complete remodeling of the Application with dna generation working on…

… the UI all all other features working under the hood
adelbke · Mar 18, 2021 · 0cea9f8 · 0cea9f8
1 parent fa824da
commit 0cea9f8
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Showing 9 changed files with 298 additions and 62 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/__pycache__/main.cpython-38.pyc b/projetsysteme/__pycache__/main.cpython-38.pyc
diff --git a/projetsysteme/__pycache__/views.cpython-38.pyc b/projetsysteme/__pycache__/views.cpython-38.pyc
diff --git a/projetsysteme/components.py b/projetsysteme/components.py
@@ -1,11 +1,15 @@
-from PyQt5.QtWidgets import QMainWindow, QHBoxLayout, QWidget, QToolBar, QPushButton
+from PyQt5.QtWidgets import QFormLayout, QInputDialog, QLabel, QMainWindow, QHBoxLayout, QMessageBox, QTextEdit, QVBoxLayout, QWidget, QToolBar, QPushButton
+# from PyQt5.QtCore import Qt
+
+from .dna import DNA
 
 class AbstractWindow(QMainWindow):
     def __init__(self, parent=None):
         """Initializer."""
         super().__init__()
+        # self.setMinimumWidth(1500)
 
-    def setupSidebarLayout(self,sidebarLayout, mainLayout):
+    def setupMainLayout(self,sidebarLayout, mainLayout):
         layout = QHBoxLayout()
         left = QWidget()
         left.setLayout(sidebarLayout)
@@ -23,15 +27,78 @@ def setupSidebarLayout(self,sidebarLayout, mainLayout):
         self.setCentralWidget(self.centralwidget)
         self.centralwidget.setLayout(layout)
 
+    def setMenuItems(self):
+        self.menu_fichier = self.menuBar().addMenu("Fichier")
+        self.menu_edit = self.menuBar().addMenu("Edit")    
+
+
+class SidebarLayout(QVBoxLayout):
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args,**kwargs)
+        self.setupButtons()
+
+
+        self.btn_creer_adn.clicked.connect(self.action_creer_adn)
+
+    def action_creer_adn(self):
+        n,result = QInputDialog.getInt(QWidget(), "Input Dialog", "Entrer la longueur:",0,0)
+        if result:
+            if n>0:
+                N=n
+                DNA.generate_dna(N)
+                print(self.parentWidget().window().mainLayout.output_ADN.setText(DNA.dna_chain))
+            else:
+                msg = QMessageBox()
+                msg.setWindowTitle("create dna")
+                msg.setText("Vous devez donner un nombre positif")
+                msg.setIcon(QMessageBox.Critical)
+                x=msg.exec_()
+
+    def setupButtons(self):
+        # setup buttons list
+        self.buttons = [
+            ('Créer ADN','creer_adn'),
+            ('ADN vers ARN','adn_vers_arn'),
+            ('ARN vers Proteine','arn_vers_proteine'),
+            ('Comp INV ADN','comp_inv_adn'),
+            ('taux GC ADN','taux_gc_adn'),
+            ('fréq codons ADN','freq_codons_adn'),
+            ('Mutation','mutation'),
+            ('Chercher Motif ADN','chercher_motif_adn'),
+            ('ADN Consensus + profil','adn_consensus_profil'),
+            ('Masse Proteïque','masse_proteique'),
+            ('Epissage d\'ADN','epissage_adn'),
+        ]
+        # create and assign buttons
+        for btn in self.buttons:
+            setattr(self,'btn_' + btn[1],QPushButton(btn[0]))
+            self.addWidget(getattr(self,'btn_' + btn[1]))
+        self.addStretch()
 
-    # automatizing setting the ToolBar for the app 
-    def setToolBar(self, menuItems):
-        tools = QToolBar()
-        self.addToolBar(tools)
-        for item in menuItems :
-            tools.addWidget(item)
 
 
+class MainLayout(QFormLayout):
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args,**kwargs)
+
+        elements = [
+            ('ADN','dna_chain'),
+            ('ARN','rna_chain'),
+            ('Proteine','protein_chain'),
+            ('Comp Inv','dna_complement')
+        ]
+        for element in elements:
+            label = QLabel(element[0])
+            textEdit = QTextEdit()
+            textEdit.setReadOnly(True)
+
+            setattr(self,'label_'+element[0], label)
+            setattr(self,'output_'+element[0],textEdit)
+            self.addRow(getattr(self,'label_'+element[0]),getattr(self,'output_'+element[0]))
+
+
+
+
 class QPrimaryButton(QPushButton):
     def __init__(self, *args, **kwargs):
         super().__init__(*args,**kwargs)

diff --git a/projetsysteme/dna.py b/projetsysteme/dna.py
@@ -1,12 +1,113 @@
 
-
+from random import randint
 class DNA():
-    chain= ""
-
-    # read from fasta file
-    def __init__(self, path: str):
-        pass
+
+    # this metaclass is here to implement getters
+    #  and setters for these static variables
+
+    class __metaclass__():
+        @property
+        def dna_chain(cls):
+            return cls._dna_chain
+
+        @dna_chain.setter
+        def dna_chain(cls, value):
+            cls._dna_chain = value
+
+        @property
+        def rna_chain(cls):
+            return cls._rna_chain
+
+        @rna_chain.setter
+        def rna_chain(cls, value):
+            cls._rna_chain = value
+
+        @property
+        def protein_chain(cls):
+            return cls._protein_chain
+
+        @protein_chain.setter
+        def protein_chain(cls, value):
+            cls._protein_chain = value
+
+        @property
+        def dna_complement(cls):
+            return cls._dna_complement
+
+        @dna_complement.setter
+        def dna_complement(cls, value):
+            cls._dna_complement = value
+
+        @property
+        def gc_rate(cls):
+            return cls._gc_rate
+
+        @gc_rate.setter
+        def gc_rate(cls, value):
+            cls._gc_rate = value
+
+    _dna_chain= ""
+    _rna_chain = ""
+    _protein_chain = ""
+    _dna_complement = ""
+    _gc_rate = 0
+
+
 
     # generate DNA Sequence from length
-    def __init__(slef, length: int):
-        pass
+    @classmethod    
+    def generate_dna(cls,length: int):
+        ADN = ''
+        for i in range(0,length):
+            ADN+='ACGT'[randint(0,3)]
+        cls.dna_chain = ADN
+        return cls.dna_chain
+
+    @classmethod
+    def translate_to_rna(cls):
+        cls.rna_chain = cls.dna_chain.replace("T", "U")
+
+    @classmethod
+    def rna_to_prot(cls):
+        from .rna_to_acid import RNA_to_acido_dic
+        rna = cls.rna_chain
+        index = 0
+        l = []
+        while index <= len(rna)-1:
+            if(len(rna[index:index+3]) == 3):
+                l.append(RNA_to_acido_dic[rna[index:index+3]])
+
+            index += 3
+        prot=''
+        print(l)
+        for ele in l:  
+            prot += ele+' ' 
+        cls.protein_chain = prot
+
+    @classmethod
+    def get_dna_complement(cls):
+        adn = cls.dna_chain
+        dna_comp=''
+        for i in range(len(adn)):
+            if adn[i] == 'A':
+                dna_comp += 'T'
+            elif adn[i] == 'T':
+                dna_comp += 'A'
+            elif adn[i] == 'C':
+                dna_comp += 'G'
+            elif adn[i] == 'G':
+                dna_comp += 'C'
+        dna_comp=dna_comp[::-1]
+
+        cls.dna_complement = dna_comp
+
+    @classmethod
+    def taux_gc(cls):
+        adn = cls.dna_chain
+        gc= int((adn.count("C")+adn.count("G")) / len(adn) * 100)
+        cls.gc_rate=gc
+
+
+DNA.generate_dna(15)
+DNA.translate_to_rna()
+print(DNA.rna_chain)
diff --git a/projetsysteme/rna_to_acid.py b/projetsysteme/rna_to_acid.py
@@ -0,0 +1,65 @@
+
+RNA_to_acido_dic = {'UUU': 'Phe',
+                    'UCU': 'Ser',
+                    'UAU': 'Tyr',
+                    'UGU': 'Cys',
+                    'UUC': 'Phe',
+                    'UCC': 'Ser',
+                    'UAC': 'Tyr',
+                    'UGC': 'Cys',
+                    'UUA': 'Leu',
+                    'UCA': 'Ser',
+                    'UAA': '---',
+                    'UGA': '---',
+                    'UUG': 'Leu',
+                    'UCG': 'Ser',
+                    'UAG': '---',
+                    'UGG': 'Trp',
+                    'CUU': 'Leu',
+                    'CCU': 'Pro',
+                    'CAU': 'His',
+                    'CGU': 'Arg',
+                    'CUC': 'Leu',
+                    'CCC': 'Pro',
+                    'CAC': 'His',
+                    'CGC': 'Arg',
+                    'CUA': 'Leu',
+                    'CCA': 'Pro',
+                    'CAA': 'Gln',
+                    'CGA': 'Arg',
+                    'CUG': 'Leu',
+                    'CCG': 'Pro',
+                    'CAG': 'Gln',
+                    'CGG': 'Arg',
+                    'AUU': 'Ile',
+                    'ACU': 'Thr',
+                    'AAU': 'Asn',
+                    'AGU': 'Ser',
+                    'AUC': 'Ile',
+                    'ACC': 'Thr',
+                    'AAC': 'Asn',
+                    'AGC': 'Ser',
+                    'AUA': 'Ile',
+                    'ACA': 'Thr',
+                    'AAA': 'Lys',
+                    'AGA': 'Arg',
+                    'AUG': 'Met',
+                    'ACG': 'Thr',
+                    'AAG': 'Lys',
+                    'AGG': 'Arg',
+                    'GUU': 'Val',
+                    'GCU': 'Ala',
+                    'GAU': 'Asp',
+                    'GGU': 'Gly',
+                    'GUC': 'Val',
+                    'GCC': 'Ala',
+                    'GAC': 'Asp',
+                    'GGC': 'Gly',
+                    'GUA': 'Val',
+                    'GCA': 'Ala',
+                    'GAA': 'Glu',
+                    'GGA': 'Gly',
+                    'GUG': 'Val',
+                    'GCG': 'Ala',
+                    'GAG': 'Glu',
+                    'GGG': 'Gly'}