Allow multiple codon tables and update list of generators in core

KarrLab · Aug 14, 2019 · 60f8b8f · 60f8b8f
1 parent 546344e
commit 60f8b8f
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Showing 2 changed files with 13 additions and 3 deletions.
diff --git a/wc_model_gen/eukaryote/complexation.py b/wc_model_gen/eukaryote/complexation.py
@@ -20,8 +20,9 @@ class ComplexationSubmodelGenerator(wc_model_gen.SubmodelGenerator):
         Options:
         * amino_acid_id_conversion (:obj:`dict`): a dictionary with amino acid standard ids
             as keys and amino acid metabolite ids as values
-        * codon_table (:obj:`int`): NCBI identifier for translation table, 
-            the default is 1 (standard table)
+        * codon_table (:obj:`dict`): a dictionary with protein subunit id as key and 
+            NCBI identifier for translation table as value, the default is 1 (standard table) 
+            for all protein
         * cds (:obj:`bool`): True indicates the sequences of protein subunits are complete CDS,
             the default if True    
         * beta (:obj:`float`, optional): ratio of Michaelis-Menten constant 
@@ -109,8 +110,13 @@ def gen_reactions(self):
                                 subunit_coefficient = subunit.coefficient if subunit.coefficient else 1
 
                                 if subunit.species_type==compl_subunit.species_type:
+
+                                    if codon_table == 1:
+                                        codon_id = 1
+                                    else:
+                                        codon_id = codon_table[subunit.species_type.id]    
 
-                                    protein_seq = subunit.species_type.get_seq(table=codon_table, cds=cds)
+                                    protein_seq = subunit.species_type.get_seq(table=codon_id, cds=cds)
                                     aa_content = {}
                                     for aa in protein_seq:
                                         aa_id = amino_acid_id_conversion[aa]

diff --git a/wc_model_gen/eukaryote/core.py b/wc_model_gen/eukaryote/core.py
@@ -7,7 +7,9 @@
 """
 
 from .initialize_model import InitializeModel
+from .complexation import ComplexationSubmodelGenerator
 from .transcription import TranscriptionSubmodelGenerator
+from .rna_degradation import RnaDegradationSubmodelGenerator
 import wc_model_gen
 
 
@@ -26,7 +28,9 @@ class EukaryoteModelGenerator(wc_model_gen.ModelGenerator):
 
     DEFAULT_COMPONENT_GENERATORS = (
         InitializeModel,
+        ComplexationSubmodelGenerator,
         TranscriptionSubmodelGenerator,
+        RnaDegradationSubmodelGenerator,
     )
 
     def clean_and_validate_options(self):