rename physical data

explanations/1_rna_circuit_simulations.ipynb

@@ -387,7 +387,7 @@
       "File \u001b[0;32m~/Kode/synbio_morpher/synbio_morpher/utils/circuit/agnostic_circuits/circuit_manager.py:751\u001b[0m, in \u001b[0;36mCircuitModeller.apply_to_circuit\u001b[0;34m(self, circuit, methods)\u001b[0m\n\u001b[1;32m    749\u001b[0m \u001b[39mfor\u001b[39;00m method, kwargs \u001b[39min\u001b[39;00m methods\u001b[39m.\u001b[39mitems():\n\u001b[1;32m    750\u001b[0m     \u001b[39mif\u001b[39;00m \u001b[39mhasattr\u001b[39m(\u001b[39mself\u001b[39m, method):\n\u001b[0;32m--> 751\u001b[0m         circuit \u001b[39m=\u001b[39m \u001b[39mgetattr\u001b[39;49m(\u001b[39mself\u001b[39;49m, method)(circuit, \u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49mkwargs)\n\u001b[1;32m    752\u001b[0m     \u001b[39melse\u001b[39;00m:\n\u001b[1;32m    753\u001b[0m         logging\u001b[39m.\u001b[39mwarning(\n\u001b[1;32m    754\u001b[0m             \u001b[39mf\u001b[39m\u001b[39m'\u001b[39m\u001b[39mCould not find method @\u001b[39m\u001b[39m{\u001b[39;00mmethod\u001b[39m}\u001b[39;00m\u001b[39m in class \u001b[39m\u001b[39m{\u001b[39;00m\u001b[39mself\u001b[39m\u001b[39m}\u001b[39;00m\u001b[39m'\u001b[39m)\n",
       "File \u001b[0;32m~/Kode/synbio_morpher/synbio_morpher/utils/circuit/agnostic_circuits/circuit_manager.py:119\u001b[0m, in \u001b[0;36mCircuitModeller.compute_interactions\u001b[0;34m(self, circuit)\u001b[0m\n\u001b[1;32m    118\u001b[0m \u001b[39mdef\u001b[39;00m \u001b[39mcompute_interactions\u001b[39m(\u001b[39mself\u001b[39m, circuit: Circuit):\n\u001b[0;32m--> 119\u001b[0m     circuit \u001b[39m=\u001b[39m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49mcompute_interactions_core(circuit)\n\u001b[1;32m    121\u001b[0m     circuit\u001b[39m.\u001b[39minteractions\u001b[39m.\u001b[39mbinding_rates_association \u001b[39m=\u001b[39m circuit\u001b[39m.\u001b[39minteractions\u001b[39m.\u001b[39mbinding_rates_association \u001b[39m*\u001b[39m \\\n\u001b[1;32m    122\u001b[0m         \u001b[39mself\u001b[39m\u001b[39m.\u001b[39minteraction_factor\n\u001b[1;32m    123\u001b[0m     circuit\u001b[39m.\u001b[39minteractions\u001b[39m.\u001b[39mbinding_rates_dissociation \u001b[39m=\u001b[39m circuit\u001b[39m.\u001b[39minteractions\u001b[39m.\u001b[39mbinding_rates_dissociation \u001b[39m*\u001b[39m \\\n\u001b[1;32m    124\u001b[0m         \u001b[39mself\u001b[39m\u001b[39m.\u001b[39minteraction_factor\n",
       "File \u001b[0;32m~/Kode/synbio_morpher/synbio_morpher/utils/circuit/agnostic_circuits/circuit_manager.py:102\u001b[0m, in \u001b[0;36mCircuitModeller.compute_interactions_core\u001b[0;34m(self, circuit)\u001b[0m\n\u001b[1;32m     99\u001b[0m input_species \u001b[39m=\u001b[39m circuit\u001b[39m.\u001b[39mget_input_species()\n\u001b[1;32m    100\u001b[0m reactant_species \u001b[39m=\u001b[39m [\n\u001b[1;32m    101\u001b[0m     r\u001b[39m.\u001b[39mspecies \u001b[39mfor\u001b[39;00m r \u001b[39min\u001b[39;00m circuit\u001b[39m.\u001b[39mqreactions\u001b[39m.\u001b[39mreactants]\n\u001b[0;32m--> 102\u001b[0m interactions \u001b[39m=\u001b[39m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49mrun_interaction_simulator(\n\u001b[1;32m    103\u001b[0m     species\u001b[39m=\u001b[39;49minput_species,\n\u001b[1;32m    104\u001b[0m     filename\u001b[39m=\u001b[39;49mfilename,\n\u001b[1;32m    105\u001b[0m     quantities\u001b[39m=\u001b[39;49m[circuit\u001b[39m.\u001b[39;49mqreactions\u001b[39m.\u001b[39;49mreactants[reactant_species\u001b[39m.\u001b[39;49mindex(s)]\u001b[39m.\u001b[39;49mquantity \u001b[39mfor\u001b[39;49;00m s \u001b[39min\u001b[39;49;00m input_species])\n\u001b[1;32m    106\u001b[0m circuit\u001b[39m.\u001b[39minteractions \u001b[39m=\u001b[39m interactions\n\u001b[1;32m    107\u001b[0m circuit\u001b[39m.\u001b[39minteractions_state \u001b[39m=\u001b[39m \u001b[39m'\u001b[39m\u001b[39mcomputed\u001b[39m\u001b[39m'\u001b[39m\n",
-      "File \u001b[0;32m~/Kode/synbio_morpher/synbio_morpher/utils/circuit/agnostic_circuits/circuit_manager.py:174\u001b[0m, in \u001b[0;36mCircuitModeller.run_interaction_simulator\u001b[0;34m(self, species, quantities, filename)\u001b[0m\n\u001b[1;32m    170\u001b[0m data \u001b[39m=\u001b[39m {s: s\u001b[39m.\u001b[39mphysical_data \u001b[39mfor\u001b[39;00m s \u001b[39min\u001b[39;00m species}\n\u001b[1;32m    171\u001b[0m \u001b[39m# if filename is not None:\u001b[39;00m\n\u001b[1;32m    172\u001b[0m \u001b[39m#     return self.interaction_simulator.run((filename, data), compute_by_filename=True)\u001b[39;00m\n\u001b[1;32m    173\u001b[0m \u001b[39m# else:\u001b[39;00m\n\u001b[0;32m--> 174\u001b[0m \u001b[39mreturn\u001b[39;00m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49minteraction_simulator\u001b[39m.\u001b[39;49mrun(data, quantities\u001b[39m=\u001b[39;49mquantities, compute_by_filename\u001b[39m=\u001b[39;49m\u001b[39mFalse\u001b[39;49;00m)\n",
+      "File \u001b[0;32m~/Kode/synbio_morpher/synbio_morpher/utils/circuit/agnostic_circuits/circuit_manager.py:174\u001b[0m, in \u001b[0;36mCircuitModeller.run_interaction_simulator\u001b[0;34m(self, species, quantities, filename)\u001b[0m\n\u001b[1;32m    170\u001b[0m data \u001b[39m=\u001b[39m {s: s\u001b[39m.\u001b[39msequence \u001b[39mfor\u001b[39;00m s \u001b[39min\u001b[39;00m species}\n\u001b[1;32m    171\u001b[0m \u001b[39m# if filename is not None:\u001b[39;00m\n\u001b[1;32m    172\u001b[0m \u001b[39m#     return self.interaction_simulator.run((filename, data), compute_by_filename=True)\u001b[39;00m\n\u001b[1;32m    173\u001b[0m \u001b[39m# else:\u001b[39;00m\n\u001b[0;32m--> 174\u001b[0m \u001b[39mreturn\u001b[39;00m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49minteraction_simulator\u001b[39m.\u001b[39;49mrun(data, quantities\u001b[39m=\u001b[39;49mquantities, compute_by_filename\u001b[39m=\u001b[39;49m\u001b[39mFalse\u001b[39;49;00m)\n",
       "File \u001b[0;32m~/Kode/synbio_morpher/synbio_morpher/srv/parameter_prediction/interactions.py:221\u001b[0m, in \u001b[0;36mInteractionSimulator.run\u001b[0;34m(self, input, quantities, compute_by_filename)\u001b[0m\n\u001b[1;32m    217\u001b[0m \u001b[39m\"\"\" Makes nested dictionary for querying interactions as \u001b[39;00m\n\u001b[1;32m    218\u001b[0m \u001b[39m{sample1: {sample2: interaction}} \"\"\"\u001b[39;00m\n\u001b[1;32m    219\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mdata_handler \u001b[39m=\u001b[39m InteractionDataHandler(\n\u001b[1;32m    220\u001b[0m     simulation_handler\u001b[39m=\u001b[39m\u001b[39mself\u001b[39m\u001b[39m.\u001b[39msimulation_handler, quantities\u001b[39m=\u001b[39mquantities)\n\u001b[0;32m--> 221\u001b[0m data \u001b[39m=\u001b[39m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49msimulator(\u001b[39minput\u001b[39;49m, compute_by_filename\u001b[39m=\u001b[39;49mcompute_by_filename)\n\u001b[1;32m    222\u001b[0m data \u001b[39m=\u001b[39m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mdata_handler\u001b[39m.\u001b[39minit_data(data)\n\u001b[1;32m    223\u001b[0m \u001b[39mreturn\u001b[39;00m data\n",
       "File \u001b[0;32m~/Kode/synbio_morpher/synbio_morpher/srv/parameter_prediction/simulator.py:172\u001b[0m, in \u001b[0;36msimulate_IntaRNA\u001b[0;34m(input, compute_by_filename, allow_self_interaction, sim_kwargs, simulator, filename)\u001b[0m\n\u001b[1;32m    170\u001b[0m \u001b[39melse\u001b[39;00m:\n\u001b[1;32m    171\u001b[0m     f \u001b[39m=\u001b[39m simulate_IntaRNA_data\n\u001b[0;32m--> 172\u001b[0m \u001b[39mreturn\u001b[39;00m f(\u001b[39minput\u001b[39;49m, allow_self_interaction\u001b[39m=\u001b[39;49mallow_self_interaction, sim_kwargs\u001b[39m=\u001b[39;49msim_kwargs, simulator\u001b[39m=\u001b[39;49msimulator)\n",
       "File \u001b[0;32m~/Kode/synbio_morpher/synbio_morpher/srv/parameter_prediction/simulator.py:209\u001b[0m, in \u001b[0;36msimulate_IntaRNA_fn\u001b[0;34m(inputs, allow_self_interaction, sim_kwargs, simulator, remove_file)\u001b[0m\n\u001b[1;32m    207\u001b[0m sim_kwargs[\u001b[39m\"\u001b[39m\u001b[39mquery\u001b[39m\u001b[39m\"\u001b[39m] \u001b[39m=\u001b[39m filename\n\u001b[1;32m    208\u001b[0m sim_kwargs[\u001b[39m\"\u001b[39m\u001b[39mtarget\u001b[39m\u001b[39m\"\u001b[39m] \u001b[39m=\u001b[39m filename\n\u001b[0;32m--> 209\u001b[0m output \u001b[39m=\u001b[39m simulator\u001b[39m.\u001b[39;49mrun(\u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49msim_kwargs)\n\u001b[1;32m    210\u001b[0m \u001b[39mif\u001b[39;00m output:\n\u001b[1;32m    211\u001b[0m     \u001b[39mif\u001b[39;00m \u001b[39mtype\u001b[39m(output) \u001b[39m==\u001b[39m \u001b[39mdict\u001b[39m:\n",

notebooks/16_Monte_Carlo_circuit_adaptability.ipynb

@@ -3187,7 +3187,7 @@
     "    \n",
     "    for i, c in enumerate(circuits):\n",
     "        circuits[i].name = make_next_name(c.name, c.subname)\n",
-    "        # sequences = {s.name: s.physical_data for s in c.model.species if s.physical_data}\n",
+    "        # sequences = {s.name: s.sequence for s in c.model.species if s.sequence}\n",
     "        sequences = load_seq_from_FASTA(c.data.source, as_type='dict')\n",
     "        circuits[i].data.source = write_mutated_circuit(\n",
     "            name=circuits[i].name, subname='ref_circuit', sequences=sequences, data_writer=data_writer)\n",

synbio_morpher/scripts/ensemble_mutation_effect_analysis/configs/test_large_scale.json

@@ -49,8 +49,8 @@
             "experiment": {
                 "purpose": "mutation_effect_on_interactions_signal",
                 "no_visualisations": false,
-                "no_numerical": true,
-                "debug_mode": 1
+                "no_numerical": false,
+                "debug_mode": 0
             },
             "interaction_simulator": {
                 "name": "IntaRNA",

synbio_morpher/scripts/mc_evolution/run_mc_evolution.py

@@ -298,7 +298,7 @@ def process_for_next_run(circuits: list, data_writer: DataWriter):
 
     for i, c in enumerate(circuits):
         circuits[i].name = make_next_name(c.name)
-        # sequences = {s.name: s.physical_data for s in c.model.species if s.physical_data}
+        # sequences = {s.name: s.sequence for s in c.model.species if s.sequence}
         sequences = load_seq_from_FASTA(c.data.source, as_type='dict')
         circuits[i].data.source = write_mutated_circuit(
             name=circuits[i].name, subname='ref_circuit', sequences=sequences, data_writer=data_writer)
@@ -452,7 +452,7 @@ def main(config=None, data_writer=None):
     def write(summary_datas, data_writer):
         data_writer.subdivide_writing('summary_datas')
         for step, sdata in summary_datas.items():
-            data_writer.output('csv', out_name='sdata_' +
+            data_writer.output(out_type='csv', out_name='sdata_' +
                                str(step), write_master=False, data=sdata)
         data_writer.unsubdivide()
 

synbio_morpher/scripts/mutation_effect_on_interactions_signal/run_mutation_effect_on_interactions_signal.py

@@ -108,6 +108,7 @@ def logging_circuit(clist: list):
                              write_to_subsystem=True, batch_size=config_file['simulation'].get('batch_size', 100),
                              methods={
                 "compute_interactions": {},
+                "write_interactions": {},
                 "init_circuits": {'batch': True},
                 "simulate_signal_batch": {'ref_circuit': None,
                                           'batch': True},

synbio_morpher/scripts/parameter_based_simulation/run_parameter_based_simulation.py

@@ -74,7 +74,7 @@ def create_circuits(config: dict, interaction_matrices: np.ndarray):
 
 def write_all(all_analytic_matrices, analytic_types, data_writer, out_type='npy'):
     for m, analytic in enumerate(analytic_types):
-        data_writer.output(out_type, out_name=analytic,
+        data_writer.output(out_type=out_type, out_name=analytic,
                            data=all_analytic_matrices[m].astype(np.float32), overwrite=True,
                            write_to_top_dir=True)
 

synbio_morpher/scripts/stitch_parameter_grid/run_stitch_parameter_grid.py

@@ -129,7 +129,7 @@ def make_indices(iteration):
     # Write full matrices
     def write_all(stitched_parameter_grids, out_type='npy'):
         for analytic_name, grid in stitched_parameter_grids.items():
-            data_writer.output(out_type, out_name=analytic_name,
+            data_writer.output(out_type=out_type, out_name=analytic_name,
                                data=grid.astype(np.float32), overwrite=True,
                                write_to_top_dir=True)
 

synbio_morpher/scripts/summarise_simulation/run_summarise_simulation.py

@@ -21,12 +21,13 @@
 
 def main(config=None, data_writer=None):
     # Set configs
-    config, data_writer = script_preamble(config, data_writer, alt_cfg_filepath=os.path.join(
+    alt_cfg_filepath = os.path.join(
             # "synbio_morpher", "scripts", "summarise_simulation", "configs", "analyse_mutated_templates_20_highmag.json"))
-            "synbio_morpher", "scripts", "summarise_simulation", "configs", "base_config.json"))
+            "synbio_morpher", "scripts", "summarise_simulation", "configs", "base_config.json")
+    config, data_writer = script_preamble(config, data_writer, alt_cfg_filepath=alt_cfg_filepath)
     config_file = load_json_as_dict(config)
 
-    # Start_experiment
+    # Start_experiments
     if data_writer is None:
         data_writer = ResultWriter(purpose=config_file.get('experiment', {}).get('purpose'))
 

synbio_morpher/utils/circuit/agnostic_circuits/circuit.py

@@ -5,19 +5,20 @@
 # This source code is licensed under the MIT-style license found in the
 # LICENSE file in the root directory of this source tree.
 
-from typing import Union
+from typing import Union, Dict
 import pandas as pd
 import numpy as np
 import logging
 
 from synbio_morpher.srv.parameter_prediction.interactions import MolecularInteractions, InteractionMatrix
 from synbio_morpher.srv.io.manage.data_manager import DataManager
 from synbio_morpher.utils.circuit.common.system_setup import construct_bioreaction_model
+from synbio_morpher.utils.evolution.mutation import Mutations
 from synbio_morpher.utils.misc.string_handling import make_circuit_name
 from synbio_morpher.utils.misc.type_handling import flatten_listlike, get_unique
 from synbio_morpher.utils.results.results import ResultCollector
 from synbio_morpher.utils.signal.signals_new import Signal
-from bioreaction.model.data_containers import BasicModel, QuantifiedReactions, MedModel
+from bioreaction.model.data_containers import BasicModel, QuantifiedReactions
 
 
 FORMAT = "[%(filename)s:%(lineno)s - %(funcName)20s() ] %(message)s"
@@ -65,7 +66,7 @@ def init_refcircuit(self, config: dict):
             assert self.interactions_state != 'uninitialised', f'The interactions should have been initialised from {config.get("interactions")}'
         self.signal: Signal  # = None
         self.mutations_args: dict = config.get('mutations_args', {})
-        self.mutations = {}
+        self.mutations: Dict[str, Mutations] = {}
 
         self.update_species_simulated_rates(self.interactions)
 

synbio_morpher/utils/circuit/agnostic_circuits/circuit_manager.py

@@ -6,7 +6,7 @@
 # LICENSE file in the root directory of this source tree.
 
 from copy import deepcopy
-from typing import List, Tuple, Union
+from typing import List, Tuple, Union, Optional
 from functools import partial
 from datetime import datetime
 import multiprocessing
@@ -37,7 +37,8 @@
 from synbio_morpher.utils.results.visualisation import VisODE
 from synbio_morpher.utils.modelling.deterministic import bioreaction_sim_dfx_expanded, bioreaction_sim_dfx_naive
 from synbio_morpher.utils.modelling.solvers import get_diffrax_solver, make_stepsize_controller
-from synbio_morpher.utils.evolution.mutation import implement_mutation
+from synbio_morpher.utils.evolution.evolver import implement_mutation
+from synbio_morpher.utils.evolution.mutation import Mutations
 from synbio_morpher.utils.results.analytics.timeseries import generate_analytics
 from synbio_morpher.utils.results.result_writer import ResultWriter
 
@@ -222,7 +223,7 @@ def compute_interactions_batch(self, circuits: List[Circuit], batch=True):
         return circuits
 
     def run_interaction_simulator(self, species: List[Species], quantities, filename=None) -> InteractionDataHandler:
-        data = {s: s.physical_data for s in species}
+        data = {s: s.sequence for s in species}
         # if filename is not None:
         #     return self.interaction_simulator.run((filename, data), compute_by_filename=True)
         # else:
@@ -539,7 +540,7 @@ def prepare_batch_params(circuits: List[Circuit]):
         for i, (circuit, analytics) in enumerate(zip(circuits, b_analytics_l)):
             if self.discard_numerical_mutations and circuit.subname != 'ref_circuit':
                 sig_data = None
-                vis_func = lambda x: x
+                vis_func = lambda **kwargs: kwargs
             else:
                 sig_data = b_new_copynumbers[i]
                 vis_func=VisODE().plot
@@ -558,7 +559,7 @@ def prepare_batch_params(circuits: List[Circuit]):
         clear_caches()
         return circuits
 
-    def make_subcircuit(self, circuit: Circuit, mutation_name: str, mutation=None):
+    def make_subcircuit(self, circuit: Circuit, mutation_name: str, mutation: Optional[Mutations] =None):
 
         subcircuit = deepcopy(circuit)
         subcircuit.reset_to_initial_state()

synbio_morpher/utils/circuit/common/system_setup.py

@@ -22,7 +22,7 @@ def get_system_type(sys_type):
 def add_data_to_species(model: BasicModel, data: Data):
     for i, s in enumerate(model.species):
         if s.name in data.data.keys():
-            model.species[i].physical_data = data.data[s.name]
+            model.species[i].sequence = data.data[s.name]
     return model