Skip to content

Commit

Permalink
Time limit (#14)
Browse files Browse the repository at this point in the history 
* testing time limits

* futher checks for time
  • Loading branch information
@Tomnl
Tomnl authored Jun 18, 2020
1 parent 074ff70 commit 5e3dad8
Show file tree
Hide file tree
Showing 7 changed files with 151 additions and 7 deletions.
9 changes: 7 additions & 2 deletions msnpy/__main__.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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
#################################
Expand Down Expand Up @@ -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":
Expand Down
62 changes: 57 additions & 5 deletions msnpy/annotation.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@

import collections
import sqlite3
import time
from typing import Sequence

import networkx as nx
Expand All @@ -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:

Expand Down Expand Up @@ -87,14 +94,16 @@ 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)

conn = sqlite3.connect(db_out)
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"])
Expand Down Expand Up @@ -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":

Expand Down Expand Up @@ -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)
Expand All @@ -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()
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -290,25 +310,31 @@ 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()

atoms = ["C", "H", "N", "O", "P", "S"]

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
Expand Down Expand Up @@ -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])
Expand All @@ -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
Expand All @@ -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])
Expand All @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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{}
Expand All @@ -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 = (
Expand All @@ -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 = (
Expand Down Expand Up @@ -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
Expand Down
5 changes: 5 additions & 0 deletions tests/data/small_adducts_neg.tsv
View file
Original file line number Diff line number Diff line change
@@ -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
Loading

0 comments on commit 5e3dad8

Please sign in to comment.