"""
GNPS Utils - Network Module
This module provides functionality to connect to GNPS and retrieve data.
Author: Shahneh
"""
import json
import requests
from modifinder.utilities.gnps_types import *
from modifinder.utilities.general_utils import parse_data_to_universal
from modifinder.exceptions import ModiFinderNetworkError
from rdkit import Chem
[docs]def usi_to_accession(usi: str) -> str:
"""
Get the accession number from a USI
param usi: str
return: str if found, None otherwise
"""
if "accession" in usi:
return usi.split(":")[-1]
else:
if isinstance(usi, str):
return usi
else:
return None
[docs]def accession_to_usi(accession: str) -> str:
"""
Get the USI from an accession id
param accession: str
return: str
"""
return "mzspec:GNPS:{}:accession:{}".format("GNPS-LIBRARY", accession)
[docs]def get_data(identifier: str) -> dict:
"""
Get data from GNPS, either from USI or Accession. if the identifier points to a known item in gnps,
it will return the full data, otherwise it will return partial data (ms2 data)
param identifier: str - USI or Accession
return: dict - dictionary of data
"""
if not identifier:
raise ModiFinderNetworkError("No identifier provided")
if not isinstance(identifier, str):
raise ModiFinderNetworkError("Identifier must be a string")
data = dict()
if _is_usi(identifier):
if _is_known(identifier):
identifier = usi_to_accession(identifier)
else:
data = _get_partial_data(identifier)
data['usi'] = identifier
data['id'] = identifier
data = parse_data_to_universal(data)
return data
link = "https://external.gnps2.org/gnpsspectrum?SpectrumID={}".format(identifier)
try:
res = requests.get(link)
parsed = res.json()
except:
raise ModiFinderNetworkError("Error in retrieving data from GNPS for identifier: {}, link: {}".format(identifier, link))
try:
data.update(parsed['annotations'][0])
except KeyError:
pass
try:
data.update(parsed['spectruminfo'])
except KeyError:
pass
try:
data['comments'] = parsed['comments']
except KeyError:
pass
data = parse_data_to_universal(data)
data['usi'] = accession_to_usi(identifier)
data['id'] = identifier
return data
[docs]def get_matched_peaks(identifier1: str, identifier2: str) -> dict:
"""
runs the gnps modified cosine matching algorithm and returns the matched peaks
param identifier1: str - USI or Accession
param identifier2: str - USI or Accession
return: dict - dictionary of matched peaks
"""
if not _is_usi(identifier1):
identifier1 = accession_to_usi(identifier1)
if not _is_usi(identifier2):
identifier2 = accession_to_usi(identifier2)
payload = {
'usi1': identifier1,
'usi2': identifier2,
'mz_min': 'None',
'mz_max':'None',
'cosine':'shifted',
'mz_tolerance':'0.1',
'grid': 'True'}
r = requests.get('https://metabolomics-usi.gnps2.org/json/mirror/', params=payload, timeout=5)
return json.loads(r.text)
def _get_partial_data(identifier: str) -> dict:
"""
Get partial data (ms2 data) from USI
param identifier: str - USI
return: dict - dictionary of data with keys: precursor_mz, precursor_charge, mz: list, intensity: list
"""
url = 'https://metabolomics-usi.gnps2.org/json/' + "?usi1=" + identifier
try:
r = requests.get(url)
data = json.loads(r.text)
except:
raise Exception("Error in retrieving data from GNPS for identifier: {}, link: {}".format(identifier, url))
data = parse_data_to_universal(data)
return data
def _is_usi(identifier: str) -> bool:
"""
Check if the identifier is a USI
param identifier: str
return: bool
"""
return "mzspec" in identifier
def _is_known(identifier: str) -> bool:
"""
Check if the identifier is a known identifier in GNPS
param identifier: str
return: bool
"""
return "accession" in identifier
[docs]def get_np_classifier(smiles):
"""
Get the NP classifier data for a molecule
Parameters
----------
smiles : str
SMILES string of the molecule.
Returns
-------
dict
Dictionary with keys: class_types (list), superclasses (list), pathways (list), isglycoside (bool).
"""
if isinstance(smiles, str):
smiles = smiles
else:
if isinstance(smiles, Chem.Mol):
smiles = Chem.MolToSmiles(smiles)
else:
raise ValueError("Invalid input for np_classifier")
try:
url = "https://npclassifier.gnps2.org/classify"
response = requests.get(url, params={"smiles": smiles}, timeout=1)
data = json.loads(response.text)
for key in data:
if data[key] == "None":
data[key] = []
final_data = {
"class_types": data["class_results"],
"superclasses": data["superclass_results"],
"pathways": data["pathway_results"],
"isglycoside": data["isglycoside"],
}
return final_data
except Exception:
return {
"class_types": [],
"superclasses": [],
"pathways": [],
"isglycoside": None,
}