EBISearch is a Python library for interacting with [EBI Search](http://www.ebi.ac.uk/ebisearch/overview.ebi>)'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
Tests
EBISearch comes with tests:
$ make test