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QueryUniprot.py
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QueryUniprot.py
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""" This module defines the class QueryUniprot which connects to APIs at
http://www.uniprot.org/uploadlists/, querying reactome pathways from uniprot id.
* map_enzyme_commission_id_to_uniprot_ids(ec_id)
Description:
map enzyme commission id to UniProt ids
Args:
ec_id (str): enzyme commission id, e.g., "ec:1.4.1.17"
Returns:
ids (set): a set of the enzyme commission ids, or empty set if no UniProt id can be obtained or the response
status code is not 200.
"""
__author__ = ""
__copyright__ = ""
__credits__ = []
__license__ = ""
__version__ = ""
__maintainer__ = ""
__email__ = ""
__status__ = "Prototype"
# import requests
# import requests_cache
from cache_control_helper import CacheControlHelper
import CachedMethods
import sys
import urllib.parse
import xmltodict
class QueryUniprot:
API_BASE_URL = "http://www.uniprot.org/uploadlists/"
TIMEOUT_SEC = 120
HANDLER_MAP = {
'map_enzyme_commission_id_to_uniprot_ids': 'uniprot/?query=({id})&format=tab&columns=id',
'get_protein': 'uniprot/{id}.xml'
}
@staticmethod
@CachedMethods.register
def uniprot_id_to_reactome_pathways(uniprot_id):
"""returns a ``set`` of reactome IDs of pathways associated with a given string uniprot ID
:param uniprot_id: a ``str`` uniprot ID, like ``"P68871"``
:returns: a ``set`` of string Reactome IDs
"""
payload = { 'from': 'ACC',
'to': 'REACTOME_ID',
'format': 'tab',
'query': uniprot_id }
contact = "[email protected]"
header = {'User-Agent': 'Python %s' % contact}
requests = CacheControlHelper()
try:
url =QueryUniprot.API_BASE_URL
res = requests.post(QueryUniprot.API_BASE_URL, data=payload, headers=header)
except requests.exceptions.Timeout:
print(url, file=sys.stderr)
print('Timeout in QueryUniprot for URL: ' + QueryUniprot.API_BASE_URL, file=sys.stderr)
return None
except KeyboardInterrupt:
sys.exit(0)
except BaseException as e:
print(url, file=sys.stderr)
print('%s received in QueryUniprot for URL: %s' % (e, url), file=sys.stderr)
return None
status_code = res.status_code
if status_code != 200:
print(QueryUniprot.API_BASE_URL, file=sys.stderr)
print('Status code ' + str(status_code) + ' for url: ' + QueryUniprot.API_BASE_URL, file=sys.stderr)
return None
# assert 200 == res.status_code
res_set = set()
for line in res.text.splitlines():
field_str = line.split("\t")[1]
if field_str != "To":
res_set.add(field_str)
return res_set
@staticmethod
def __access_api(handler):
api_base_url = 'http://www.uniprot.org'
url = api_base_url + '/' + handler
#print(url)
contact = "[email protected]"
header = {'User-Agent': 'Python %s' % contact}
requests = CacheControlHelper()
try:
res = requests.get(url, timeout=QueryUniprot.TIMEOUT_SEC, headers=header)
except requests.exceptions.Timeout:
print(url, file=sys.stderr)
print('Timeout in QueryUniprot for URL: ' + url, file=sys.stderr)
return None
except requests.exceptions.ChunkedEncodingError:
print(url, file=sys.stderr)
print('ChunkedEncodingError for URL: ' + url, file=sys.stderr)
return None
except BaseException as e:
print(url, file=sys.stderr)
print('%s received in QueryUniprot for URL: %s' % (e, url), file=sys.stderr)
return None
status_code = res.status_code
if status_code != 200:
print(url, file=sys.stderr)
print('Status code ' + str(status_code) + ' for url: ' + url, file=sys.stderr)
return None
return res.text
@staticmethod
def map_enzyme_commission_id_to_uniprot_ids(ec_id):
res_set = set()
if not isinstance(ec_id, str):
return res_set
ec_id_encoded = urllib.parse.quote_plus(ec_id)
handler = QueryUniprot.HANDLER_MAP['map_enzyme_commission_id_to_uniprot_ids'].format(id=ec_id_encoded)
res = QueryUniprot.__access_api(handler)
if res is not None:
res = res[res.find('\n')+1:]
for line in res.splitlines():
res_set.add(line)
return res_set
@staticmethod
def __get_entity(entity_type, entity_id):
if entity_id[:10] == 'UniProtKB:':
entity_id = entity_id[10:]
handler = QueryUniprot.HANDLER_MAP[entity_type].format(id=entity_id)
results = QueryUniprot.__access_api(handler)
entity = None
if results is not None:
obj = xmltodict.parse(results)
if 'uniprot' in obj.keys():
if 'entry' in obj['uniprot'].keys():
entity = obj['uniprot']['entry']
return entity
@staticmethod
def get_protein_gene_symbol(entity_id):
ret_symbol = "None"
if not isinstance(entity_id, str):
return ret_symbol
entity_obj = QueryUniprot.__get_entity("get_protein", entity_id)
if entity_obj is not None:
if 'gene' in entity_obj.keys():
if "name" in entity_obj["gene"].keys():
gene_name_obj = entity_obj["gene"]["name"]
if not type(gene_name_obj) == list:
gene_name_obj = [gene_name_obj]
for name_dict in gene_name_obj:
# print(name_dict)
if "primary" in name_dict.values() and "#text" in name_dict.keys():
ret_symbol = name_dict["#text"]
return ret_symbol
@staticmethod
def __get_name(entity_type, entity_id):
entity_obj = QueryUniprot.__get_entity(entity_type, entity_id)
name = "UNKNOWN"
if entity_obj is not None:
if 'protein' in entity_obj.keys():
if 'recommendedName' in entity_obj['protein'].keys():
if 'fullName' in entity_obj['protein']['recommendedName'].keys():
name = entity_obj['protein']['recommendedName']['fullName']
if isinstance(name, dict):
name = name['#text']
return name
@staticmethod
def get_protein_name(protein_id):
if not isinstance(protein_id, str):
return "UNKNOWN"
return QueryUniprot.__get_name("get_protein", protein_id)
@staticmethod
def get_citeable_accession_for_accession(accession_number):
res_acc = None
res_tab = QueryUniprot.__access_api("uniprot/" + accession_number + ".tab")
if res_tab is None:
return res_acc
res_lines = res_tab.splitlines()
if len(res_lines) > 1:
res_acc = res_lines[1].split("\t")[0]
return res_acc
if __name__ == '__main__':
print(QueryUniprot.get_citeable_accession_for_accession("P35354"))
print(QueryUniprot.get_citeable_accession_for_accession("A8K802"))
print(QueryUniprot.get_citeable_accession_for_accession("Q16876"))
# print(QueryUniprot.uniprot_id_to_reactome_pathways("P68871"))
# print(QueryUniprot.uniprot_id_to_reactome_pathways("Q16621"))
# print(QueryUniprot.uniprot_id_to_reactome_pathways("P09601"))
print(CachedMethods.cache_info())
print(QueryUniprot.map_enzyme_commission_id_to_uniprot_ids("ec:1.4.1.17")) # small results
print(QueryUniprot.map_enzyme_commission_id_to_uniprot_ids("ec:1.3.1.110")) # empty result
print(QueryUniprot.map_enzyme_commission_id_to_uniprot_ids("ec:1.2.1.22")) # large results
print(QueryUniprot.map_enzyme_commission_id_to_uniprot_ids("ec:4.4.1.xx")) # fake id
print(QueryUniprot.map_enzyme_commission_id_to_uniprot_ids("R-HSA-1912422")) # wrong id
print(QueryUniprot.get_protein_gene_symbol('UniProtKB:P20848'))
print(QueryUniprot.get_protein_gene_symbol("UniProtKB:P01358"))
print(QueryUniprot.get_protein_gene_symbol("UniProtKB:Q96P88"))
print(QueryUniprot.get_protein_name('UniProtKB:P01358'))
print(QueryUniprot.get_protein_name('UniProtKB:P20848'))
print(QueryUniprot.get_protein_name('UniProtKB:Q9Y471'))
print(QueryUniprot.get_protein_name('UniProtKB:O60397'))
print(QueryUniprot.get_protein_name('UniProtKB:Q8IZJ3'))
print(QueryUniprot.get_protein_name('UniProtKB:Q7Z2Y8'))
print(QueryUniprot.get_protein_name('UniProtKB:Q8IWN7'))
print(QueryUniprot.get_protein_name('UniProtKB:Q156A1'))