Source code for indra.databases.hgnc_client

from __future__ import absolute_import, print_function, unicode_literals
from builtins import dict, str
import os
import re
import csv
import xml.etree.ElementTree as ET
import requests
# Python3
try:
    from functools import lru_cache
# Python2
except ImportError:
    from functools32 import lru_cache
from indra.util import read_unicode_csv, UnicodeXMLTreeBuilder as UTB

hgnc_url = 'http://rest.genenames.org/fetch/'


[docs]def get_uniprot_id(hgnc_id): """Return the UniProt ID corresponding to the given HGNC ID. Parameters ---------- hgnc_id : str The HGNC ID to be converted. Note that the HGNC ID is a number that is passed as a string. It is not the same as the HGNC gene symbol. Returns ------- uniprot_id : str The UniProt ID corresponding to the given HGNC ID. """ uniprot_id = uniprot_ids.get(hgnc_id) # The lookup can yield an empty string. Instead return None. if not uniprot_id: return None return uniprot_id
[docs]def get_entrez_id(hgnc_id): """Return the Entrez ID corresponding to the given HGNC ID. Parameters ---------- hgnc_id : str The HGNC ID to be converted. Note that the HGNC ID is a number that is passed as a string. It is not the same as the HGNC gene symbol. Returns ------- entrez_id : str The Entrez ID corresponding to the given HGNC ID. """ entrez_id = entrez_ids.get(hgnc_id) # The lookup can yield an empty string. Instead return None. if not entrez_id: return None return entrez_id
[docs]def get_hgnc_from_entrez(entrez_id): """Return the HGNC ID corresponding to the given Entrez ID. Parameters ---------- entrez_id : str The EntrezC ID to be converted, a number passed as a strig. Returns ------- hgnc_id : str The HGNC ID corresponding to the given Entrez ID. """ hgnc_id = entrez_ids_reverse.get(entrez_id) return hgnc_id
[docs]def get_hgnc_name(hgnc_id): """Return the HGNC symbol corresponding to the given HGNC ID. Parameters ---------- hgnc_id : str The HGNC ID to be converted. Returns ------- hgnc_name : str The HGNC symbol corresponding to the given HGNC ID. """ try: hgnc_name = hgnc_names[hgnc_id] except KeyError: xml_tree = get_hgnc_entry(hgnc_id) if xml_tree is None: return None hgnc_name_tag =\ xml_tree.find("result/doc/str[@name='symbol']") if hgnc_name_tag is None: return None hgnc_name = hgnc_name_tag.text.strip() return hgnc_name
[docs]def get_hgnc_id(hgnc_name): """Return the HGNC ID corresponding to the given HGNC symbol. Parameters ---------- hgnc_name : str The HGNC symbol to be converted. Example: BRAF Returns ------- hgnc_id : str The HGNC ID corresponding to the given HGNC symbol. """ return hgnc_ids.get(hgnc_name)
[docs]def get_hgnc_from_mouse(mgi_id): """Return the HGNC ID corresponding to the given MGI mouse gene ID. Parameters ---------- mgi_id : str The MGI ID to be converted. Example: "2444934" Returns ------- hgnc_id : str The HGNC ID corresponding to the given MGI ID. """ if mgi_id.startswith('MGI:'): mgi_id = mgi_id[4:] return mouse_map.get(mgi_id)
[docs]def get_hgnc_from_rat(rgd_id): """Return the HGNC ID corresponding to the given RGD rat gene ID. Parameters ---------- rgd_id : str The RGD ID to be converted. Example: "1564928" Returns ------- hgnc_id : str The HGNC ID corresponding to the given RGD ID. """ if rgd_id.startswith('RGD:'): rgd_id = rgd_id[4:] return rat_map.get(rgd_id)
[docs]def get_rat_id(hgnc_id): """Return the RGD rat ID corresponding to the given HGNC ID. Parameters ---------- hgnc_id : str The HGNC ID to be converted. Example: "" Returns ------- rgd_id : str The RGD ID corresponding to the given HGNC ID. """ for k, v in rat_map.items(): if v == hgnc_id: return k
[docs]def get_mouse_id(hgnc_id): """Return the MGI mouse ID corresponding to the given HGNC ID. Parameters ---------- hgnc_id : str The HGNC ID to be converted. Example: "" Returns ------- mgi_id : str The MGI ID corresponding to the given HGNC ID. """ for k, v in mouse_map.items(): if v == hgnc_id: return k
[docs]@lru_cache(maxsize=1000) def get_hgnc_entry(hgnc_id): """Return the HGNC entry for the given HGNC ID from the web service. Parameters ---------- hgnc_id : str The HGNC ID to be converted. Returns ------- xml_tree : ElementTree The XML ElementTree corresponding to the entry for the given HGNC ID. """ url = hgnc_url + 'hgnc_id/%s' % hgnc_id headers = {'Accept': '*/*'} res = requests.get(url, headers=headers) if not res.status_code == 200: return None xml_tree = ET.XML(res.content, parser=UTB()) return xml_tree
def _read_hgnc_maps(): hgnc_file = os.path.dirname(os.path.abspath(__file__)) + \ '/../resources/hgnc_entries.tsv' csv_rows = read_unicode_csv(hgnc_file, delimiter='\t', encoding='utf-8') hgnc_names = {} hgnc_ids = {} hgnc_withdrawn = [] uniprot_ids = {} entrez_ids = {} entrez_ids_reverse = {} mouse_map = {} rat_map = {} for row in csv_rows: hgnc_id = row[0][5:] hgnc_status = row[3] if hgnc_status == 'Approved': hgnc_name = row[1] hgnc_names[hgnc_id] = hgnc_name hgnc_ids[hgnc_name] = hgnc_id elif hgnc_status == 'Symbol Withdrawn': descr = row[2] m = re.match(r'symbol withdrawn, see ([^ ]*)', descr) new_name = m.groups()[0] hgnc_withdrawn.append(hgnc_id) hgnc_names[hgnc_id] = new_name # Uniprot uniprot_id = row[6] uniprot_ids[hgnc_id] = uniprot_id # Entrez entrez_id = row[5] entrez_ids[hgnc_id] = entrez_id entrez_ids_reverse[entrez_id] = hgnc_id # Mouse mgi_id = row[7] if mgi_id: mgi_ids = mgi_id.split(', ') for mgi_id in mgi_ids: if mgi_id.startswith('MGI:'): mgi_id = mgi_id[4:] mouse_map[mgi_id] = hgnc_id # Rat rgd_id = row[8] if rgd_id: rgd_ids = rgd_id.split(', ') for rgd_id in rgd_ids: if rgd_id.startswith('RGD:'): rgd_id = rgd_id[4:] rat_map[rgd_id] = hgnc_id return (hgnc_names, hgnc_ids, hgnc_withdrawn, uniprot_ids, entrez_ids, entrez_ids_reverse, mouse_map, rat_map) (hgnc_names, hgnc_ids, hgnc_withdrawn, uniprot_ids, entrez_ids, entrez_ids_reverse, mouse_map, rat_map) = \ _read_hgnc_maps()