https://github.com/tlnagy/pyuniprot

A simple Python 2/3 script for retrieving protein data in the CSV format via UniProt's RESTful API.
https://github.com/tlnagy/pyuniprot

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A simple Python 2/3 script for retrieving protein data in the CSV format via UniProt's RESTful API.

• Host: GitHub
• URL: https://github.com/tlnagy/pyuniprot
• Owner: tlnagy
• Created: 2014-06-13T21:03:42.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2014-09-13T21:26:30.000Z (about 10 years ago)
• Last Synced: 2024-10-12T14:54:47.392Z (about 1 month ago)
• Language: Python
• Homepage:
• Size: 207 KB
• Stars: 1
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
pyuniprot

=======

A simple and easy-to-use Python frontend for [UniProt](http://www.uniprot.org)'s REST API. It outputs a CSV file populated with the requested columns and information from Uniprot. 

## Features

- Accepts either JSON piped via command-line or a configuration file for requests

- Automatic conversion from Uniprot's tab format to the more widely used csv format

## Installation

Either clone it to your computer or download it as a zip file. To run it you will need a Python interpreter installed (I highly recommend the free [Anaconda](https://store.continuum.io/cshop/anaconda/) package manager for this) and the following command: 

```bash

python pyuniprot.py

```

The other option is to run `chmod +x pyuniprot.py` so you can then use it like so:

```bash

./pyuniprot.py

```

## Usage

A request can either be given via stdin as a JSON file or via the `conf.py` file. Requests should be formatted in the following manner:

```

request = {

    'columns':'id,entry name,reviewed,protein names,sequence',

    'query':'sonic hedgehog AND organism:human',

    'output':'output'

}

```

where `columns` is a comma-separated list of the columns of information that you would like Uniprot, `query` is the Uniprot query, i.e. what you would type into the search bar on , and `output` is the name of the output file. The release date of Uniprot version accessed will be appended to this name, e.g. output_2014_07.csv.

The following are some examples of the possible columns:

- clusters

- database (usage: database(PDB) )

- domains

- id

- existence

- families

- features

- genes

- go-id

- keywords

- last-modified

- length

- protein names

- sequence

- taxon

- virus hosts

Please see  for the complete list of available columns and detailed information on building queries. 

## License 

BSD