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https://github.com/rvhonorato/cazy-parser

A way to extract specific information from CAZy
https://github.com/rvhonorato/cazy-parser

carbohydrates cazy data-mining enzymes scrapper text-mining

Last synced: 20 days ago
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A way to extract specific information from CAZy

Host: GitHub
URL: https://github.com/rvhonorato/cazy-parser
Owner: rvhonorato
License: gpl-3.0
Created: 2016-08-18T12:26:40.000Z (over 8 years ago)
Default Branch: main
Last Pushed: 2024-11-16T10:45:08.000Z (about 1 month ago)
Last Synced: 2024-11-16T11:26:25.465Z (about 1 month ago)
Topics: carbohydrates, cazy, data-mining, enzymes, scrapper, text-mining
Language: Python
Homepage:
Size: 120 KB
Stars: 13
Watchers: 3
Forks: 8
Open Issues: 1
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md

Awesome Lists containing this project

README

        # cazy-parser

_A way to extract specific information from the Carbohydrate-Active enZYmes._

[![Downloads](https://pepy.tech/badge/cazy-parser)](https://pepy.tech/project/cazy-parser)

[![status](http://joss.theoj.org/papers/f709afe5d720fc6eee82fca277942a46/status.svg)](http://joss.theoj.org/papers/f709afe5d720fc6eee82fca277942a46)

[![unittests](https://github.com/rvhonorato/cazy-parser/actions/workflows/unittests.yml/badge.svg?branch=main)](https://github.com/rvhonorato/cazy-parser/actions/workflows/unittests.yml)

[![Codacy Badge](https://app.codacy.com/project/badge/Grade/33f087332ec24da689268a13d2f4ca23)](https://www.codacy.com/gh/rvhonorato/cazy-parser/dashboard?utm_source=github.com&utm_medium=referral&utm_content=rvhonorato/cazy-parser&utm_campaign=Badge_Grade)

[![Codacy Badge](https://app.codacy.com/project/badge/Coverage/33f087332ec24da689268a13d2f4ca23)](https://www.codacy.com/gh/rvhonorato/cazy-parser/dashboard?utm_source=github.com&utm_medium=referral&utm_content=rvhonorato/cazy-parser&utm_campaign=Badge_Coverage)

Make sure to visit and cite the CAZy website!

- http://www.cazy.org/

- Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B (2014) The Carbohydrate-active enzymes database (CAZy) in 2013. **Nucleic Acids Res** 42:D490–D495. [PMID: [24270786](http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=24270786)].

License: [GNU GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)

[RV Honorato. CAZy-parser a way to extract information from the Carbohydrate-Active enZYmes Database. _The Journal of Open Source Software_, 1(8), dec 2016.](https://github.com/openjournals/joss-papers/blob/master/joss.00053/10.21105.joss.00053.pdf)

doi: 10.21105/joss.00053

## Recommendation

[`cazy_webscraper`](https://github.com/HobnobMancer/cazy_webscraper) provides broader functionality by integrating CAZy data with external resources (protein sequences, taxonomy, and structures) to build comprehensive local databases for large-scale analyses. It also includes additional features for taxonomic exploration and structural analysis that aren't available here.

## Introduction

_cazy-parser_ is a tool that extract information from [CAZy](http://www.cazy.org/) in a more usable and readable format. Firstly, a script reads the HTML structure and creates a mirror of the database as a tab delimited file. Secondly, information is extracted from the database according to user inputted parameters and presented to the user as a set of accession codes.

## Install / Upgrade

```text

pip install --upgrade cazy-parser

```

## Usage (internet connection required)

```text

cazy-parser -h

usage: cazy-parser [-h] [-f FAMILY] [-s SUBFAMILY] [-c CHARACTERIZED] [-v] {GH,GT,PL,CA,AA}

positional arguments:

  {GH,GT,PL,CA,AA}

optional arguments:

  -h, --help            show this help message and exit

  -f FAMILY, --family FAMILY

  -s SUBFAMILY, --subfamily SUBFAMILY

  -c CHARACTERIZED, --characterized CHARACTERIZED

  -v, --version         show version

```

### Example

Extract all fasta sequences from family 43 of Glycoside Hydrolase subfamily 1

```text

$ cazy-parser GH -f 43 -s 1

 [2022-05-26 16:39:21,511 91 INFO] ------------------------------------------

 [2022-05-26 16:39:21,511 92 INFO]

 [2022-05-26 16:39:21,511 93 INFO] ┌─┐┌─┐┌─┐┬ ┬   ┌─┐┌─┐┬─┐┌─┐┌─┐┬─┐

 [2022-05-26 16:39:21,511 94 INFO] │  ├─┤┌─┘└┬┘───├─┘├─┤├┬┘└─┐├┤ ├┬┘

 [2022-05-26 16:39:21,511 95 INFO] └─┘┴ ┴└─┘ ┴    ┴  ┴ ┴┴└─└─┘└─┘┴└─ v2.0.1

 [2022-05-26 16:39:21,511 96 INFO]

 [2022-05-26 16:39:21,511 97 INFO] ------------------------------------------

 [2022-05-26 16:39:21,511 183 INFO] Fetching links for Glycoside-Hydrolases, url: http://www.cazy.org/Glycoside-Hydrolases.html

 [2022-05-26 16:39:22,454 189 INFO] Only using links of family 43 subfamily 1

 [2022-05-26 16:39:23,029 26 INFO] Dowloading 1415 fasta sequences...

 [2022-05-26 16:40:32,187 51 INFO] Dumping fasta sequences to file GH43_1_26052022.fasta

```

This will generate the following file `GH43_1_DDMMYYY.fasta` containing the fasta sequences.

## To-do and how to contribute

Please refer to [CONTRIBUTING](CONTRIBUTING.md) 🤓