From d695413f0b39f0bff47ae4209f150aaf84b18979 Mon Sep 17 00:00:00 2001 From: Sebastian Prillo <10426884+sprillo@users.noreply.github.com> Date: Tue, 21 Jul 2020 20:39:40 -0700 Subject: [PATCH 1/6] Add Turbo Compass. --- .../Test Data/rsem_tpmTable_2cells.txt | 42128 ++++++++++++++++ .../Test Data/rsem_tpmTable_4cells.txt | 42128 ++++++++++++++++ compass/compass/algorithm.py | 37 +- compass/global_state.py | 76 + compass/globals.py | 5 +- compass/main.py | 130 +- compass/turbo_compass.py | 366 + conftest.py | 21 + setup.py | 4 +- tests/data/select_reactions.txt | 1 + .../data/selected_reactions_for_each_cell.txt | 4 + tests/test_compass.py | 146 + tests/test_global_state.py | 39 + tests/test_models.py | 6 + tests/test_turbo_compass.py | 346 + 15 files changed, 85399 insertions(+), 38 deletions(-) create mode 100644 compass/Resources/Test Data/rsem_tpmTable_2cells.txt create mode 100644 compass/Resources/Test Data/rsem_tpmTable_4cells.txt create mode 100644 compass/global_state.py create mode 100644 compass/turbo_compass.py create mode 100644 conftest.py create mode 100644 tests/data/select_reactions.txt create mode 100644 tests/data/selected_reactions_for_each_cell.txt create mode 100644 tests/test_compass.py create mode 100644 tests/test_global_state.py create mode 100644 tests/test_turbo_compass.py diff --git a/compass/Resources/Test Data/rsem_tpmTable_2cells.txt b/compass/Resources/Test Data/rsem_tpmTable_2cells.txt new file mode 100644 index 0000000..f0f9204 --- /dev/null +++ b/compass/Resources/Test Data/rsem_tpmTable_2cells.txt @@ -0,0 +1,42128 @@ +Gene Sybmol WT-d_S141_L007_R1_001 Ob-DHA-e_S154_L007_R1_001 +Xkr4 0.0 0.0 +LOC102640625 60.25 92.35 +LOC102640704 0.0 0.0 +Xkr9 9.6 15.74 +LOC102638355 0.87 0.55 +LOC102634683 1.04 0.21 +LOC102634599 0.26 0.7 +Eif4g3 16.53 22.62 +LOC102634927 0.41 0.6 +1700095J12Rik 0.0 0.0 +LOC102634789 1.4 0.42 +Mir6399 0.0 0.0 +Hp1bp3 26.75 38.27 +Sh2d5 0.0 0.0 +Kif17 0.0 0.0 +Gm2666 0.0 0.0 +Ddost 62.01 55.53 +Pink1 75.09 137.74 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+LOC102633328 0.0 0.0 0.0 0.0 +Rpl11 408.35 425.73 431.38 413.92 +Id3 56.38 61.21 60.95 57.02 +E2f2 0.7 0.37 0.67 0.21 +Asap3 7.94 4.37 5.81 3.35 +Tcea3 67.08 81.03 58.05 83.05 +LOC102638555 0.0 0.02 0.0 0.0 +Zfp46 1.26 1.53 1.84 1.23 +Hnrnpr 10.93 11.06 11.11 10.78 +Gm17388 1.33 1.03 1.58 1.01 +LOC102633481 0.0 0.0 0.0 0.0 +Htr1d 0.0 0.0 0.0 0.08 +Luzp1 3.09 5.04 3.56 5.04 +Kdm1a 6.39 8.88 6.09 9.0 +LOC102633670 0.0 0.0 0.16 0.45 +4930549C01Rik 0.0 0.0 0.0 0.0 +LOC102638435 0.0 0.0 0.0 0.0 +Lactbl1 0.0 0.0 0.0 0.0 +Ephb2 1.17 3.21 1.08 7.7 +LOC102633796 0.0 0.0 0.34 0.0 +C1qb 28.1 65.98 51.3 63.53 +C1qc 26.98 79.42 52.12 69.71 +C1qa 32.28 61.86 57.38 55.83 +Epha8 0.0 0.0 0.0 0.0 +Zbtb40 1.87 1.33 1.41 1.89 +LOC102633949 0.0 0.0 0.0 0.0 +LOC102634021 0.0 0.0 0.0 0.0 +Gm7609 8.55 8.16 8.83 9.09 +LOC102634099 0.0 0.0 0.0 0.0 +Gm13003 0.0 0.0 0.0 0.0 +LOC102634171 0.08 0.0 0.06 0.04 +Wnt4 1.36 1.51 0.6 2.46 +Cdc42 59.1 118.19 75.46 125.97 +LOC102634326 0.62 0.19 0.4 0.19 +Gm13011 0.0 0.0 0.0 0.0 +Cela3b 0.0 0.0 0.0 0.0 +C130026I21Rik 0.0 0.0 0.0 0.0 +1700013G24Rik 0.0 0.0 0.0 0.0 +Hspg2 2.52 4.08 2.06 4.86 +Mir7018 0.0 0.0 0.0 0.0 +Ldlrad2 2.53 2.66 0.79 2.47 +Usp48 10.17 12.7 10.82 12.55 +Rap1gap 2.45 2.87 1.92 2.71 +Rap1gapos 0.0 0.0 0.0 0.76 +Alpl 9.97 21.55 10.58 19.99 +LOC102634516 0.0 0.0 0.0 0.0 +Ece1 61.02 98.63 73.38 96.19 diff --git a/compass/compass/algorithm.py b/compass/compass/algorithm.py index c93e8ee..aa83ca6 100644 --- a/compass/compass/algorithm.py +++ b/compass/compass/algorithm.py @@ -2,6 +2,7 @@ Run the procedure for COMPASS """ from __future__ import print_function, division, absolute_import +import numpy as np import pandas as pd from tqdm import tqdm from random import shuffle @@ -13,6 +14,7 @@ from .. import models from . import cache from ..globals import BETA, EXCHANGE_LIMIT +import compass.global_state as global_state import cplex @@ -75,7 +77,7 @@ def singleSampleCompass(data, model, media, directory, sample_index, args): logger.info("Processing Sample %i/%i: %s", sample_index, len(expression.columns), sample_name) - + global_state.set_current_cell_name(sample_name) # Run core compass algorithm # Evaluate reaction penalties @@ -198,7 +200,7 @@ def compass_exchange(model, problem, reaction_penalties, select_reactions=None, uptake_scores[met_id] = 0.0 secretion_scores[met_id] = 0.0 - continue + continue # In test mode this always continues! # Rectify exchange reactions # Either find existing pos and neg exchange reactions @@ -226,7 +228,7 @@ def compass_exchange(model, problem, reaction_penalties, select_reactions=None, reactions = [r for r in reactions if ((r.id)[:-4] in selected_reaction_ids)] - for reaction in reactions: + for reaction in reactions: # This only effectively loops over exchange reactions in fact. if reaction.is_exchange and met_id in reaction.products: if uptake_rxn is None: uptake_rxn = reaction.id @@ -319,8 +321,8 @@ def compass_exchange(model, problem, reaction_penalties, select_reactions=None, problem.objective.set_name('reaction_penalties') problem.objective.set_sense(problem.objective.sense.minimize) - problem.solve() - value = problem.solution.get_objective_value() + global_state.set_current_reaction_id(secretion_rxn) + value = solve_problem_wrapper(problem) secretion_scores[met_id] = value # Clear Secretion constraint @@ -371,8 +373,8 @@ def compass_exchange(model, problem, reaction_penalties, select_reactions=None, problem.objective.set_name('reaction_penalties') problem.objective.set_sense(problem.objective.sense.minimize) - problem.solve() - value = problem.solution.get_objective_value() + global_state.set_current_reaction_id(uptake_rxn) + value = solve_problem_wrapper(problem) uptake_scores[met_id] = value # Clear Secretion constraint @@ -436,7 +438,6 @@ def compass_reactions(model, problem, reaction_penalties, select_reactions=None, reactions = [r for r in reactions if ((r.id)[:-4] in selected_reaction_ids)] - for reaction in tqdm(reactions, file=sys.stderr): if reaction.is_exchange: @@ -474,8 +475,8 @@ def compass_reactions(model, problem, reaction_penalties, select_reactions=None, problem.objective.set_name('reaction_penalties') problem.objective.set_sense(problem.objective.sense.minimize) - problem.solve() - value = problem.solution.get_objective_value() + global_state.set_current_reaction_id(reaction.id) + value = solve_problem_wrapper(problem) reaction_scores[reaction.id] = value # Remove Constraint @@ -552,11 +553,23 @@ def maximize_reaction(model, problem, rxn, use_cache=True): problem.objective.set_name(rxn) problem.objective.set_sense(problem.objective.sense.maximize) - problem.solve() - rxn_max = problem.solution.get_objective_value() + global_state.set_current_reaction_id(rxn) + rxn_max = solve_problem_wrapper(problem) # Save the result model_cache = cache.load(model) model_cache[rxn] = rxn_max return rxn_max + + +def solve_problem_wrapper(problem) -> float: + r""" + Only solve the problem if the reaction is selected for the cell. Else, + skip the computation and return np.nan. + """ + if global_state.current_reaction_is_selected_for_current_cell(): + problem.solve() + return problem.solution.get_objective_value() + else: + return np.nan diff --git a/compass/global_state.py b/compass/global_state.py new file mode 100644 index 0000000..edd9da3 --- /dev/null +++ b/compass/global_state.py @@ -0,0 +1,76 @@ +r""" +This module contains global state. It is used for e.g. determining whether +to skip the computation of a reaction for a cell when --selected-reactions-for-each-cell +is provided. +""" +import os +from typing import Optional + +_current_cell_name = -1 +_current_reaction_id = "" +# This will hold an object of the class SelectedReactionsForEachCell that +# will allow us to know +_selected_reactions_for_each_cell = None + + +class _SelectedReactionsForEachCell(): + def __init__(self, path: Optional[str]): + r""" + :param path: Path to file containing the reactions for each cell. + The file contains one line per cell of interest. Each line is + comma-separated. It starts with the name of the cell, and is + followed by the reaction ids of interest. + E.g. 'cell42,BUP2_pos,BUP2_neg,DHPM2_pos' is a valid line. + If no path is provided, then no (cells, reaction) pairs will + be excluded by this method. + """ + if path is None: + reactions_for_cells = None + else: + reactions_for_cells = {} + if not os.path.exists(path): + raise Exception(f"cannot find selected reactions for each cell: file {path}") + + with open(path) as f: + for line in f: + # Must be careful to remove newlines from end of file. + tokens = [token.rstrip("\n") for token in line.split(',')] + cell_name, reactions_for_this_cell = tokens[0], tokens[1:] + reactions_for_cells[cell_name] = reactions_for_this_cell + self.reactions_for_cells = reactions_for_cells + + def is_selected(self, cell_name: str, reaction_id: str) -> bool: + r""" + Whether the reaction_id is selected for cell_name. + """ + if self.reactions_for_cells is None: + # No file was supplied: everything is selected by default. + return True + return reaction_id in self.reactions_for_cells.get(cell_name, []) + + +def init_selected_reactions_for_each_cell(path: Optional[str]) -> None: + global _selected_reactions_for_each_cell + _selected_reactions_for_each_cell = _SelectedReactionsForEachCell(path) + + +def set_current_cell_name(cell_name: str) -> None: + global _current_cell_name + _current_cell_name = cell_name + + +def set_current_reaction_id(reaction_id: str) -> None: + global _current_reaction_id + _current_reaction_id = reaction_id + + +def get_current_cell_name() -> str: + return _current_cell_name + + +def get_current_reaction_id() -> str: + return _current_reaction_id + + +def current_reaction_is_selected_for_current_cell() -> bool: + return _selected_reactions_for_each_cell.is_selected(_current_cell_name, _current_reaction_id) diff --git a/compass/globals.py b/compass/globals.py index 663c2cb..9e67107 100644 --- a/compass/globals.py +++ b/compass/globals.py @@ -33,8 +33,7 @@ def init_logger(directory="."): fh = logging.FileHandler(log_file, mode='w') fh.name = 'logfile' - formatter = logging.Formatter( - '%(message)s') + formatter = logging.Formatter("%(levelname)s %(lineno)s %(name)s: %(message)s") fh.setLevel(logging.DEBUG) fh.setFormatter(formatter) @@ -42,7 +41,7 @@ def init_logger(directory="."): # Add stream to stdout sh = logging.StreamHandler(sys.stdout) - formatter = logging.Formatter('%(message)s') + formatter = logging.Formatter("%(levelname)s %(lineno)s %(name)s: %(message)s") sh.setFormatter(formatter) sh.setLevel(logging.INFO) logger.addHandler(sh) diff --git a/compass/main.py b/compass/main.py index 30c75f4..429991d 100644 --- a/compass/main.py +++ b/compass/main.py @@ -23,6 +23,8 @@ from .models import init_model from .compass.penalties import eval_reaction_penalties from . import globals +import compass.global_state as global_state +from compass.turbo_compass import turbo_compass_entry def parseArgs(): @@ -97,6 +99,45 @@ def parseArgs(): type=int, default=1, metavar="N") + parser.add_argument("--turbo", + help="If you are willing to sacrifice some accuracy in favour of speed, " + "you can run Compass with --turbo specifying the minimum tolerated " + "Spearman R2 (MIN_SR2) of the output matrix as compared to the ground " + "truth Compass matrix. This option is mutually exclusive with " + "--calc-metabolites. By default MIN_SR2=1.0, i.e. no approximation " + "is performed. Even setting MIN_SR2=0.95 can speed up Compass 5x, " + "producing an extremely fidelitous reaction score matrix.", + type=float, + default=1.0, + metavar="MIN_SR2") + + parser.add_argument("--turbo-increments", + help="Turbo Compass runs by incrementally computing only subsets of the " + "reaction score matrix. This argument indicates what percentage is" + "computed in each iteration.", + type=float, + default=0.01, + metavar="INC") + + parser.add_argument("--turbo-min-pct", + help="The minimum tolerated Spearman R2 (SR2) only has to hold for MIN_PCT " + "of the reactions. Requiring 100 pct of reactions to meet the SR2 condition " + "is typically too taxing since SR2 computation is pedantic and " + "leads to there always being some reaction that fails it. Setting this " + "argument to e.g. 0.99 is enough to fix the artifact without compromising " + "the reconstruction quality. In general, decreasing this argument will " + "cause Compass to run faster but produce more reactions that violate the " + "SR2 condition.", + type=float, + default=0.99, + metavar="MIN_PCT") + + parser.add_argument("--turbo-max-iters", + help="Maximum number of iterative matrix completion steps.", + type=int, + default=1000000, # Infinity + metavar="MAX_ITERS") + parser.add_argument( "--and-function", help="Which function used to aggregate AND associations", @@ -110,6 +151,18 @@ def parseArgs(): required=False, metavar="FILE") + parser.add_argument( + "--selected-reactions-for-each-cell", + help=argparse.SUPPRESS, + # help="Compute Compass scores only for the reactions listed for each cell, " + # "in the given file. FILE is expected to have one comma-separated line per cell of interest: the " + # "first string in each file is the cell's name, and it is followed by the reaction ids " + # "(which are directional or exchange reactions - in general, they look like what " + # "you see in the reaction.tsv file you get after you run Compass)." + # "E.g. 'cell42,BUP2_pos,BUP2_neg,DHPM2_pos' is a valid line.", + required=False, + metavar="FILE") # Not part of public API + # Hidden argument. Used for batch jobs parser.add_argument("--collect", action="store_true", help=argparse.SUPPRESS) @@ -161,6 +214,9 @@ def parseArgs(): if args['select_reactions']: args['select_reactions'] = os.path.abspath(args['select_reactions']) + if args['selected_reactions_for_each_cell']: + args['selected_reactions_for_each_cell'] = os.path.abspath(args['selected_reactions_for_each_cell']) + if args['temp_dir'] == "/_tmp": args['temp_dir'] = os.path.join(args['output_dir'], '_tmp') @@ -172,6 +228,11 @@ def parseArgs(): "'lambda' parameter cannot be less than 0 or greater than 1" ) + if args['turbo'] < 0 or args['turbo'] > 1: + parser.error( + "'turbo' parameter cannot be less than 0 or greater than 1" + ) + if args['generate_cache'] and \ (args['no_reactions'] or not args['calc_metabolites']): @@ -223,7 +284,15 @@ def entry(): logger.debug("\nCOMPASS Started: {}".format(start_time)) # Parse arguments and decide what course of action to take + if args['turbo'] < 1.0: + turbo_compass_entry() + return + + global_state.init_selected_reactions_for_each_cell( + args.get('selected_reactions_for_each_cell', None)) + if args['single_sample'] is not None: + eval_reaction_penalties_wrapper(args, logger) singleSampleCompass(data=args['data'], model=args['model'], media=args['media'], directory=args['temp_dir'], sample_index=args['single_sample'], args=args) @@ -239,21 +308,7 @@ def entry(): return # Time to evaluate the reaction expression - success_token = os.path.join(args['temp_dir'], 'success_token_penalties') - penalties_file = os.path.join(args['temp_dir'], 'penalties.txt.gz') - if os.path.exists(success_token): - logger.info("Reaction Penalties already evaluated") - logger.info("Resuming execution from previous run...") - else: - logger.info("Evaluating Reaction Penalties...") - penalties = eval_reaction_penalties(args['data'], args['model'], - args['media'], args['species'], - args) - penalties.to_csv(penalties_file, sep='\t', compression='gzip') - with open(success_token, 'w') as fout: - fout.write('Success!') - - args['penalties_file'] = penalties_file + eval_reaction_penalties_wrapper(args, logger) # Now run the individual cells through cplex in parallel # This is either done by sending to Torque queue, or running on the @@ -292,8 +347,6 @@ def runCompassParallel(args): partial_map_fun = partial(_parallel_map_fun, args=args) - pool = multiprocessing.Pool(args['num_processes']) - logger.info( "Processing {} samples using {} processes" .format(n_samples, args['num_processes']) @@ -305,8 +358,16 @@ def runCompassParallel(args): pbar = tqdm(total=n_samples) - for _ in pool.imap_unordered(partial_map_fun, range(n_samples)): - pbar.update() + if args['num_processes'] == 1: + # Don't even spawn a process! Just run in main thread. + logger.info("Since num-processes=1, will not spawn subprocess: I will just run in the main thread.") + for i in range(n_samples): + _parallel_map_fun(i, args.copy(), redirect_stderr_and_stdout=False) + pbar.update() + else: + pool = multiprocessing.Pool(args['num_processes']) + for _ in pool.imap_unordered(partial_map_fun, range(n_samples)): + pbar.update() collectCompassResults(args['data'], args['temp_dir'], args['output_dir'], args) @@ -314,7 +375,7 @@ def runCompassParallel(args): logger.info("COMPASS Completed Successfully") -def _parallel_map_fun(i, args): +def _parallel_map_fun(i, args, redirect_stderr_and_stdout: bool = True): data = args['data'] model = args['model'] @@ -331,8 +392,9 @@ def _parallel_map_fun(i, args): with open(out_file, 'w') as fout, open(err_file, 'w') as ferr: stdout_bak = sys.stdout stderr_bak = sys.stderr - sys.stdout = fout - sys.stderr = ferr + if redirect_stderr_and_stdout: + sys.stdout = fout + sys.stderr = ferr globals.init_logger(sample_dir) @@ -364,6 +426,8 @@ def _parallel_map_fun(i, args): end_time = datetime.datetime.now() logger.debug("\nElapsed Time: {}".format(end_time-start_time)) + sys.stdout = stdout_bak + sys.stderr = stderr_bak def collectCompassResults(data, temp_dir, out_dir, args): @@ -488,3 +552,25 @@ def load_config(args): newArgs[key] = str(newArgs[key]) args.update(newArgs) + + +def eval_reaction_penalties_wrapper(args, logger) -> None: + r""" + If the penalties_file already exists, then nothing is done (for it is cached). + Else, the reaction penalties are computed. + """ + success_token = os.path.join(args['temp_dir'], 'success_token_penalties') + penalties_file = os.path.join(args['temp_dir'], 'penalties.txt.gz') + if os.path.exists(success_token): + logger.info("Reaction Penalties already evaluated") + logger.info("Resuming execution from previous run...") + else: + logger.info("Evaluating Reaction Penalties...") + penalties = eval_reaction_penalties(args['data'], args['model'], + args['media'], args['species'], + args) + penalties.to_csv(penalties_file, sep='\t', compression='gzip') + with open(success_token, 'w') as fout: + fout.write('Success!') + + args['penalties_file'] = penalties_file diff --git a/compass/turbo_compass.py b/compass/turbo_compass.py new file mode 100644 index 0000000..078299c --- /dev/null +++ b/compass/turbo_compass.py @@ -0,0 +1,366 @@ +from collections import defaultdict +import logging +import numpy as np +import os +import pandas as pd +import sys +import tempfile +from typing import List, Tuple +from unittest.mock import patch + +from turbo_mc.iterative_models.matrix_oracle import MatrixOracle +from turbo_mc.models.exclude_constant_columns_model_wrapper import ExcludeConstantColumnsModelWrapper +from turbo_mc.models.column_normalizer_model_wrapper import ColumnNormalizerModelWrapper +from turbo_mc.models.matrix_completion_fast_als import MatrixCompletionFastALS +from turbo_mc.models.cv_matrix_completion_model import TrainValSplitCVMatrixCompletionModel +from turbo_mc.iterative_models.iterative_matrix_completion_model import IterativeMCMWithGuaranteedSpearmanR2 + +import compass + + +logger = logging.getLogger("compass") + + +class CompassResourceManager(): + r""" + Hackily exposes some new interfaces in Compass, e.g. determining which cells + Compass is being run on, the reaction ids, etc. + Thus, this class knows the details of where Compass output data files are located, + how to parse them, etc. + """ + def __init__(self, compass_args: List[str]): + r""" + :param compass_args: Arguments used to call Compass (as obtained from sys.argv) + E.g. ["compass", "--media", "media1", "--data", "compass/Resources/Test Data/rsem_tpmTable_full.txt"] + """ + self.compass_args = compass_args[:] # Dependency injection + with patch.object(sys, 'argv', self.compass_args): + self.compass_parsed_args = compass.main.parseArgs() + + def get_cell_names(self) -> List[str]: + r""" + Returns the list of cell names on which Compass is being run. + """ + logger.info("CompassResourceManager getting cell names ...") + data = pd.read_csv(self.compass_parsed_args['data'], sep='\t', nrows=0, index_col=0) + if "--single-sample" in self.compass_args: + sample_number = int(self.compass_parsed_args['single_sample']) + return [data.columns[sample_number]] + else: + return list(data.columns) + + def get_reaction_ids(self) -> List[str]: + r""" + Returns the list of reaction ids on which Compass is being run. + """ + logger.info("CompassResourceManager getting reactions ids ...") + # Run Compass on one cell, patching CPLEX to do nothing. + with tempfile.TemporaryDirectory() as output_dir_name: + logger.info( + f"CompassResourceManager created temporary output directory " + f"'{output_dir_name}' for calling Compass ...") + compass_args = self.compass_args[:] + set_argument(compass_args, "--single-sample", "0") + set_argument(compass_args, "--output-dir", output_dir_name) + + def cplex_solve_stub(self): + class DummySolution(): + def get_objective_value(self): + return 0 + self.solution = DummySolution() + with patch.object(sys, 'argv', compass_args),\ + patch.object(compass.compass.algorithm.cplex.Cplex, 'solve', new=cplex_solve_stub): + compass.main.entry() + reaction_scores = CompassResourceManager(compass_args).get_reaction_scores() + reaction_ids = list(reaction_scores.index) + return reaction_ids + + def get_reaction_scores(self) -> pd.DataFrame: + r""" + Returns the reaction score DataFrame + """ + logger.info("CompassResourceManager getting reactions scores ...") + if "--single-sample" in self.compass_args: + reaction_scores_path = os.path.join(self.compass_parsed_args['temp_dir'], 'reactions.txt') + else: + reaction_scores_path = os.path.join(self.compass_parsed_args['output_dir'], 'reactions.tsv') + logger.info(f"Trying to read reaction scores from '{reaction_scores_path}' ...") + reaction_scores = pd.read_csv(reaction_scores_path, sep="\t", index_col=0) + return reaction_scores + + def get_temporary_directory(self) -> str: + r""" + Returns the directory where the temporary data is stored. + """ + return self.compass_parsed_args['temp_dir'] + + +class CompassOracle(MatrixOracle): + def __init__(self, compass_args: List[str]): + r""" + :param args: Arguments with which Compass is being run. + """ + logger.info("Initializing CompassOracle ...") + # Let's first figure out on what cells and reactions Compass is being run on. + self.compass_args = compass_args[:] + compass_resource_manager = CompassResourceManager(compass_args=compass_args) + self.cell_names = np.array(compass_resource_manager.get_cell_names()) + self.reaction_ids = np.array(compass_resource_manager.get_reaction_ids()) + cache_dir = os.path.join( + compass_resource_manager.get_temporary_directory(), + "turbo_compass_cache") + # Write out cell names and reaction ids just for logging / debugging. + self._save_cell_names_and_reaction_ids_for_debugging(cache_dir) + # Caching + self.cache_filepath = os.path.join(cache_dir, "turbo_compass_cache.txt") + # Just make sure that the cache works before even starting! + self._cache_observations([], [], [], self.cache_filepath) + # Load the cache + self._load_cache() + + def _load_cache(self): + logger.info("CompassOracle trying to load its cache ...") + rows, cols, vals = [], [], [] + with open(self.cache_filepath, "r") as cache_file: + for line in cache_file: + row, col, val = line.strip('\n').split(' ') + rows.append(int(row)), cols.append(int(col)), vals.append(float(val)) + logger.info(f"CompassOracle loaded {len(vals)} observations from the cache!") + self._add_observations(rows, cols, vals) + + def _save_cell_names_and_reaction_ids_for_debugging(self, cache_dir: str) -> None: + r""" + This is only used for logging / debugging purposes. + If the cache already exists, will validate its contents. + """ + cell_names_filepath = os.path.join(cache_dir, "cell_names.txt") + reaction_ids_filepath = os.path.join(cache_dir, "reaction_ids.txt") + + def validate_cache_and_write_out_list_of_strings(filepath, names: List[str]) -> None: + r""" + Writes out the list of strings 'names' to filepath, with one string per line. + First checks to see if the names are already cached. If they are, checks + that they are correct. + """ + # If the cache already exists, check that it has the right content! + # Or else, something is VERY wrong with the cache and we should raise. + output_str = '\n'.join(names) + '\n' + if os.path.exists(filepath): + with open(filepath) as f: + file_contents = f.read() + if not file_contents == output_str: + raise Exception(f"CompassOracle cache file '{filepath}' seems to be corrupted!") + else: + # All is well! No need to write anything. + logger.info(f"CompassOracle cache file '{filepath}' is healthy!") + return + # Cache does not exist yet, create. + logger.info(f"Creating CompassOracle cache file '{filepath}' ...") + if not os.path.exists(os.path.dirname(filepath)): + os.makedirs(os.path.dirname(filepath)) + with open(filepath, "w") as cache_file: + cache_file.write(output_str) + validate_cache_and_write_out_list_of_strings(cell_names_filepath, list(self.cell_names)) + validate_cache_and_write_out_list_of_strings(reaction_ids_filepath, list(self.reaction_ids)) + + def shape(self) -> Tuple[int, int]: + r""" + Simply returns the shape of the cell X reaction matrix. + """ + return len(self.cell_names), len(self.reaction_ids) + + def _observe_entries( + self, + rows: List[int], + cols: List[int] + ) -> np.array: + # Start by running Compass on the selected cells (rows) and reactions (cols). + assert("--selected-reactions-for-each-cell" not in self.compass_args) + compass_args_to_observe_entries = self.compass_args[:] + with tempfile.NamedTemporaryFile("w") as selected_reactions_file: + # Create list of selected cells and reactions + logger.info("CompassOracle populating the file with the selected cells and reactions ...") + self._populate_selected_reactions_file(rows, cols, selected_reactions_file.name) + # Now run Compass + set_argument( + compass_args_to_observe_entries, + "--selected-reactions-for-each-cell", + selected_reactions_file.name) + with tempfile.TemporaryDirectory() as output_dir_name: + logger.info( + f"CompassOracle created temporary output directory " + f"'{output_dir_name}' for running Compass") + # output_dir_name = "_observe_entries" # TODO: Remove this line. + set_argument(compass_args_to_observe_entries, "--output-dir", output_dir_name) + logger.info("CompassOracle running Compass for the selected subset of the reaction score matrix ...") + with patch.object(sys, 'argv', compass_args_to_observe_entries): + compass.main.entry() + logger.info( + "CompassOracle successfully ran Compass. " + "Now will retrieve the computed reaction scores ...") + # Retrieve reaction scores. + compass_resource_manager = CompassResourceManager(compass_args_to_observe_entries) + reaction_scores = compass_resource_manager.get_reaction_scores() + # Check that rows and cols agree + assert(list(reaction_scores.columns) == list(self.cell_names)) + assert(list(reaction_scores.index) == list(self.reaction_ids)) + vals = reaction_scores.to_numpy().T[(rows, cols)] + logger.info("CompassOracle caching the latest Compass results ...") + self._cache_observations(rows, cols, list(vals), self.cache_filepath) + return vals + + def _populate_selected_reactions_file( + self, + rows: List[int], + cols: List[int], + filename: str + ) -> None: + r""" + Populates the file which will be later passed to Compass via the + --selected-reactions-for-each-cell argument. + """ + with open(filename, "w") as file: + row_to_cols_mapping = defaultdict(list) + for (r, c) in zip(rows, cols): + row_to_cols_mapping[r].append(c) + for row, columns in row_to_cols_mapping.items(): + cell_name = self.cell_names[row] + reaction_ids = self.reaction_ids[columns] + tokens = [cell_name] + list(reaction_ids) + line_for_this_cell = ','.join(tokens) + '\n' + file.write(line_for_this_cell) + + @staticmethod + def _cache_observations( + rows: List[int], + cols: List[int], + vals: List[float], + cache_filepath: str): + r""" + Adds the newly observed (row, col, val) triples to the cache. The structure of + the cache is one line per observation, e.g.: + 1 5 1356.7 + 37 134 0.0 + 123 4567 8901.2 + ... + """ + assert(len(rows) == len(cols)) + assert(len(rows) == len(vals)) + output_str = "" + for row, col, val in zip(rows, cols, vals): + output_str += f"{row} {col} {val}\n" + if not os.path.exists(os.path.dirname(cache_filepath)): + os.makedirs(os.path.dirname(cache_filepath)) + with open(cache_filepath, "a+") as cache_file: + cache_file.write(output_str) + + +def set_argument(args: List, arg_name: str, val: str) -> None: + r""" + Modifies args list in place, setting 'arg_name' argument to 'val'. + If 'arg_name' does not exist already, it is created. + """ + if not isinstance(arg_name, str) or not isinstance(val, str): + raise ValueError(f"{arg_name} and {val} should be strings!") # pragma: no cover + for i in range(len(args) - 1): + if args[i] == arg_name: + args[i + 1] = str(val) + return + args.append(arg_name) + args.append(val) + + +def pop_argument(args: List[str], arg: str) -> Tuple[List[str], str]: + r""" + Removes the argument from the parameter list and returns the new parameter + list and the popped parameter's value. If the argument is not present, returns + the original arguments and the empty string. + e.g. pop_argument(['compass', '--turbo', '0.95']) == (['compass'], '0.95') + after the operation. + """ + if arg not in args: + return args[:], "" + for i in range(len(args) - 1): + if args[i] == arg: + return args[:i] + args[(i + 2):], args[i + 1] + assert(False) + + +def turbo_compass_entry() -> None: + # Exctract turbo arguments. + logger.info("******** Turbo Compass started ********") + compass_parsed_args = compass.main.parseArgs() + requested_cv_spearman_r2, increments, min_pct_meet_sr2_requirement, max_iters =\ + compass_parsed_args['turbo'],\ + compass_parsed_args['turbo_increments'],\ + compass_parsed_args['turbo_min_pct'],\ + compass_parsed_args['turbo_max_iters'] + logger.info( + f"Running Turbo Compass with arguments:\n" + f"--turbo={requested_cv_spearman_r2}\n" + f"--turbo-increments={increments}\n" + f"--turbo-min-pct={min_pct_meet_sr2_requirement}\n" + f"--turbo-max-iters={max_iters}") + + # Remove turbo arguments from the command line call, and create the CompassOracle for the new command line. + compass_args = sys.argv[:] + compass_args, _ = pop_argument(compass_args, '--turbo') + compass_args, _ = pop_argument(compass_args, '--turbo-increments') + compass_args, _ = pop_argument(compass_args, '--turbo-min-pct') + compass_args, _ = pop_argument(compass_args, '--turbo-max-iters') + logger.info("Turbo Compass creating the CompassOracle ...") + compass_matrix_oracle = CompassOracle(compass_args[:]) + + model =\ + IterativeMCMWithGuaranteedSpearmanR2( + cv_model=lambda state: + TrainValSplitCVMatrixCompletionModel( + ExcludeConstantColumnsModelWrapper( + ColumnNormalizerModelWrapper( + MatrixCompletionFastALS( + n_factors=max(1, int(min(state.R, state.C) * state.sampled_density * 0.5)), + lam=10.0, + n_epochs=100, + verbose=False))), + train_ratio=0.8, + verbose=True, + finally_refit_model=None), + requested_cv_spearman_r2=requested_cv_spearman_r2, + sampling_density=increments, + finally_refit_model=lambda state: + ExcludeConstantColumnsModelWrapper( + ColumnNormalizerModelWrapper( + MatrixCompletionFastALS( + n_factors=int(min(state.R, state.C) * state.sampled_density * 0.5), + lam=10.0, + n_epochs=300, + verbose=False))), + min_pct_meet_sr2_requirement=min_pct_meet_sr2_requirement, + verbose=True, + plot_progress=False, + max_iterations=max_iters + ) + + # Fit iterative model. This is the core procedure of Turbo Compass (here is where all the magic happens) + logger.info("Turbo Compass performing iterative matrix completion ...") + np.random.seed(1) + model.fit(compass_matrix_oracle) + X_imputed = model.impute_all().T + logger.info("Iterative matrix completion was successfull!") + + # Write out imputation + logger.info("Turbo Compass writing out imputation ...") + if "--single-sample" in compass_args: + if not os.path.isdir(compass_parsed_args['temp_dir']): + os.makedirs(compass_parsed_args['temp_dir']) + reaction_scores_path = os.path.join(compass_parsed_args['temp_dir'], 'reactions.txt') + else: + if not os.path.isdir(compass_parsed_args['output_dir']): + os.makedirs(compass_parsed_args['output_dir']) + reaction_scores_path = os.path.join(compass_parsed_args['output_dir'], 'reactions.tsv') + cell_names = compass_matrix_oracle.cell_names[:] + reaction_ids = compass_matrix_oracle.reaction_ids[:] + X_imputed_df = pd.DataFrame(data=X_imputed, index=reaction_ids, columns=cell_names) + X_imputed_df.to_csv(reaction_scores_path, sep="\t") + logger.info("Turbo Compass completed successfully!") + return diff --git a/conftest.py b/conftest.py new file mode 100644 index 0000000..e446d0a --- /dev/null +++ b/conftest.py @@ -0,0 +1,21 @@ +import pytest + + +def pytest_addoption(parser): + parser.addoption( + "--runslow", action="store_true", default=False, help="run slow tests" + ) + + +def pytest_configure(config): + config.addinivalue_line("markers", "slow: mark test as slow to run") + + +def pytest_collection_modifyitems(config, items): + if config.getoption("--runslow"): + # --runslow given in cli: do not skip slow tests + return + skip_slow = pytest.mark.skip(reason="need --runslow option to run") + for item in items: + if "slow" in item.keywords: + item.add_marker(skip_slow) diff --git a/setup.py b/setup.py index 5787a49..69d7d72 100644 --- a/setup.py +++ b/setup.py @@ -49,7 +49,9 @@ 'python-libsbml>=5.13', 'six>=1.10', 'scikit-learn>=0.19', - 'scipy>=1.0'], + 'scipy>=1.0', + 'turbo-mc @ git+ssh://git@github.com/sprillo/turbo-mc.git@' + 'master#egg=turbo-mc'], # 'cplex>=12.7.0.0' also required, but installed separately diff --git a/tests/data/select_reactions.txt b/tests/data/select_reactions.txt new file mode 100644 index 0000000..685b19f --- /dev/null +++ b/tests/data/select_reactions.txt @@ -0,0 +1 @@ +10FTHF5GLUtl diff --git a/tests/data/selected_reactions_for_each_cell.txt b/tests/data/selected_reactions_for_each_cell.txt new file mode 100644 index 0000000..4d868d6 --- /dev/null +++ b/tests/data/selected_reactions_for_each_cell.txt @@ -0,0 +1,4 @@ +WT-d_S141_L007_R1_001,10FTHF5GLUtl_pos +Ob-DHA-e_S154_L007_R1_001,10FTHF5GLUtl_pos,10FTHF5GLUtm_pos +Ob-DHA-b_S132_L007_R1_001 + diff --git a/tests/test_compass.py b/tests/test_compass.py new file mode 100644 index 0000000..09e14ee --- /dev/null +++ b/tests/test_compass.py @@ -0,0 +1,146 @@ +import os +import numpy as np +import pandas as pd +import pytest +import sys +import tempfile +from unittest.mock import patch + +import compass.main + + +@pytest.mark.slow +@pytest.mark.parametrize("num_processes", ["1", "2"]) +def test_compass_smoke_test(num_processes): + r""" + Just checks that Compass runs end-to-end without crashing in a very + minimalistic setting. + Takes 54s on my laptop. + We use 1 process to turn multi-processing off, which can otherwise + hide errors. We also try with 2 processes to excercise multiprocessing. + You can also manually run this from the command line as follows: + $ compass --media media1 --data compass/Resources/Test\ Data/rsem_tpmTable_2cells.txt \ + --output-dir _test_compass_smoke_test --num-processes 1 --test-mode + """ + with tempfile.TemporaryDirectory() as output_dir_name: + print(f"created temporary output directory '{output_dir_name}'") + compass_args = [ + "compass", + "--media", "media1", + "--data", "compass/Resources/Test Data/rsem_tpmTable_2cells.txt", + "--output-dir", output_dir_name, + "--num-processes", num_processes, + "--test-mode", + ] + with patch.object(sys, 'argv', compass_args): + compass.main.entry() + # Try to read the reactions file + reaction_scores_path = os.path.join(output_dir_name, "reactions.tsv") + reaction_scores_df = pd.read_csv(reaction_scores_path, sep="\t", index_col=0) + assert(reaction_scores_df.shape == (106, 2)) + + +@pytest.mark.slow +def test_compass_smoke_test_2(): + r""" + Same test as above, but now runs on ALL reactions (does not use --test-mode) + To avoid this test being slow due to CPLEX, CPLEX is stubbed. + Takes 30s on my laptop. + We use 1 process to turn multi-processing off, which can otherwise + hide errors. Also, we _must_ turn multiprocessing off or else the + subprocesses won't have CPLEX stubbed and so the test would take forever. + You can also manually run this from the command line as follows, but do note + that CPLEX _WON'T BE STUBBED_ so it will take a while: + $ compass --media media1 --data compass/Resources/Test\ Data/rsem_tpmTable_2cells.txt \ + --output-dir _test_compass_smoke_test_2 --num-processes 1 + """ + with tempfile.TemporaryDirectory() as output_dir_name: + print(f"created temporary output directory '{output_dir_name}'") + compass_args = [ + "compass", + "--media", "media1", + "--data", "compass/Resources/Test Data/rsem_tpmTable_2cells.txt", + "--output-dir", output_dir_name, + "--num-processes", "1" + ] + + def cplex_solve_stub(self): + class DummySolution(): + def get_objective_value(self): + return 42.0 + self.solution = DummySolution() + with patch.object(sys, 'argv', compass_args),\ + patch.object(compass.compass.algorithm.cplex.Cplex, 'solve', new=cplex_solve_stub): + compass.main.entry() + # Try to read the reactions file + reaction_scores_path = os.path.join(output_dir_name, "reactions.tsv") + reaction_scores_df = pd.read_csv(reaction_scores_path, sep="\t", index_col=0) + assert(reaction_scores_df.shape == (10211, 2)) + + +@pytest.mark.slow +def test_compass_select_reactions_argument(): + r""" + Runs Compass with the '--select_reactions' argument in a minimalistic + setting, checking that the outputted reaction scores are correct. + Takes 10s on my laptop. + """ + with tempfile.TemporaryDirectory() as output_dir_name: + print(f"created temporary output directory '{output_dir_name}'") + compass_args = [ + "compass", + "--media", "media1", + "--data", "compass/Resources/Test Data/rsem_tpmTable_2cells.txt", + "--output-dir", output_dir_name, + "--single-sample", "1", + "--select_reactions", "tests/data/select_reactions.txt"] + with patch.object(sys, 'argv', compass_args): + compass.main.entry() + # Check that contents of outputted reaction scores are correct + reaction_scores_path = os.path.join(output_dir_name, "_tmp", "reactions.txt") + reaction_scores_df = pd.read_csv(reaction_scores_path, sep="\t", index_col=0) + assert(list(reaction_scores_df.index) == ["10FTHF5GLUtl_pos"]) + assert(list(reaction_scores_df.columns) == ["Ob-DHA-e_S154_L007_R1_001"]) + np.testing.assert_almost_equal(reaction_scores_df.to_numpy(), np.array([[3226.7257585068633]])) + + +@pytest.mark.slow +def test_compass_select_reactions_for_each_cell_argument(): + r""" + Runs Compass with the '--selected-reactions-for-each-cell' argument in a minimalistic + setting, checking that the outputted reaction scores are correct. + Takes 25s on my laptop. + """ + with tempfile.TemporaryDirectory() as output_dir_name: + print(f"created temporary output directory '{output_dir_name}'") + compass_args = [ + "compass", + "--media", "media1", + "--data", "compass/Resources/Test Data/rsem_tpmTable_4cells.txt", + "--selected-reactions-for-each-cell", "tests/data/selected_reactions_for_each_cell.txt", + "--output-dir", output_dir_name + ] + with patch.object(sys, 'argv', compass_args): + compass.main.entry() + # Check that contents of outputted reaction scores are correct + reaction_scores_path = os.path.join(output_dir_name, "reactions.tsv") + reaction_scores_df = pd.read_csv(reaction_scores_path, sep="\t", index_col=0) + assert(len(reaction_scores_df.index) == 10211) + # I will only check the top 3 x 4 rows of the matrix. + assert(list(reaction_scores_df.index)[:3] == [ + "10FTHF5GLUtl_pos", + "10FTHF5GLUtm_pos", + "10FTHF6GLUtl_pos" + ]) + assert(list(reaction_scores_df.columns) == [ + "WT-d_S141_L007_R1_001", + "Ob-DHA-e_S154_L007_R1_001", + "WT-1012-c_S135_L007_R1_001", + "Ob-DHA-b_S132_L007_R1_001" + ]) + np.testing.assert_almost_equal( + reaction_scores_df.iloc[:3, :], + np.array( + [[3284.4609894639148, 3226.7257585068633, np.nan, np.nan], + [np.nan, 4142.645986483619, np.nan, np.nan], + [np.nan, np.nan, np.nan, np.nan]])) diff --git a/tests/test_global_state.py b/tests/test_global_state.py new file mode 100644 index 0000000..ceea724 --- /dev/null +++ b/tests/test_global_state.py @@ -0,0 +1,39 @@ +import tempfile + +from compass.global_state import _SelectedReactionsForEachCell + + +def test_SelectedReactionsForEachCell(): + r""" + Test that information of which reactions should be computed for each cell is loaded correctly. + """ + state = _SelectedReactionsForEachCell("tests/data/selected_reactions_for_each_cell.txt") + assert(state.is_selected("WT-d_S141_L007_R1_001", "10FTHF5GLUtl_pos")) + assert(not state.is_selected("WT-d_S141_L007_R1_001", "10FTHF5GLUtm_pos")) + assert(state.is_selected("Ob-DHA-e_S154_L007_R1_001", "10FTHF5GLUtl_pos")) + assert(state.is_selected("Ob-DHA-e_S154_L007_R1_001", "10FTHF5GLUtm_pos")) + assert(not state.is_selected("Ob-DHA-b_S132_L007_R1_001", "10FTHF5GLUtl_pos")) + assert(not state.is_selected("Ob-DHA-b_S132_L007_R1_001", "10FTHF5GLUtm_pos")) + assert(not state.is_selected("unseen_cell", "10FTHF5GLUtl_pos")) + assert(not state.is_selected("WT-d_S141_L007_R1_001", "unseen_reaction")) + assert(not state.is_selected("unseen_cell", "unseen_reaction")) + + +def test_by_default_all_cells_and_reactions_are_selected(): + r""" + If no file with selected reactions is provided, all cells and + reactions should be valid. + """ + state = _SelectedReactionsForEachCell(None) + assert(state.is_selected("any_cell", "any_reaction")) + + +def test_with_empty_file_nothing_is_selected(): + r""" + If an empty file is supplied, nothing should be computed. + (This is just a border case I ran into. It basically guarantees that turbo Compass + is idempotent.) + """ + with tempfile.NamedTemporaryFile("w+") as file: + state = _SelectedReactionsForEachCell(file.name) + assert(not state.is_selected("some_cell", "some_reaction")) diff --git a/tests/test_models.py b/tests/test_models.py index f4eab60..560d703 100644 --- a/tests/test_models.py +++ b/tests/test_models.py @@ -1,7 +1,10 @@ from compass import models from compass.models.MetabolicModel import MetabolicModel +import pytest + +@pytest.mark.slow def test_sbml_3(): model = models.load_metabolic_model("RECON1_xml") assert isinstance(model, MetabolicModel) @@ -9,6 +12,7 @@ def test_sbml_3(): assert len(model.species) == 2766 +@pytest.mark.slow def test_sbml_2(): model = models.load_metabolic_model("RECON2.2") assert isinstance(model, MetabolicModel) @@ -16,6 +20,7 @@ def test_sbml_2(): assert len(model.species) == 6047 +@pytest.mark.slow def test_mat(): model = models.load_metabolic_model("RECON2_mat") assert isinstance(model, MetabolicModel) @@ -23,6 +28,7 @@ def test_mat(): assert len(model.species) == 5063 +@pytest.mark.slow def test_to_json(): model = models.load_metabolic_model("RECON2.2") json = model.to_JSON() diff --git a/tests/test_turbo_compass.py b/tests/test_turbo_compass.py new file mode 100644 index 0000000..4f072f6 --- /dev/null +++ b/tests/test_turbo_compass.py @@ -0,0 +1,346 @@ +import hashlib +import numpy as np +import os +import pandas as pd +import pytest +import sys +import tempfile +from unittest.mock import patch + +import compass.global_state as global_state +import compass.main +from compass.turbo_compass import CompassResourceManager, CompassOracle, set_argument,\ + pop_argument + + +COMPASS_ARGS = [ + "compass", + "--media", "media1", + "--data", "compass/Resources/Test Data/rsem_tpmTable_full.txt" +] + + +def test_set_argument(): + args = ['compass', '--turbo', '0.95'] + set_argument(args, '--turbo', '1.0') + assert(args == ['compass', '--turbo', '1.0']) + args = ['compass'] + set_argument(args, '--turbo', '0.6') + assert(args == ['compass', '--turbo', '0.6']) + + +def test_pop_argument(): + args = ['compass', '--turbo', '0.95'] + assert(pop_argument(args, '--turbo') == (['compass'], '0.95')) + args = ['compass', '--turbo', '0.95', '--num-processes', '2'] + assert(pop_argument(args, '--num-processes') == (['compass', '--turbo', '0.95'], '2')) + args = ['compass', '--num-processes', '2', '--turbo', '0.95'] + assert(pop_argument(args, '--num-processes') == (['compass', '--turbo', '0.95'], '2')) + args = ['compass', '--num-processes', '2'] + assert(pop_argument(args, '--turbo-min-pct') == (['compass', '--num-processes', '2'], '')) + + +@pytest.mark.slow +def test_compass_resource_manager_get_cell_names(): + r""" + Tests that the CompassResourceManager correctly finds the cell names. + """ + compass_args = COMPASS_ARGS + compass_resource_manager = CompassResourceManager(compass_args=compass_args) + cell_names = compass_resource_manager.get_cell_names() + assert(len(cell_names) == 40) # There should be 40 cells + assert(cell_names[0] == 'WT-d_S141_L007_R1_001') # This should be the first cell. + + +@pytest.mark.slow +def test_compass_resource_manager_get_reaction_ids(): + r""" + Tests that the CompassResourceManager correctly finds the reaction ids. + """ + compass_args = COMPASS_ARGS + compass_resource_manager = CompassResourceManager(compass_args=compass_args) + reaction_ids = compass_resource_manager.get_reaction_ids() + assert(len(reaction_ids) == 10211) # There should be 10211 reactions + assert(reaction_ids[0] == '10FTHF5GLUtl_pos') # This should be the first reaction. + + +@pytest.mark.slow +def test_compass_oracle_shape(): + r""" + Tests that the CompassOracle returns the correct shape of the underlying matrix. + Takes 30s on my laptop. + """ + compass_args = COMPASS_ARGS + compass_oracle = CompassOracle(compass_args=compass_args) + matrix_shape = compass_oracle.shape() + assert(matrix_shape == (40, 10211)) # There should be 40 cells and 10211 reactions. + + +@pytest.mark.slow +def test_compass_oracle_populate_selected_reactions_file(): + r""" + Tests that the CompassOracle correctly populates the file passed to + --selected-reactions-for-each-cell (necessary for running Compass to + obtain only a subset of the reaction scores.) + Takes 30s on my laptop. + """ + compass_args = COMPASS_ARGS + with tempfile.NamedTemporaryFile("w+") as selected_reactions_file: + compass_oracle = CompassOracle(compass_args=compass_args) + compass_oracle._populate_selected_reactions_file( + [0, 2, 2], + [0, 0, 1], + selected_reactions_file.name + ) + # Check that the written cells and reactions are correct + print(f"Checking contents of '{selected_reactions_file.name}'") + with open(selected_reactions_file.name, "r") as file: + file_content = file.read() + assert( + file_content + == "WT-d_S141_L007_R1_001,10FTHF5GLUtl_pos\n" + "WT-1012-c_S135_L007_R1_001,10FTHF5GLUtl_pos,10FTHF5GLUtm_pos\n") + + +@pytest.mark.slow +def test_compass_oracle_observe_entries(): + r""" + Tests that the CompassOracle correctly runs Compass under the hood to compute the + requested reaction scores. This is the key method of the CompassOracle object. + """ + compass_args = COMPASS_ARGS + compass_oracle = CompassOracle(compass_args=compass_args) + vals = compass_oracle.observe_entries( + [[0, 0], [0, 2], [1, 2]] + ) + np.testing.assert_almost_equal(vals, np.array([3284.4609895, 3716.8335506, 3620.9471307])) + vals = compass_oracle.observe_entries( + [[1, 0]] + ) + np.testing.assert_almost_equal(vals, np.array([3226.725758506863])) + + +def test_compass_oracle_cache_observations(): + r""" + Tests that the caching method of the CompassOracle works as expected. + """ + with tempfile.NamedTemporaryFile() as output_file: + CompassOracle._cache_observations( + [], [], [], output_file.name + ) # This tests that adding no observations works too. + CompassOracle._cache_observations( + [1], [2], [3.14], output_file.name + ) + CompassOracle._cache_observations( + [3, 5], [4, 6], [2.71, -1.0], output_file.name + ) + with open(output_file.name, "r") as f: + cache_contents = f.read() + assert(cache_contents == "1 2 3.14\n3 4 2.71\n5 6 -1.0\n") + + +@pytest.mark.slow +@pytest.mark.parametrize("num_processes", ["1", "2"]) +def test_turbo_compass_smoke_test(num_processes): + r""" + Just checks that turbo Compass runs end-to-end without crashing in a very + minimalistic setting. + Takes 80s on my laptop. + We use 1 process to turn multi-processing off, which can otherwise + hide errors. We also try with 2 processes to excercise multiprocessing. + You can also manually run this from the command line as follows: + $ compass --media media1 --data compass/Resources/Test\ Data/rsem_tpmTable_2cells.txt \ + --output-dir _test_turbo_compass_smoke_test --num-processes 1 --test-mode \ + --turbo 0.7 --turbo-increments 0.5 + """ + with tempfile.TemporaryDirectory() as output_dir_name: + print(f"created temporary output directory '{output_dir_name}'") + compass_args = [ + "compass", + "--media", "media1", + "--data", "compass/Resources/Test Data/rsem_tpmTable_2cells.txt", + "--output-dir", output_dir_name, + "--num-processes", num_processes, + "--test-mode", + "--turbo", "0.7", + "--turbo-increments", "0.5" + ] + + with patch.object(sys, 'argv', compass_args): + compass.main.entry() + # Try to read the reactions file + reaction_scores_path = os.path.join(output_dir_name, "reactions.tsv") + reaction_scores_df = pd.read_csv(reaction_scores_path, sep="\t", index_col=0) + assert(reaction_scores_df.shape == (106, 2)) + + +@pytest.mark.slow +def test_turbo_compass_smoke_test_2(): + r""" + Same test as above, but now runs on ALL reactions (does not use --test-mode) + To avoid this test being slow due to CPLEX, CPLEX is stubbed. + Takes 75s on my laptop. + We use 1 process to turn multi-processing off, which can otherwise + hide errors. Also, we _must_ turn multiprocessing off or else the + subprocesses won't have CPLEX stubbed and so the test would take forever. + You can also manually run this from the command line as follows, but do note + that CPLEX _WON'T BE STUBBED_ so it will take a while: + $ compass --media media1 --data compass/Resources/Test\ Data/rsem_tpmTable_2cells.txt \ + --output-dir _test_turbo_compass_smoke_test_2 --num-processes 1 \ + --turbo 0.7 --turbo-increments 0.5 + """ + with tempfile.TemporaryDirectory() as output_dir_name: + print(f"created temporary output directory '{output_dir_name}'") + compass_args = [ + "compass", + "--media", "media1", + "--data", "compass/Resources/Test Data/rsem_tpmTable_2cells.txt", + "--output-dir", output_dir_name, + "--num-processes", "1", + "--turbo", "0.7", + "--turbo-increments", "0.5" + ] + + def cplex_solve_stub(self): + class DummySolution(): + def get_objective_value(self): + return 42.0 + self.solution = DummySolution() + with patch.object(sys, 'argv', compass_args),\ + patch.object(compass.compass.algorithm.cplex.Cplex, 'solve', new=cplex_solve_stub): + compass.main.entry() + # Try to read the reactions file + reaction_scores_path = os.path.join(output_dir_name, "reactions.tsv") + reaction_scores_df = pd.read_csv(reaction_scores_path, sep="\t", index_col=0) + assert(reaction_scores_df.shape == (10211, 2)) + + +@pytest.mark.slow +def test_turbo_compass_caching(): + r""" + Tests that Turbo Compass caching works. + Takes 3m30s on my laptop. + """ + with tempfile.TemporaryDirectory() as output_dir_name: + print(f"created temporary output directory '{output_dir_name}'") + compass_args = [ + "compass", + "--media", "media1", + "--data", "compass/Resources/Test Data/rsem_tpmTable_4cells.txt", + "--output-dir", output_dir_name, + "--num-processes", "4", + "--turbo", "0.7", + "--turbo-increments", "0.25", + "--turbo-max-iters", "2" + ] + cache_path = os.path.join(output_dir_name, "_tmp", "turbo_compass_cache", "turbo_compass_cache.txt") + np.random.seed(1) + + def cplex_solve_stub(self): + class DummySolution(): + def get_objective_value(self): + return np.random.uniform(1000.0, 10000.0) + self.solution = DummySolution() + with patch.object(sys, 'argv', compass_args),\ + patch.object(compass.compass.algorithm.cplex.Cplex, 'solve', new=cplex_solve_stub): + # First run + compass.main.entry() + # Check that exactly one half of the matrix was queried + cache = pd.read_csv(cache_path, sep=" ", header=None) + assert(cache.shape == (2 * 10211, 3)) + + # Second run + compass.main.entry() + # Check that 3/4 of the matrix was queried + cache = pd.read_csv(cache_path, sep=" ", header=None) + assert(cache.shape == (3 * 10211, 3)) + + # Third run + compass.main.entry() + # Check that all of the matrix was queried + cache = pd.read_csv(cache_path, sep=" ", header=None) + assert(cache.shape == (4 * 10211, 3)) + + # Fourth run: Even when we observe all the data, Turbo Compass should + # not crash (i.e. Turbo Compass should be idempotent) + compass.main.entry() + # Check that all of the matrix was queried + cache = pd.read_csv(cache_path, sep=" ", header=None) + assert(cache.shape == (4 * 10211, 3)) + + +@pytest.mark.slow +def test_turbo_compass_on_40_cells_stubbing_cplex_to_a_rank_1_matrix(): + r""" + Runs turbo Compass on a 40 cells x 10211 reactions matrix. CPLEX is stubbed + to produce a rank-1 reaction score matrix. + Takes 11m on my computer (using 12 processes). + NOTE: Don't try to run this on the command line since it relies on CPLEX patching! + (it will take forever if not) + """ + with tempfile.TemporaryDirectory() as output_dir_name: + print(f"created temporary output directory '{output_dir_name}'") + compass_args = [ + "compass", + "--media", "media1", + "--data", "compass/Resources/Test Data/rsem_tpmTable_full.txt", + "--output-dir", output_dir_name, + "--turbo", "0.95", + "--turbo-increments", "0.05", + "--turbo-min-pct", "0.99" + ] + + def hash_str(s: str, mod: int = 10000) -> int: + r""" + Hashes the string modulo 'mod', returning an integer between + 0 and mod-1. + """ + res = int(hashlib.sha1(s.encode()).hexdigest(), 16) % mod + return res + + def reaction_score(cell_name: str, reaction_id: str) -> float: + r""" + Each cell and reaction has a latent number between 0 and 100. + Each entry of the reaction score matrix is the product of these + two latent numbers (i.e. the reaction score matrix has rank 1). + """ + return np.sqrt(hash_str(cell_name)) * np.sqrt(hash_str(reaction_id)) + + def cplex_solve_stub(self): + class HardcodedSolution(): + def __init__(self, objective_value: float): + self.objective_value = objective_value + + def get_objective_value(self) -> float: + return self.objective_value + current_cell_name = global_state.get_current_cell_name() + current_reaction_id = global_state.get_current_reaction_id() + self.solution = HardcodedSolution( + objective_value=reaction_score( + current_cell_name, + current_reaction_id + )) + with patch.object(sys, 'argv', compass_args),\ + patch.object(compass.compass.algorithm.cplex.Cplex, 'solve', new=cplex_solve_stub): + compass.main.entry() + # Check that the solution makes sense: + # (1) Retrieve the imputed solution + imputed_reaction_scores_df = CompassResourceManager(compass_args).get_reaction_scores() + # (2) Compute the ground truth solution + true_reaction_scores_df = imputed_reaction_scores_df.copy() + for reaction_id in true_reaction_scores_df.index: + for cell_name in true_reaction_scores_df.columns: + true_reaction_scores_df.loc[reaction_id, cell_name] =\ + reaction_score(cell_name, reaction_id) + # (3) Compute the spearman correlation for each reaction + X_true = true_reaction_scores_df.to_numpy().T + X_imputed = imputed_reaction_scores_df.to_numpy().T + from turbo_mc.models.cv_matrix_completion_model import compute_spearman_r2s + cv_spearman_r2s = compute_spearman_r2s(X_true, X_imputed) + # (4) Check that the median reconstruction quality of the reactions is good. + # NOTE: Because of caching in Compass' maximize_reaction, constant reactions + # never hit cplex.solve() and are hardcoded by Compass as 0 (rather than using my + # low rank approximation). Thus, true_reaction_scores_df is actually wrong for + # these reactions. They are approximately 30%. To avoid these 30% wrong reactions + # (that have a SR2 of 0.0), we look at the MEDIAN SR2 in this test, as follows: + assert(np.sort(cv_spearman_r2s)[len(cv_spearman_r2s) // 2] > 0.95) From 5e0241f8f4dded79b199a3764fbae72209224368 Mon Sep 17 00:00:00 2001 From: Sebastian Prillo <10426884+sprillo@users.noreply.github.com> Date: Tue, 21 Jul 2020 22:55:08 -0700 Subject: [PATCH 2/6] nit docs --- compass/global_state.py | 2 +- compass/turbo_compass.py | 5 ++--- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/compass/global_state.py b/compass/global_state.py index edd9da3..08c02be 100644 --- a/compass/global_state.py +++ b/compass/global_state.py @@ -9,7 +9,7 @@ _current_cell_name = -1 _current_reaction_id = "" # This will hold an object of the class SelectedReactionsForEachCell that -# will allow us to know +# will allow us to know what reactions are selected for each cell. _selected_reactions_for_each_cell = None diff --git a/compass/turbo_compass.py b/compass/turbo_compass.py index 078299c..5619ceb 100644 --- a/compass/turbo_compass.py +++ b/compass/turbo_compass.py @@ -98,7 +98,7 @@ def get_temporary_directory(self) -> str: class CompassOracle(MatrixOracle): def __init__(self, compass_args: List[str]): r""" - :param args: Arguments with which Compass is being run. + :param compass_args: Arguments with which Compass is being run. """ logger.info("Initializing CompassOracle ...") # Let's first figure out on what cells and reactions Compass is being run on. @@ -190,7 +190,6 @@ def _observe_entries( logger.info( f"CompassOracle created temporary output directory " f"'{output_dir_name}' for running Compass") - # output_dir_name = "_observe_entries" # TODO: Remove this line. set_argument(compass_args_to_observe_entries, "--output-dir", output_dir_name) logger.info("CompassOracle running Compass for the selected subset of the reaction score matrix ...") with patch.object(sys, 'argv', compass_args_to_observe_entries): @@ -287,8 +286,8 @@ def pop_argument(args: List[str], arg: str) -> Tuple[List[str], str]: def turbo_compass_entry() -> None: - # Exctract turbo arguments. logger.info("******** Turbo Compass started ********") + # Extract turbo arguments. compass_parsed_args = compass.main.parseArgs() requested_cv_spearman_r2, increments, min_pct_meet_sr2_requirement, max_iters =\ compass_parsed_args['turbo'],\ From 457777ee82c8b77c9c56d3fd8b115e6a2f213616 Mon Sep 17 00:00:00 2001 From: Sebastian Prillo <10426884+sprillo@users.noreply.github.com> Date: Thu, 23 Jul 2020 12:03:28 -0700 Subject: [PATCH 3/6] Remove slow marker from one test --- tests/test_compass.py | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/test_compass.py b/tests/test_compass.py index 09e14ee..dc9c729 100644 --- a/tests/test_compass.py +++ b/tests/test_compass.py @@ -78,7 +78,6 @@ def get_objective_value(self): assert(reaction_scores_df.shape == (10211, 2)) -@pytest.mark.slow def test_compass_select_reactions_argument(): r""" Runs Compass with the '--select_reactions' argument in a minimalistic From 3909e97cb0513d716a08cc00eed4a726133c6ac8 Mon Sep 17 00:00:00 2001 From: Sebastian Prillo <10426884+sprillo@users.noreply.github.com> Date: Thu, 23 Jul 2020 12:58:31 -0700 Subject: [PATCH 4/6] Better indentation in test --- tests/test_turbo_compass.py | 42 ++++++++++++++++++------------------- 1 file changed, 21 insertions(+), 21 deletions(-) diff --git a/tests/test_turbo_compass.py b/tests/test_turbo_compass.py index 4f072f6..d9656e0 100644 --- a/tests/test_turbo_compass.py +++ b/tests/test_turbo_compass.py @@ -323,24 +323,24 @@ def get_objective_value(self) -> float: with patch.object(sys, 'argv', compass_args),\ patch.object(compass.compass.algorithm.cplex.Cplex, 'solve', new=cplex_solve_stub): compass.main.entry() - # Check that the solution makes sense: - # (1) Retrieve the imputed solution - imputed_reaction_scores_df = CompassResourceManager(compass_args).get_reaction_scores() - # (2) Compute the ground truth solution - true_reaction_scores_df = imputed_reaction_scores_df.copy() - for reaction_id in true_reaction_scores_df.index: - for cell_name in true_reaction_scores_df.columns: - true_reaction_scores_df.loc[reaction_id, cell_name] =\ - reaction_score(cell_name, reaction_id) - # (3) Compute the spearman correlation for each reaction - X_true = true_reaction_scores_df.to_numpy().T - X_imputed = imputed_reaction_scores_df.to_numpy().T - from turbo_mc.models.cv_matrix_completion_model import compute_spearman_r2s - cv_spearman_r2s = compute_spearman_r2s(X_true, X_imputed) - # (4) Check that the median reconstruction quality of the reactions is good. - # NOTE: Because of caching in Compass' maximize_reaction, constant reactions - # never hit cplex.solve() and are hardcoded by Compass as 0 (rather than using my - # low rank approximation). Thus, true_reaction_scores_df is actually wrong for - # these reactions. They are approximately 30%. To avoid these 30% wrong reactions - # (that have a SR2 of 0.0), we look at the MEDIAN SR2 in this test, as follows: - assert(np.sort(cv_spearman_r2s)[len(cv_spearman_r2s) // 2] > 0.95) + # Check that the solution makes sense: + # (1) Retrieve the imputed solution + imputed_reaction_scores_df = CompassResourceManager(compass_args).get_reaction_scores() + # (2) Compute the ground truth solution + true_reaction_scores_df = imputed_reaction_scores_df.copy() + for reaction_id in true_reaction_scores_df.index: + for cell_name in true_reaction_scores_df.columns: + true_reaction_scores_df.loc[reaction_id, cell_name] =\ + reaction_score(cell_name, reaction_id) + # (3) Compute the spearman correlation for each reaction + X_true = true_reaction_scores_df.to_numpy().T + X_imputed = imputed_reaction_scores_df.to_numpy().T + from turbo_mc.models.cv_matrix_completion_model import compute_spearman_r2s + cv_spearman_r2s = compute_spearman_r2s(X_true, X_imputed) + # (4) Check that the median reconstruction quality of the reactions is good. + # NOTE: Because of caching in Compass' maximize_reaction, constant reactions + # never hit cplex.solve() and are hardcoded by Compass as 0 (rather than using my + # low rank approximation). Thus, true_reaction_scores_df is actually wrong for + # these reactions. They are approximately 30%. To avoid these 30% wrong reactions + # (that have a SR2 of 0.0), we look at the MEDIAN SR2 in this test, as follows: + assert(np.sort(cv_spearman_r2s)[len(cv_spearman_r2s) // 2] > 0.95) From 673dda1a35c4c4e9cae8fb075de1abde066eb8d3 Mon Sep 17 00:00:00 2001 From: Sebastian Prillo <10426884+sprillo@users.noreply.github.com> Date: Mon, 31 Oct 2022 08:13:03 -0700 Subject: [PATCH 5/6] Use https instead of ssh in setup.py --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 69d7d72..731ddc6 100644 --- a/setup.py +++ b/setup.py @@ -50,7 +50,7 @@ 'six>=1.10', 'scikit-learn>=0.19', 'scipy>=1.0', - 'turbo-mc @ git+ssh://git@github.com/sprillo/turbo-mc.git@' + 'turbo-mc @ git+https://github.com/sprillo/turbo-mc.git@' 'master#egg=turbo-mc'], # 'cplex>=12.7.0.0' also required, but installed separately From ff081c1de4ea1631e5d49307eb764c5451f613b0 Mon Sep 17 00:00:00 2001 From: Sebastian Prillo <10426884+sprillo@users.noreply.github.com> Date: Sat, 19 Nov 2022 12:55:47 -0800 Subject: [PATCH 6/6] Check that model and media are cached, and if not, ask user to generate cache first --- compass/turbo_compass.py | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/compass/turbo_compass.py b/compass/turbo_compass.py index 5619ceb..ec30a80 100644 --- a/compass/turbo_compass.py +++ b/compass/turbo_compass.py @@ -1,3 +1,4 @@ +from copy import deepcopy from collections import defaultdict import logging import numpy as np @@ -8,6 +9,8 @@ from typing import List, Tuple from unittest.mock import patch +from .compass import cache + from turbo_mc.iterative_models.matrix_oracle import MatrixOracle from turbo_mc.models.exclude_constant_columns_model_wrapper import ExcludeConstantColumnsModelWrapper from turbo_mc.models.column_normalizer_model_wrapper import ColumnNormalizerModelWrapper @@ -94,6 +97,25 @@ def get_temporary_directory(self) -> str: """ return self.compass_parsed_args['temp_dir'] + def _check_cache_is_present(self): + """ + Makes sure that the model and media are cached in the compass resources. + Recall that this data contains the reaction maximums, that are used many + times, which is why it is good to cache them first. + """ + compass_args = deepcopy(self.compass_args) + model = self.compass_parsed_args["model"] + media = self.compass_parsed_args["media"] + if media is None: + raise ValueError(f"Please explicitly provide the media used with --media") + cache.load(model, media) + if len(cache._cache[(model, media)]) == 0: + raise ValueError( + f"Cache not present for model '{model}' and media '{media}'." + " Please generate it first by running compass (NOT turbo-compass) " + f"with the --generate-cache flag." + ) + class CompassOracle(MatrixOracle): def __init__(self, compass_args: List[str]): @@ -104,6 +126,7 @@ def __init__(self, compass_args: List[str]): # Let's first figure out on what cells and reactions Compass is being run on. self.compass_args = compass_args[:] compass_resource_manager = CompassResourceManager(compass_args=compass_args) + compass_resource_manager._check_cache_is_present() self.cell_names = np.array(compass_resource_manager.get_cell_names()) self.reaction_ids = np.array(compass_resource_manager.get_reaction_ids()) cache_dir = os.path.join(