https://github.com/bebatut/ebisearch

A Python library for interacting with EBI Search's API
https://github.com/bebatut/ebisearch

api api-client ebi

Last synced: 12 days ago
JSON representation

A Python library for interacting with EBI Search's API

• Host: GitHub
• URL: https://github.com/bebatut/ebisearch
• Owner: bebatut
• License: mit
• Created: 2017-03-24T16:07:20.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2017-05-31T07:05:55.000Z (over 7 years ago)
• Last Synced: 2024-10-06T09:11:38.896Z (about 1 month ago)
• Topics: api, api-client, ebi
• Language: Python
• Homepage:
• Size: 37.1 KB
• Stars: 2
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

Awesome Lists containing this project

README

        
EBISearch

=========

.. image:: https://travis-ci.org/bebatut/ebisearch.svg?branch=master

    :target: https://travis-ci.org/bebatut/ebisearch

.. image:: https://badge.fury.io/py/ebisearch.svg

    :target: https://badge.fury.io/py/ebisearch

.. image:: https://anaconda.org/bioconda/ebisearch/badges/installer/conda.svg

    :target: https://anaconda.org/bioconda/ebisearch

EBISearch is a Python library for interacting with `EBI Search `_'s API.

Usage

-----

EBISearch is easy to use

.. code-block:: bash

    $ ebisearch --help

    Usage: ebisearch [OPTIONS] COMMAND [ARGS]...

    

    Options:

      --help  Show this message and exit.

    

    Commands:

      get_domains        Get domains

      get_entries        Get entry content

      get_fields         Get retrievable fields

      get_query_results  Get results for a query

    $ get_entries --help

    Usage: ebisearch get_entries [OPTIONS]

      Return content of entries on a specific domain in EBI

    Options:

      --domain TEXT    Domain id in EBI (accessible with get_domains)

      --entry_id TEXT  (Multiple) Entry identifier to retrieve

      --field TEXT     (Multiple) Field to export (accessible with get_fields with

                       retrieva    ble as type

      --field_url      Include the field links

      --view_url       Include other view links

      --file PATH      (Optional) File to export the entry content

      --help           Show this message and exit.

It can also be used as a Python library:

.. code-block:: python

    >>> import ebisearch

    >>> ebisearch.get_entries(

            domain="metagenomics_runs",

            entryids="ERR1135279,SRR2135754",

            fields="id,experiment_type")

    [{'fields': {'experiment_type': ['metagenomic'], 'id': ['ERR1135279']}, 'source': 'metagenomics_runs', 'id': 'ERR1135279'}, {'fields': {'experiment_type': ['metagenomic'], 'id': ['SRR2135754']}, 'source': 'metagenomics_runs', 'id': 'SRR2135754'}]

    >>> ebisearch.get_number_of_results(

            domain="metagenomics_runs",

            query="experiment_type:(metagenomic)")

    13227

Installation

------------

To install EBISearch, simply:

.. code-block:: bash

    $ pip install ebisearch

or

.. code-block:: bash

    $ conda install ebisearch

Tests

-----

EBISearch comes with tests:

.. code-block:: bash

    $ make test