An example script for retrieving RNAcentral ids for a given sequence.

retrieve_rnacentral_id.py

"""
Copyright [2009-present] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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     http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
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An example Python script showing how to retrieve the RNAcentral id for an RNA sequence.

Usage:
python retrieve_rnacentral_id.py
"""

import hashlib
import requests # pip install requests


def get_md5(sequence):
	"""
	Calculate md5 for an RNA sequence
	"""
	# RNAcentral stores DNA md5 hashes
	sequence = sequence.replace('U','T')
	# get the md5 digest
	m = hashlib.md5()
	m.update(sequence)
	return m.hexdigest()

# get the RNAcentral id
def get_rnacentral_id(md5):
	"""
	Parse json output and return the RNAcentral id.
	"""
	url = 'https://rnacentral.org/api/v1/rna'
	r = requests.get(url, params = {'md5': md5})
	data = r.json()
	if data['count'] > 0:
		return data['results'][0]['rnacentral_id']
	else:
		return 'RNAcentral id not found'

# This sequence has an RNAcentral id
sequence = 'CUGAAUAAAUAAGGUAUCUUAUAUCUUUUAAUUAACAGUUAAACGCUUCCAUAAAGCUUUUAUCCA'
md5 = get_md5(sequence)
print get_rnacentral_id(md5)  # URS00002C9E9D

# This sequence doesn't have an RNAcentral id
sequence = 'Not an RNA sequence'
md5 = get_md5(sequence)
print get_rnacentral_id(md5) # RNAcentral id not found

Hi Anton,

A minor comment: the years in the copyright notice need updating

Matthieu