Merge pull request #80 from Fxe/dev

Dev

Author: Fxe

modelseedpy/core/msatpcorrection.py

@@ -262,7 +262,7 @@ def expand_model_to_genome_scale(self):
         # it is not detrimental to run this twice
         self.restore_noncore_reactions(noncore=True, othercompartment=False)
         # Extending model with non core reactions while retaining ATP accuracy
-        self.filtered_noncore = self.modelutl.reaction_expansion_test(self.noncore_reactions,tests)        
+        self.filtered_noncore = self.modelutl.reaction_expansion_test(self.noncore_reactions, tests)
         # Removing filtered reactions
         for item in self.filtered_noncore:
             print("Removing "+item[0].id+" "+item[1])

modelseedpy/core/msbuilder.py

@@ -650,4 +650,7 @@ def gapfill_model(original_mdl, target_reaction, template, media):
             else:
                 rxn.upper_bound = 0
                 rxn.lower_bound = -100
-        return original_mdl
+        return original_mdl
+
+def build_metabolic_model(genome, media=None, atp_test_medias=None, core_template=None, genome_scale_template=None):
+    pass

modelseedpy/core/msgapfill.py

@@ -57,7 +57,7 @@ def run_gapfilling(self, media=None, target=None, minimum_obj=0.01, binary_check
         })
         pkgmgr.getpkg("KBaseMediaPkg").build_package(media)
 
-        #Filtering breaking reactions out of the database
+        # Filtering breaking reactions out of the database
         if prefilter and self.test_conditions:
             pkgmgr.getpkg("GapfillingPkg").filter_database_based_on_tests(self.test_conditions)
 
@@ -68,14 +68,16 @@ def run_gapfilling(self, media=None, target=None, minimum_obj=0.01, binary_check
         logger.debug('gapfill solution objective value %f (%s) for media %s', sol.objective_value, sol.status, media)
 
         if sol.status != 'optimal':
-            logger.warning("No solution found for %s", media)
+            logger.debug("No solution found for %s", media)
             return None
 
         self.last_solution = pkgmgr.getpkg("GapfillingPkg").compute_gapfilled_solution() 
         if self.test_conditions:
-            self.last_solution = pkgmgr.getpkg("GapfillingPkg").run_test_conditions(self.test_conditions, self.last_solution, self.test_condition_iteration_limit)
+            self.last_solution = pkgmgr.getpkg("GapfillingPkg").run_test_conditions(
+                self.test_conditions, self.last_solution, self.test_condition_iteration_limit)
             if self.last_solution is None:
-                logger.warning("no solution could be found that satisfied all specified test conditions in specified iterations!")
+                logger.debug("No solution could be found that satisfied all \
+                              specified test conditions in specified iterations!")
                 return None
         if binary_check:
             return pkgmgr.getpkg("GapfillingPkg").binary_check_gapfilling_solution()

modelseedpy/core/msgenome.py

@@ -1,24 +1,24 @@
 import logging
 import re
-import copy  # !!! the import is never used
 from cobra.core.dictlist import DictList
 
 logger = logging.getLogger(__name__)
 
+DEFAULT_SPLIT = ' '
+
 
 def normalize_role(s):
-    # print(s)
     s = s.strip().lower()
-    s = re.sub('[\W_]+', '', s)
+    s = re.sub(r'[\W_]+', '', s)
     return s
 
 
-def read_fasta(f, split='|', h_func=None):
+def read_fasta(f, split=DEFAULT_SPLIT, h_func=None):
     with open(f, 'r') as fh:
         return parse_fasta_str(fh.read(), split, h_func)
 
 
-def parse_fasta_str(faa_str, split='|', h_func=None):
+def parse_fasta_str(faa_str, split=DEFAULT_SPLIT, h_func=None):
     features = []
     seq = None
     for line in faa_str.split('\n'):
@@ -32,7 +32,8 @@ def parse_fasta_str(faa_str, split='|', h_func=None):
             elif split:
                 header_data = line[1:].split(split, 1)
                 seq_id = header_data[0]
-                desc = header_data[1]  # The unit test throws an error when this is commented
+                if len(header_data) > 1:
+                    desc = header_data[1]  # The unit test throws an error when this is commented
 
             seq = MSFeature(seq_id, "", desc)
         else:
@@ -108,10 +109,10 @@ def from_protein_sequences_hash(sequences):
         genome = MSGenome()
         genome.features += features
         return genome
-    
+
     def alias_hash(self):
         return {alias: gene for gene in self.features for alias in gene.aliases}
-    
+
     def search_for_gene(self, query):
         if query in self.features:
             return self.features.get_by_id(query)

modelseedpy/core/msmodelutl.py

@@ -74,9 +74,9 @@ def __init__(self,model):
         self.test_objective = None
         self.score = None
 
-    def printlp(self,lpfilename="debug.lp"):
+    def printlp(self, lpfilename="debug.lp"):
         with open(lpfilename, 'w') as out:
-                out.write(str(self.model.solver))
+            out.write(str(self.model.solver))
 
     def build_metabolite_hash(self):
         self.metabolite_hash = {}
@@ -345,7 +345,7 @@ def add_gapfilling_solution_to_kbase_model(self,newmodel,gapfilled_reactions,gfi
                     kbrxn["gapfill_data"][gfid]["0"] = [gapfilled_reactions["reversed"][rxn],1,[]]
         return rxn_table
 
-    def apply_test_condition(self,condition,model = None):
+    def apply_test_condition(self, condition, model=None):
         """Applies constraints and objective of specified condition to model
         
         Parameters
@@ -363,7 +363,7 @@ def apply_test_condition(self,condition,model = None):
         Raises
         ------
         """
-        if model == None:
+        if model is None:
             model = self.model
             pkgmgr = self.pkgmgr
         else:
@@ -375,7 +375,7 @@ def apply_test_condition(self,condition,model = None):
             model.objective.direction = "min"
         pkgmgr.getpkg("KBaseMediaPkg").build_package(condition["media"])
 
-    def test_single_condition(self,condition,apply_condition=True,model=None):
+    def test_single_condition(self, condition, apply_condition=True, model=None):
         """Runs a single test condition to determine if objective value on set media exceeds threshold
         
         Parameters
@@ -395,14 +395,14 @@ def test_single_condition(self,condition,apply_condition=True,model=None):
         Raises
         ------
         """
-        if model == None:
+        if model is None:
             model = self.model
         if apply_condition:
-            self.apply_test_condition(condition,model)
+            self.apply_test_condition(condition, model)
         new_objective = model.slim_optimize()
         value = new_objective
         if "change" in condition and condition["change"]:
-            if self.test_objective != None:
+            if self.test_objective is not None:
                 value = new_objective - self.test_objective
         self.score = value
         if model.solver.status != 'optimal':
@@ -418,7 +418,7 @@ def test_single_condition(self,condition,apply_condition=True,model=None):
         self.test_objective = new_objective
         return True
 
-    def test_condition_list(self,condition_list,model=None):
+    def test_condition_list(self, condition_list: list, model=None):
         """Runs a set of test conditions to determine if objective values on set medias exceed thresholds
         
         Parameters
@@ -443,7 +443,7 @@ def test_condition_list(self,condition_list,model=None):
                 return False
         return True
 
-    def reaction_expansion_test(self,reaction_list,condition_list):
+    def reaction_expansion_test(self, reaction_list: list, condition_list: list):
         """Adds reactions in reaction list one by one and appplies tests, filtering reactions that fail
         
         Parameters
@@ -461,10 +461,15 @@ def reaction_expansion_test(self,reaction_list,condition_list):
         Raises
         ------
         """
-        print("Expansion started!")
         tic = time.perf_counter()
+
+        logger.info(f"Expansion started! reaction list: {len(reaction_list)} conditions: {len(condition_list)}")
+
         filtered_list = []
         for condition in condition_list:
+
+            logger.debug(f'testing condition {condition}')
+
             currmodel = self.model
             with currmodel:
                 self.apply_test_condition(condition)

modelseedpy/fbapkg/gapfillingpkg.py

@@ -450,9 +450,11 @@ def binary_check_gapfilling_solution(self, solution=None, flux_values=None):
             self.model.optimize()
             new_solution = self.compute_gapfilled_solution()
         return new_solution
-    
-    #This function is designed to KO all gapfilled reactions not included in the solution
+
     def knockout_gf_reactions_outside_solution(self,solution = None,flux_values = None):
+        """
+        This function is designed to KO all gap filled reactions not included in the solution
+        """
         if solution == None:
             solution = self.compute_gapfilled_solution()
         if flux_values == None:
@@ -500,18 +502,18 @@ def run_test_conditions(self,condition_list,solution = None,max_iterations = 10)
             return None
         return solution
 
-    def filter_database_based_on_tests(self,test_conditions):
+    def filter_database_based_on_tests(self, test_conditions):
         filetered_list = []
         with self.model:
             rxnlist = []
             for reaction in self.model.reactions:
                 if reaction.id in self.gapfilling_penalties:
                     if "reverse" in self.gapfilling_penalties[reaction.id]:
-                        rxnlist.append([reaction,"<"])
+                        rxnlist.append([reaction, "<"])
                     if "forward" in self.gapfilling_penalties[reaction.id]:
-                        rxnlist.append([reaction,">"])
+                        rxnlist.append([reaction, ">"])
             self.pkgmgr.getpkg("ObjConstPkg").constraints["objc"]["1"].lb = 0
-            filtered_list = self.modelutl.reaction_expansion_test(rxnlist,test_conditions)
+            filtered_list = self.modelutl.reaction_expansion_test(rxnlist, test_conditions)
         #Now constraining filtered reactions to zero
         for item in filtered_list:
             logger.debug("Filtering:",item[0].id,item[1])

modelseedpy/fbapkg/kbasemediapkg.py

@@ -60,4 +60,4 @@ def build_package(self, media_or_parameters, default_uptake=None, default_excret
                                         self.variables["logconc"][met.id].lb = ln(mediacpd.concentration)
                                         self.variables["logconc"][met.id].ub = ln(mediacpd.concentration)
                 else:
-                    logger.warn('Media compound: ', mediacpd.id,' not found in model.')
+                    logger.info(f'Media compound: {mediacpd.id} not found in model.')