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: about 1 month 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 9 years ago)
- Default Branch: master
- Last Pushed: 2017-05-31T07:05:55.000Z (about 9 years ago)
- Last Synced: 2025-11-27T17:53:27.364Z (8 months ago)
- Topics: api, api-client, ebi
- Language: Python
- Homepage:
- Size: 37.1 KB
- Stars: 2
- Watchers: 1
- 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