added codon frequency functionality

adelbke · Mar 18, 2021 · 23ecf22 · 23ecf22
1 parent ef632d6
commit 23ecf22
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Showing 5 changed files with 49 additions and 21 deletions.
diff --git a/projetsysteme/__pycache__/components.cpython-38.pyc b/projetsysteme/__pycache__/components.cpython-38.pyc
diff --git a/projetsysteme/__pycache__/dna.cpython-38.pyc b/projetsysteme/__pycache__/dna.cpython-38.pyc
diff --git a/projetsysteme/components.py b/projetsysteme/components.py
@@ -54,6 +54,7 @@ def __init__(self, *args, **kwargs):
         self.btn_arn_vers_proteine.clicked.connect(self.action_arn_vers_proteine)
         self.btn_comp_inv_adn.clicked.connect(self.action_comp_inv_adn)
         self.btn_taux_gc_adn.clicked.connect(self.action_taux_gc_adn)
+        self.btn_freq_codons_adn.clicked.connect(self.action_freq_codons_adn)
 
 
     def action_creer_adn(self):
@@ -71,22 +72,36 @@ def action_creer_adn(self):
                 x=msg.exec_()
 
     def action_adn_vers_arn(self):
+        if DNA.dna_chain == "":
+            return
         DNA.translate_to_rna()
         MainLayout._instance.output_rna_chain.setText(DNA.rna_chain)
+
 
     def action_arn_vers_proteine(self):
+        if DNA.rna_chain == "":
+            return
         DNA.rna_to_prot()
         MainLayout._instance.output_protein_chain.setText(DNA.protein_chain)
 
     def action_comp_inv_adn(self):
+        if DNA.dna_chain == "":
+            return
         DNA.get_dna_complement()
         MainLayout._instance.output_dna_complement.setText(DNA.dna_complement)
 
     def action_taux_gc_adn(self):
+        if DNA.dna_chain == "":
+            return
         DNA.taux_gc()
-        MainLayout._instance.output_taux_gc.setText(DNA.gc_rate)
-
+        MainLayout._instance.output_taux_gc.setText(str(DNA.gc_rate)+'%')
+    
 
+    def action_freq_codons_adn(self):
+        if DNA.dna_chain == "":
+            return
+        DNA.taux_codons()
+        MainLayout._instance.output_codon_frequency.setText(str(DNA.codon_frequency))
 
     def setupButtons(self):
         # setup buttons list
@@ -118,13 +133,14 @@ def __init__(self, *args, **kwargs):
             return None
         super().__init__(*args,**kwargs)
         MainLayout._instance = self
-
+        chain_width = 50
         elements = [
-            ('ADN','dna_chain'),
-            ('ARN','rna_chain'),
-            ('Proteine','protein_chain'),
-            ('Comp Inv','dna_complement'),
-            ('Taux GC','taux_gc')
+            ('ADN','dna_chain',chain_width),
+            ('ARN','rna_chain',chain_width),
+            ('Proteine','protein_chain',chain_width),
+            ('Comp Inv','dna_complement',chain_width),
+            ('Taux GC','taux_gc',4),
+            ('Fréquence Codons','codon_frequency',4)
         ]
         for element in elements:
             label = QLabel(element[0])
@@ -134,7 +150,7 @@ def __init__(self, *args, **kwargs):
             textEdit.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
             textEdit.setLineWrapMode(QTextEdit.NoWrap)
             singleWidth = textEdit.fontMetrics().boundingRect('A').width()
-            textEdit.setFixedWidth(singleWidth*50)
+            textEdit.setFixedWidth(singleWidth*element[2])
 
 
             setattr(self,'label_'+element[1], label)

diff --git a/projetsysteme/dna.py b/projetsysteme/dna.py
@@ -1,16 +1,16 @@
-
 from random import randint
 class DNA():
 
     # this metaclass is here to implement getters
     #  and setters for these static variables
 
 
-    _dna_chain= ""
-    _rna_chain = ""
-    _protein_chain = ""
-    _dna_complement = ""
-    _gc_rate = 0
+    dna_chain= ""
+    rna_chain = ""
+    protein_chain = ""
+    dna_complement = ""
+    gc_rate = 0
+    codon_frequency=0
 
 
 
@@ -65,10 +65,22 @@ def taux_gc(cls):
         gc= int((adn.count("C")+adn.count("G")) / len(adn) * 100)
         cls.gc_rate=gc
 
-    # @classmethod
-    # def taux_codons()
+    @classmethod
+    def taux_codons(cls):
+        if cls.rna_chain == "":
+            cls.translate_to_rna()
+        from .rna_to_acid import RNA_to_acido_dic
+        rna = cls.rna_chain
+        freq = 0
+        for index in range(0,len(rna),3):
+            if index+3 < len(rna) and RNA_to_acido_dic[rna[index:index+3]] != "---":
+                freq= freq+1
+        cls.codon_frequency = freq
+
 
 
-# DNA.generate_dna(15)
-# DNA.translate_to_rna()
-# print(DNA.rna_chain)
+# DNA.generate_dna(31)
+# DNA.taux_codons()
+# DNA.rna_to_prot()
+# print(DNA.protein_chain)
+# print(DNA.codon_frequency)
diff --git a/projetsysteme/style.css b/projetsysteme/style.css
@@ -669,7 +669,7 @@ QTextEdit {
   background-color: #19232D;
   color: #F0F0F0;
   border-radius: 4px;
-  border: 1px solid #32414B;
+  border: 1px solid #5c778a;
   max-height: 1rem;
 }