help show this help message and exit
--path PATH Path to store CARD ontology.
-q QUIET, --quiet QUIET
Do not print process information
```
The update command `card-trick update` will download the latest version of the
database. If already exists in the path provided (or default) it would update it.
Database in obo format is stored in your home directory in the .card-trick
directory or in the directory stated using option --path
Obo format file would be parsed into a csv file for later analysis.
All information for each entry in CARD ontology database are stored in the
csv file.
### Search ontology database
```
usage: card-trick search -i INPUT -t {ARO,gene,antibiotic,target,any}
[-f {json,csv,tsv,all}] [-o OUTPUT_NAME] [-p PATH] [-b]
[-i2 INPUT_2] [t2 {ARO,gene,antibiotic,target,any}] [-b2] [-q] [-h]
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
Input term to search in CARD ontology. Provide a unique
term o several using --batch option
-f {json,csv,tsv,all}, --format_output {json,csv,tsv,all}
Output format. csv, tsv or json
-o OUTPUT_NAME, --output_name OUTPUT_NAME
Output name.
-p PATH, --path PATH
Path containing CARD ontology. Default is user’s home
directory.
-t {ARO,gene,antibiotic,target,any}, --term {ARO,gene,antibiotic,target,any}
The type of term provided to search.
-b, --batch Provide this option if input is a file containing
multiple terms, one per line.
-i2 INPUT_2, --input_2 INPUT_2
Input term to search in results retrieved from first
input. Provide a unique term o several using --batch
option
-t2 {ARO,gene,antibiotic,target,any}, --term_2 {ARO,gene,antibiotic,target,any}
The type of term provided to search for the second
input. Default: any
-b2, --batch_2 Provide this option if input_2 is a file containing
multiple terms, one per line.
-q, --quiet Do not print process information
```
The command `card-trick search` will return matches as a dataframe and print
into a default tabular file.
There are several possibilities to search the dataframe. This module can search for:
* gene entries
* ARO terms
* antibiotic to which a gene confers resistance
* antibiotic to target a gene
No output is print to STDOUT as card-trick would retrieve all information from
CARD ontology database and might be too much information.
There is a possibility to generate a batch search of multiple terms using option
batch.
Also, there is a possibility to link several searches: Use option --input_2, --term_2 or --batch_2
e.g. CTX genes that have a resistance to ceftazidime
Examples
```
## Different term options:
card-trick search -t antibiotic -i tigecycline
card-trick search -t target -i tigecycline
card-trick search -t gene -i ctx
card-trick search -t ARO -i ARO:3003032
card-trick search -t any -i ctx
## Using path database provided
card-trick search -t gene -i ctx --path /folder/to/card_ontology
## Batch example
card-trick search -t ARO --batch -i batch_entry_file.txt
## Multiple search
card-trick search -t gene -i ctx --path /folder/to/card_ontology -i2 ceftazidime -t2 antibiotic
card-trick search -t gene -i ctx --path /folder/to/card_ontology --batch_2 -i2 file.txt -t2 any
## Output
card-trick search -t ARO --batch -i batch_entry_file.txt -f tsv -o example_name
```
## Using in a python script or program
Here is a simple code example to download, parse and search the database.
If the database is download and parsed as a csv, just load the information to a
pandas dataframe
```
import card_trick
import pandas as pd
CARD_folder=/path/to/your/database/ontology/card
## uptade database in a path
aro_obo_file = card_trick.ontology_functions.update_ontology(CARD_folder, False)
## get ontology and save it in csv
card_trick.ontology_functions.parse_ontology(aro_obo_file, False)
## load information
csv_file = CARD_folder + '/aro.obo.csv'
card_ontology = pd.read_csv(csv_file, sep=',', index_col=0)
## search for examples IDs
AROS_identified = ('ARO:3000026', 'ARO:3004058')
term = 'ARO'
information_ontology = card_trick_caller.get_info_CARD(AROS_identified, term, card_ontology)
```
نیازمندی
| مقدار | نام |
|---|---|
| >=2.2 | pronto |
| - | requests |
نحوه نصب
نصب پکیج whl card-trick-0.2.1:
pip install card-trick-0.2.1.whl
نصب پکیج tar.gz card-trick-0.2.1:
pip install card-trick-0.2.1.tar.gz