bebatut / ebisearch

A Python library for interacting with EBI Search's API

EBISearch

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

Usage

EBISearch is easy to use

$ 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:

>>> 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:

$ pip install ebisearch

or

$ conda install ebisearch

Tests

EBISearch comes with tests:

$ make test