seed2lp 2.0.0__py3-none-any.whl

tests/fba.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+Description:
+Test seed2lp
+"""
+from os import path
+from .utils import search_seed
+
+##### ###### ##### DIRECTORIES AND FILES ###################
+TEST_DIR = path.dirname(path.abspath(__file__))
+
+# All reaction are not reversible 
+# except import/export reaction for exchange metabolite S1, S2 C and G
+INFILE = path.join(TEST_DIR,'network/sbml/toy_paper_no_reversible.sbml')
+######################################################## 
+
+
+################### FIXED VARIABLES ####################
+RUN_MODE="fba"
+######################################################## 
+
+
+################# EXPECTED SOLUTIONS ###################
+
+# Seeds for Reasoning, filter, Gues-Check, Guess-Check Diversty and Hybrid
+SEEDS_SUBMIN_TAF= [{"M_B_c", "M_D_c", "M_E_c"},
+                {"M_B_c", "M_D_c", "M_I_c"},
+                {"M_B_c", "M_D_c", "M_H_c"},
+                {"M_B_c", "M_I_c", "M_S2_e"},
+                {"M_B_c", "M_E_c", "M_S2_e"},
+                {"M_B_c", "M_H_c", "M_S2_e"},
+                {"M_A_c", "M_D_c", "M_I_c", "M_S1_e"},
+                {"M_D_c", "M_I_c", "M_J_c", "M_S1_e"},
+                {"M_A_c", "M_D_c", "M_E_c", "M_S1_e"},
+                {"M_A_c", "M_D_c", "M_H_c", "M_S1_e"},
+                {"M_A_c", "M_E_c", "M_S1_e", "M_S2_e"},
+                {"M_A_c", "M_H_c", "M_S1_e", "M_S2_e"},
+                {"M_H_c", "M_J_c", "M_S1_e", "M_S2_e"},
+                {"M_E_c", "M_J_c", "M_S1_e", "M_S2_e"},
+                {"M_A_c", "M_I_c", "M_S1_e", "M_S2_e"},
+                {"M_I_c", "M_J_c", "M_S1_e", "M_S2_e"},
+                {"M_D_c", "M_H_c", "M_J_c", "M_S1_e"},
+                {"M_D_c", "M_E_c", "M_J_c", "M_S1_e"}
+                ]
+SIZE_SUBMIN_TAF=len(SEEDS_SUBMIN_TAF)
+
+SEEDS_MIN_TAF = [{"M_B_c", "M_D_c", "M_E_c"} ,
+            {"M_B_c", "M_D_c", "M_I_c"} ,
+            {"M_B_c", "M_D_c", "M_H_c"} ,
+            {"M_B_c", "M_I_c", "M_S2_e"} ,
+            {"M_B_c", "M_E_c", "M_S2_e"} ,
+            {"M_B_c", "M_H_c", "M_S2_e"}
+            ]
+SIZE_MIN_TAF=len(SEEDS_MIN_TAF)
+
+
+SEEDS_SUBMIN_TAS= [{"M_F_c"},
+                {"M_B_c", "M_D_c", "M_E_c"},
+                {"M_B_c", "M_D_c", "M_I_c"},
+                {"M_B_c", "M_D_c", "M_H_c"},
+                {"M_B_c", "M_I_c", "M_S2_e"},
+                {"M_B_c", "M_E_c", "M_S2_e"},
+                {"M_B_c", "M_H_c", "M_S2_e"},
+                {"M_A_c", "M_D_c", "M_I_c", "M_S1_e"},
+                {"M_D_c", "M_I_c", "M_J_c", "M_S1_e"},
+                {"M_A_c", "M_D_c", "M_E_c", "M_S1_e"},
+                {"M_A_c", "M_D_c", "M_H_c", "M_S1_e"},
+                {"M_A_c", "M_E_c", "M_S1_e", "M_S2_e"},
+                {"M_A_c", "M_H_c", "M_S1_e", "M_S2_e"},
+                {"M_H_c", "M_J_c", "M_S1_e", "M_S2_e"},
+                {"M_E_c", "M_J_c", "M_S1_e", "M_S2_e"},
+                {"M_A_c", "M_I_c", "M_S1_e", "M_S2_e"},
+                {"M_I_c", "M_J_c", "M_S1_e", "M_S2_e"},
+                {"M_D_c", "M_H_c", "M_J_c", "M_S1_e"},
+                {"M_D_c", "M_E_c", "M_J_c", "M_S1_e"}
+                ]
+SIZE_SUBMIN_TAS=len(SEEDS_SUBMIN_TAS)
+
+SEEDS_MIN_TAS = [{"M_F_c"}]
+SIZE_MIN_TAS=len(SEEDS_MIN_TAS)
+
+######################################################## 
+
+
+
+
+
+
+######################### TESTS ########################
+#TODO: 
+#     - test with accumulation
+#     - test keep import reaction and topological injection
+#     - find Network to have different value in Reasoning / Filter / Gues_check / Guess_Check_Div
+#     - find Network to have different value with accumulation authorized
+#     - test without maximization for hybrid
+#     - test unsat
+#     - test possible_seeds (subset of seed that maximize number of producible targets)
+#     - test changing objective
+#     - test target file
+
+# solve values: 'all'
+# optim values: 'submin', 'min'
+
+# ---------------------- TARGET ARE FORBIDDEN ----------------------
+# ----------- SUBSETMIN ----------- 
+def test_submin_taf():
+    solve="all"
+    optim="submin"
+    list_solution=search_seed(INFILE, RUN_MODE, solve, optim)
+    for solution in list_solution:
+        assert set(solution) in SEEDS_SUBMIN_TAF
+    assert len(list_solution) == SIZE_SUBMIN_TAF
+
+
+# ----------- MINIMIZE ----------- 
+def test_min_taf():
+    solve="all"
+    optim="min"
+    list_solution=search_seed(INFILE, RUN_MODE, solve, optim)
+    for solution in list_solution:
+        assert set(solution) in SEEDS_MIN_TAF
+    assert len(list_solution) == SIZE_MIN_TAF
+
+
+# ---------------------- TARGET AS SEEDS ----------------------
+# ----------- SUBSETMIN ----------- 
+def test_submin_tas():
+    solve="all"
+    optim="submin"
+    targets_as_seeds=True
+    list_solution=search_seed(INFILE, RUN_MODE, solve, optim, targets_as_seeds)
+    for solution in list_solution:
+        assert set(solution) in SEEDS_SUBMIN_TAS
+    assert len(list_solution) == SIZE_SUBMIN_TAS
+
+
+# ----------- MINIMIZE ----------- 
+def test_min_tas():
+    solve="all"
+    optim="min"
+    targets_as_seeds=True
+    list_solution=search_seed(INFILE, RUN_MODE, solve, optim, targets_as_seeds)
+    for solution in list_solution:
+        assert set(solution) in SEEDS_MIN_TAS
+    assert len(list_solution) == SIZE_MIN_TAS

tests/full_network.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+Description:
+Test seed2lp
+"""
+from os import path
+from .utils import search_seed
+
+################ DIRECTORIES AND FILES ###################
+TEST_DIR = path.dirname(path.abspath(__file__))
+
+# In This Network, The reaction R2 J + A -> C is deleted
+# C is alone in the network, with an import/export reaction, 
+# therefore C is always a seed by design in Full Network
+# J is alone never involved in any reaction, J is never a seed
+# All reaction are not reversible 
+# except import/export reaction for exchange metabolite S1, S2 C and G
+INFILE = path.join(TEST_DIR,'network/sbml/toy_paper_no_rev_rm_R2.sbml')
+######################################################## 
+
+
+################### FIXED VARIABLES ####################
+RUN_MODE="full"
+######################################################## 
+
+
+################ EXPECTED SOLUTIONS ##################
+# Same results for subset minimal and minimize
+SEEDS_REASONING = [{'M_C_c', 'M_F_c', 'M_S1_e', 'M_S2_e'},
+                    {'M_C_c', 'M_I_c', 'M_S1_e', 'M_S2_e'},
+                    {'M_C_c', 'M_H_c', 'M_S1_e', 'M_S2_e'},
+                    {'M_C_c', 'M_E_c', 'M_S1_e', 'M_S2_e'}
+                    ]
+SIZE_REASONING=len(SEEDS_REASONING)
+
+# Same results for Filter, Guess-Check and Guess-Check Diversity
+# Same results for subset minimal and minimize
+# F is an objective reactant (therefore a target), and it is choosen 
+# event if target is forbidden because in Full Network mode, 
+# all metabolite are Target and can't be forbidden
+SEEDS_HYB_COBRA = [{'M_C_c', 'M_F_c', 'M_S1_e', 'M_S2_e'}]
+SIZE_HYB_COBRA=len(SEEDS_HYB_COBRA)
+
+# metabolite A is a seed for hybrid only to create an export reaction
+# When B is a seed, The reaction S1 -> A+B is not activated in FBA
+# A is therefore not accumlated
+SEEDS_SUBMIN_HYBRID = [{'M_C_c', 'M_F_c', 'M_S1_e', 'M_S2_e'},
+                       {'M_A_c', 'M_C_c', 'M_I_c', 'M_S1_e', 'M_S2_e'},
+                       {'M_B_c', 'M_C_c', 'M_I_c', 'M_S1_e', 'M_S2_e'},
+                       {'M_A_c', 'M_C_c', 'M_H_c', 'M_S1_e', 'M_S2_e'},
+                       {'M_B_c', 'M_C_c', 'M_H_c', 'M_S1_e', 'M_S2_e'},
+                       {'M_A_c', 'M_C_c', 'M_E_c', 'M_S1_e', 'M_S2_e'},
+                       {'M_B_c', 'M_C_c', 'M_E_c', 'M_S1_e', 'M_S2_e'}
+                        ]
+SIZE_SUBMIN_HYBRID=len(SEEDS_SUBMIN_HYBRID)
+
+# F is an objective reactant (therefore a target), and it is choosen 
+# event if target is forbidden because in Full Network mode, 
+# all metabolite are Target and can't be forbidden
+SEEDS_MIN_HYBRID = [{'M_C_c', 'M_F_c', 'M_S1_e', 'M_S2_e'}]
+SIZE_MIN_HYBRID=len(SEEDS_MIN_HYBRID)
+
+######################################################## 
+
+
+
+######################### TESTS ########################
+#TODO: 
+#     - test with accumulation
+#     - test keep import reaction and topological injection
+#     - find Network to have different value in Filter / Gues_check / Guess_Check_Div
+#     - find Network to have different value with accumulation authorized
+#     - test without maximization for hybrid
+#     - test unsat
+#     - test possible_seeds (subset of seed that maximize number of producible targets)
+#     - test changing objective
+
+# solve values: 'reasoning', 'filter', 'guess_check', 'guess_check_div', 'hybrid'
+# optim values: 'submin', 'min'
+
+# ----------- SUBSETMIN ----------- 
+def test_reasoning_submin():
+    solve="reasoning"
+    optim="submin"
+    list_solution=search_seed(INFILE, RUN_MODE, solve, optim)
+    for solution in list_solution:
+        assert set(solution) in SEEDS_REASONING
+    assert len(list_solution) == SIZE_REASONING
+
+def test_filter_submin():
+    solve="filter"
+    optim="submin"
+    list_solution=search_seed(INFILE, RUN_MODE, solve, optim)
+    for solution in list_solution:
+        assert set(solution) in SEEDS_HYB_COBRA
+    assert len(list_solution) == SIZE_HYB_COBRA 
+
+def test_gc_submin():
+    solve="guess_check"
+    optim="submin"
+    list_solution=search_seed(INFILE, RUN_MODE, solve, optim)
+    for solution in list_solution:
+        assert set(solution) in SEEDS_HYB_COBRA
+    assert len(list_solution) == SIZE_HYB_COBRA 
+
+def test_gcd_submin():
+    solve="guess_check_div"
+    optim="submin"
+    list_solution=search_seed(INFILE, RUN_MODE, solve, optim)
+    for solution in list_solution:
+        assert set(solution) in SEEDS_HYB_COBRA
+    assert len(list_solution) == SIZE_HYB_COBRA 
+
+
+def test_hybrid_submin():
+    solve="hybrid"
+    optim="submin"
+    list_solution=search_seed(INFILE, RUN_MODE, solve, optim)
+    for solution in list_solution:
+        assert set(solution) in SEEDS_SUBMIN_HYBRID
+    assert len(list_solution) == SIZE_SUBMIN_HYBRID
+
+
+# ----------- MINIMIZE ----------- 
+def test_reasoning_min():
+    solve="reasoning"
+    optim="min"
+    list_solution=search_seed(INFILE, RUN_MODE, solve, optim)
+    for solution in list_solution:
+        assert set(solution) in SEEDS_REASONING
+    assert len(list_solution) == SIZE_REASONING
+
+def test_filter_min():
+    solve="filter"
+    optim="min"
+    list_solution=search_seed(INFILE, RUN_MODE, solve, optim)
+    for solution in list_solution:
+        assert set(solution) in SEEDS_HYB_COBRA
+    assert len(list_solution) == SIZE_HYB_COBRA 
+
+def test_gc_min():
+    solve="guess_check"
+    optim="min"
+    list_solution=search_seed(INFILE, RUN_MODE, solve, optim)
+    for solution in list_solution:
+        assert set(solution) in SEEDS_HYB_COBRA
+    assert len(list_solution) == SIZE_HYB_COBRA 
+
+def test_gcd_min():
+    solve="guess_check_div"
+    optim="min"
+    list_solution=search_seed(INFILE, RUN_MODE, solve, optim)
+    for solution in list_solution:
+        assert set(solution) in SEEDS_HYB_COBRA
+    assert len(list_solution) == SIZE_HYB_COBRA 
+
+
+def test_hybrid_min():
+    solve="hybrid"
+    optim="min"
+    list_solution=search_seed(INFILE, RUN_MODE, solve, optim)
+    for solution in list_solution:
+        assert set(solution) in SEEDS_MIN_HYBRID
+    assert len(list_solution) == SIZE_MIN_HYBRID

tests/normalization.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+Description:
+Test seed2lp
+"""
+from os import path
+from .utils import get_network
+import re
+
+##### ###### ##### DIRECTORIES AND FILES ###################
+TEST_DIR = path.dirname(path.abspath(__file__))
+
+# All reaction are not reversible 
+# except import/export reaction for exchange metabolite S1, S2 C and G
+INFILE = path.join(TEST_DIR,'network/sbml/toy_paper.sbml')
+######################################################## 
+
+
+################### FIXED VARIABLES ####################
+
+######################################################## 
+
+
+
+################# EXPECTED SOLUTIONS ###################
+EXCH = {"R_EX_S1", "R_EX_S2", "R_EX_C", "R_EX_G"}
+
+DEL = {"R_R2"}
+
+# For exchange reaction when import reaction deleted
+# The deletion is on ASP facts with atom reaction and bounds prefixed with "rm_" 
+# and product or reactant prefixed with "rm_" 
+REV = {'R_BIOMASS', 'R_EX_S1', 'R_EX_S2', 'R_EX_C', 'R_EX_G'}
+
+META_EXCH = {"R_R7"}
+
+FORBID_TAF = {"M_F_c"}
+
+RM_RXN = ['rm_reaction("rev_R_EX_S1").',
+        'rm_reaction("rev_R_EX_S2").',
+        'rm_reaction("rev_R_EX_C").',
+        'rm_reaction("rev_R_EX_G").',
+        'rm_bounds("rev_R_EX_S1","0.0000000000","1000.0000000000").',
+        'rm_bounds("rev_R_EX_S2","0.0000000000","1000.0000000000").',
+        'rm_bounds("rev_R_EX_C","0.0000000000","1000.0000000000").',
+        'rm_bounds("rev_R_EX_G","0.0000000000","1000.0000000000").',
+        'rm_product("M_S1_e","1.0000000000","rev_R_EX_S1","exchange","M_S1_e","toy_paper").',
+        'rm_product("M_S2_e","1.0000000000","rev_R_EX_S2","exchange","M_S2_e","toy_paper").',
+        'rm_product("M_C_c","1.0000000000","rev_R_EX_C","exchange","M_C_c","toy_paper").',
+        'rm_product("M_G_c","1.0000000000","rev_R_EX_G","exchange","M_G_c","toy_paper").'
+        ]
+SIZE_RM_RXN=len(RM_RXN)
+
+SEED_TI = ['seed("M_S1_e","exchange","M_S1_e").',
+        'seed("M_S2_e","exchange","M_S2_e").',
+        'seed("M_C_c","exchange","M_C_c").',
+        'seed("M_G_c","exchange","M_G_c").'
+        ]
+SIZE_SEED_TI=len(SEED_TI)
+
+
+MATCH_RM = 'rm_'
+MATCH_SEED = 'seed\('
+
+######################################################## 
+
+def test_exchange():
+    run_mode = "full"
+    targets_as_seeds = False
+    topological_injection = False
+    keep_import_reactions = False
+
+    network = get_network(INFILE, run_mode, targets_as_seeds, 
+                    topological_injection, keep_import_reactions)
+    assert set(network.exchanged_reactions) == EXCH
+
+
+def test_delete():
+    run_mode = "full"
+    targets_as_seeds = False
+    topological_injection = False
+    keep_import_reactions = False
+
+    network = get_network(INFILE, run_mode, targets_as_seeds, 
+                    topological_injection, keep_import_reactions)
+    assert set(network.deleted_reactions) == DEL
+
+
+def test_rev_modified():
+    run_mode = "full"
+    targets_as_seeds = False
+    topological_injection = False
+    keep_import_reactions = False
+
+    network = get_network(INFILE, run_mode, targets_as_seeds, 
+                    topological_injection, keep_import_reactions)
+    assert set(network.reversible_modified_reactions.keys()) == REV
+
+
+# import reaction removed, prefixed by "rm_" on atom 
+# reaction reaction and bounds 
+# and 
+def test_rm_rxn():
+    run_mode = "full"
+    targets_as_seeds = False
+    topological_injection = False
+    keep_import_reactions = False
+
+    network = get_network(INFILE, run_mode, targets_as_seeds, 
+                    topological_injection, keep_import_reactions)
+    network.convert_to_facts()
+
+    rm_list_found=re.findall(MATCH_RM, network.facts)
+    size_rm_found=len(rm_list_found)
+    assert size_rm_found == SIZE_RM_RXN
+
+    seed_list_found=re.findall(MATCH_SEED, network.facts)
+    size_seed_found=len(seed_list_found)
+    assert size_seed_found == 0
+    
+    for rm in RM_RXN:
+        assert rm in network.facts
+    
+# import reaction kept, no prefix on atom reaction
+def test_kir():
+    run_mode = "full"
+    targets_as_seeds = False
+    topological_injection = False
+    keep_import_reactions = True
+
+    network = get_network(INFILE, run_mode, targets_as_seeds, 
+                    topological_injection, keep_import_reactions)
+    network.convert_to_facts()
+    
+    rm_list_found=re.findall(MATCH_RM, network.facts)
+    size_rm_found=len(rm_list_found)
+    assert size_rm_found == 0
+
+    seed_list_found=re.findall(MATCH_SEED, network.facts)
+    size_seed_found=len(seed_list_found)
+    assert size_seed_found == 0
+
+
+# import reaction kept, no prefix on atom reaction
+# atom seed added product or reactant (dependeing way it is written on sbml)
+def test_ti():
+    run_mode = "full"
+    targets_as_seeds = False
+    topological_injection = True
+    keep_import_reactions = True
+
+    network = get_network(INFILE, run_mode, targets_as_seeds, 
+                    topological_injection, keep_import_reactions)
+    network.convert_to_facts()
+
+    rm_list_found=re.findall(MATCH_RM, network.facts)
+    size_rm_found=len(rm_list_found)
+    assert size_rm_found == 0
+
+    seed_list_found=re.findall(MATCH_SEED, network.facts)
+    size_seed_found=len(seed_list_found)
+    assert size_seed_found == SIZE_SEED_TI
+    for seed in SEED_TI:
+        assert seed in network.facts
+
+
+
+def test_taf():
+    run_mode = "target"
+    targets_as_seeds = False
+    topological_injection = False
+    keep_import_reactions = False
+    network = get_network(INFILE, run_mode, targets_as_seeds, 
+                    topological_injection, keep_import_reactions)
+    assert set(network.forbidden_seeds) == FORBID_TAF
+
+
+def test_tas():
+    run_mode = "target"
+    targets_as_seeds = True
+    topological_injection = False
+    keep_import_reactions = False
+    network = get_network(INFILE, run_mode, targets_as_seeds, 
+                    topological_injection, keep_import_reactions)
+    # check if list is empty
+    assert not network.forbidden_seeds