diff --git a/msnpy/__main__.py b/msnpy/__main__.py index 29f5fa7..b848879 100644 --- a/msnpy/__main__.py +++ b/msnpy/__main__.py @@ -226,6 +226,10 @@ def main(): # pragma: no cover action='store_true', required=False, help="Filter the spectral tree annotations.") + parser_ast.add_argument('-t', '--time_limit', + default=None, type=float, required=False, + help="Time limit (seconds) for each tree to be processed for annotation") + ################################# # RANK SPECTRAL TREES ################################# @@ -375,10 +379,11 @@ def main(): # pragma: no cover ppm=args.ppm, adducts=adducts, rules=args.rules, - mf_db=args.mf_db) + mf_db=args.mf_db, + time_limit=args.time_limit) if args.filter: - st = filter_mf(st, args.output_db) + st = filter_mf(st, args.output_db, args.time_limit) save_trees(st, args.output_trees, format="json") if args.step == "rank-spectral-trees": diff --git a/msnpy/annotation.py b/msnpy/annotation.py index 02ee040..8a987cb 100644 --- a/msnpy/annotation.py +++ b/msnpy/annotation.py @@ -22,6 +22,7 @@ import collections import sqlite3 +import time from typing import Sequence import networkx as nx @@ -30,6 +31,12 @@ from .processing import mz_tol, mz_pair_diff_tol +def is_time_left(start_time, time_limit): + if time_limit and start_time and time.time() - start_time >= time_limit: + return False + else: + return True + class ApiMfdb: @@ -87,7 +94,7 @@ def select_mf(self, min_tol: float, max_tol: float, adducts: dict = None, rules: def annotate_mf(spectral_trees: Sequence[nx.classes.ordered.OrderedDiGraph], db_out: str, ppm: float, adducts: dict = {"[M+H]+": 1.0072764}, rules: bool = True, mf_db: str = "http://mfdb.bham.ac.uk", - prefix_inp: str = ""): + prefix_inp: str = "", time_limit: float = None): db = ApiMfdb(url=mf_db) @@ -95,6 +102,8 @@ def annotate_mf(spectral_trees: Sequence[nx.classes.ordered.OrderedDiGraph], db_ cursor = conn.cursor() for G in spectral_trees: + start_time = time.time() + print("Annotate precursors and fragments for Group {}".format(G.graph["id"])) if prefix_inp == "": prefix = "_{}".format(G.graph["id"]) @@ -131,6 +140,8 @@ def annotate_mf(spectral_trees: Sequence[nx.classes.ordered.OrderedDiGraph], db_ nodes_done = [] rows = [] for edge in G.edges(data=True): + if not is_time_left(start_time, time_limit): + break if edge[2]['mzdiff'] > 0.5 and edge[2]['type'] == "e": @@ -192,6 +203,10 @@ def annotate_mf(spectral_trees: Sequence[nx.classes.ordered.OrderedDiGraph], db_ # None, None, None, None, None, 0,) # rows.append(values) + if not is_time_left(start_time, time_limit): + print("Could not complete - time out for group {}".format(G.graph["id"])) + continue + cursor.executemany(""" INSERT INTO MF{} (MZ_ID, MF_ID, C, H, N, O, P, S, ADDUCT, MASS, MZ, PPM_ERROR, PRECURSOR, MSLEVEL, DBE, LEWIS, SENIOR, HC, NOPSC, flag) @@ -215,7 +230,8 @@ def annotate_mf(spectral_trees: Sequence[nx.classes.ordered.OrderedDiGraph], db_ return spectral_trees -def mf_tree(G: nx.classes.ordered.OrderedDiGraph, path_db: str, max_mslevel: int, prefix: str): +def mf_tree(G: nx.classes.ordered.OrderedDiGraph, path_db: str, max_mslevel: int, prefix: str, time_limit: float = None, + start_time=None): conn = sqlite3.connect(path_db) cursor = conn.cursor() @@ -257,6 +273,10 @@ def mf_tree(G: nx.classes.ordered.OrderedDiGraph, path_db: str, max_mslevel: int record = tuple(filter(lambda x: x is not None, record)) for i in range(0, len(record), 6): + if not is_time_left(start_time, time_limit): + print('Time limit reached - no annotated tree for graph {}'.format(G.graph["id"])) + return False + ids = record[i:i + 6] cursor.execute(""" SELECT MZ_ID, MF_ID, C, H, N, O, P, S, ADDUCT, MASS @@ -290,16 +310,20 @@ def mf_tree(G: nx.classes.ordered.OrderedDiGraph, path_db: str, max_mslevel: int if "mf" not in node[1]: GG.remove_node(node[0]) GG.graph["id"] = "{}_{}".format(GG.graph["id"], mf_prec[0]) + mft.append(GG) conn.close() return mft -def filter_mf(trees: Sequence[nx.classes.ordered.OrderedDiGraph], path_db: str): +def filter_mf(trees: Sequence[nx.classes.ordered.OrderedDiGraph], path_db: str, time_limit: float = None): #http://www.sqlstyle.guide/ + print('filter mf') + + conn = sqlite3.connect(path_db) cursor = conn.cursor() @@ -307,8 +331,10 @@ def filter_mf(trees: Sequence[nx.classes.ordered.OrderedDiGraph], path_db: str): annotated_trees = [] for G in trees: + start_time = time.time() prefix = "_{}".format(G.graph["id"]) + print("Filtering group {}".format(G.graph["id"])) ################################################################ # TABLES: EDGES AND MZ_PREC_FRAG @@ -364,6 +390,8 @@ def filter_mf(trees: Sequence[nx.classes.ordered.OrderedDiGraph], path_db: str): # Insert all inital edges for edge in [edge for edge in G.edges(data=True) if edge[2]["type"] == "e" and edge[2]["mzdiff"] > 0.5]: + if not is_time_left(start_time, time_limit): + break # Set IDs to search sqlite database mz_id_prec, mz_id_frag, mz_id_nl = edge[0], edge[1], "{}__{}".format(edge[0], edge[1]) @@ -376,6 +404,9 @@ def filter_mf(trees: Sequence[nx.classes.ordered.OrderedDiGraph], path_db: str): # Number of C in the fragment MF plus the number of C in the neutral mass should be equal to the number of C in the precursor MF # Apply for N, O, P and S. for atom in atoms: + if not is_time_left(start_time, time_limit): + break + sub_queries.append("MF3.{} <= MF1.{} AND MF3.{} + MF2.{} = MF1.{}".format(atom, atom, atom, atom, atom)) # APPLY CONSTRAINS & INSERT EDGES @@ -402,9 +433,13 @@ def filter_mf(trees: Sequence[nx.classes.ordered.OrderedDiGraph], path_db: str): if max_mslevel is None: max_mslevel = 1 for loop in range(1, max_mslevel + 1): + if not is_time_left(start_time, time_limit): + break # loop through neutral losses (i.e. type is e) for edge in [edge for edge in G.edges(data=True) if edge[2]["type"] == "e" and edge[2]["mzdiff"] > 0.5]: + if not is_time_left(start_time, time_limit): + break # Define constrains as above mz_id_prec, mz_id_frag, mz_id_nl = edge[0], edge[1], "{}__{}".format(edge[0], edge[1]) @@ -414,6 +449,8 @@ def filter_mf(trees: Sequence[nx.classes.ordered.OrderedDiGraph], path_db: str): 'MF1.FLAG >= 0 AND MF2.FLAG >= 0 AND MF3.FLAG >= 0'] for atom in atoms: + if not is_time_left(start_time, time_limit): + break sub_queries.append("MF3.{} <= MF1.{} AND MF3.{} + MF2.{} = MF1.{}".format(atom, atom, atom, atom, atom)) # Apply constrains & Update edges @@ -500,6 +537,8 @@ def filter_mf(trees: Sequence[nx.classes.ordered.OrderedDiGraph], path_db: str): """.format(prefix, prefix, prefix, prefix), (loop, loop, loop, loop, )) records = cursor.fetchall() for record in records: + if not is_time_left(start_time, time_limit): + break # Set the flag for the fragment/precursor MF to a minus value (i.e. -flag) # If all related fragment masses (if exists) have no MF annotation @@ -512,7 +551,9 @@ def filter_mf(trees: Sequence[nx.classes.ordered.OrderedDiGraph], path_db: str): """.format(prefix, prefix, prefix, prefix, prefix), values) conn.commit() - # UPDATE COLUMN FLAG IN TABLE EDGES FOR PERCURSOR, NEUTRAL LOSS AND FRAGMENT BASED ON MF TABLE + # UPDATE COLUMN FLAG IN TABLE EDGES FOR PRECURSOR, NEUTRAL LOSS AND FRAGMENT BASED ON MF TABLE + if not is_time_left(start_time, time_limit): + break cursor.execute(""" UPDATE EDGES{} @@ -525,6 +566,8 @@ def filter_mf(trees: Sequence[nx.classes.ordered.OrderedDiGraph], path_db: str): ); """.format(prefix, prefix, prefix)) + elapsed_time = time.time() - start_time + cursor.execute(""" UPDATE EDGES{} SET MF_ID_NL_FLAG = ( @@ -540,6 +583,7 @@ def filter_mf(trees: Sequence[nx.classes.ordered.OrderedDiGraph], path_db: str): ); """.format(prefix, prefix, prefix)) + cursor.execute(""" UPDATE EDGES{} SET MF_ID_PREC_FLAG = ( @@ -571,8 +615,16 @@ def filter_mf(trees: Sequence[nx.classes.ordered.OrderedDiGraph], path_db: str): """.format(prefix)) improvement.append(cursor.fetchone()[0]) + if not is_time_left(start_time, time_limit): + print('Time limit reached - no annotated tree for graph {}'.format(G.graph["id"])) + continue + print("MF AFTER CONSTRAINS: ", ", ".join(map(str, improvement))) - annotated_trees.extend(mf_tree(G, path_db, max_mslevel, prefix)) + + mf_tree_out = mf_tree(G, path_db, max_mslevel, prefix, time_limit, start_time) + + if mf_tree_out: + annotated_trees.extend(mf_tree_out) conn.close() return annotated_trees diff --git a/tests/data/small_adducts_neg.tsv b/tests/data/small_adducts_neg.tsv new file mode 100644 index 0000000..2d2756a --- /dev/null +++ b/tests/data/small_adducts_neg.tsv @@ -0,0 +1,5 @@ +label exact_mass ion_mode +[M-H]- -1.007276 neg +[M+Cl]- 34.969402 neg +[M+HCOO]- 44.99765 neg +[M+CH3COO]- 59.01385 neg diff --git a/tests/data/time_limit_test_spectral_tree.json b/tests/data/time_limit_test_spectral_tree.json new file mode 100644 index 0000000..ad480e3 --- /dev/null +++ b/tests/data/time_limit_test_spectral_tree.json @@ -0,0 +1,64 @@ +{'directed': True, 'multigraph': False, 'graph': {'id': 1}, 'nodes': 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'623.3419_6_4'}, {'mzdiff': 0.0138245, 'type': 'e', 'order': 11, 'source': '623.3593_4_35', 'target': '623.3455_6_5'}, {'mzdiff': -0.0967712, 'type': 'e', 'order': 12, 'source': '623.3593_4_35', 'target': '623.4561_6_6'}, {'mzdiff': 417.2468414, 'type': 'e', 'order': 13, 'source': '623.3593_4_35', 'target': '206.1124_7_0'}]} \ No newline at end of file diff --git a/tests/test_annotation.py b/tests/test_annotation.py index 1567518..ce7d258 100644 --- a/tests/test_annotation.py +++ b/tests/test_annotation.py @@ -144,6 +144,20 @@ def test_filter_mf(self): records = cursor.fetchall() self.assertListEqual(records, [('MF_1',), ('EDGES_1',), ('MZ_PREC_FRAG_1',)]) + + def test_time_limit_annotate(self): + ann_time = annotate_mf(spectral_trees=self.trees, db_out=self.db_single_adduct, ppm=10.0, + adducts={"[M+H]+": 1.0072764}, rules=True, + mf_db="http://mfdb.bham.ac.uk", time_limit=0.001) + + # check no annotation performed and we output un-annotated trees + + def test_time_limit_mf_filter(self): + filter_ann_time = filter_mf(self.trees, self.db_single_adduct_filtered, time_limit=0.001) + + # check no annotation performed and we output un-annotated trees + + def test_mf_tree(self): mft = mf_tree(self.trees[0], self.db_single_adduct_filtered, max_mslevel=5, prefix="_1")