Beispiel #1
0
 def on_button_melt(self):
     if execBash('xdotool search --name meltviewer').decode() == '':
         proc =  subprocess.Popen(
             ['python3m',
             '/home/kablag/private/workspace/snpick/meltviewer.py'],
             stdout=subprocess.PIPE
         )
         time.sleep(1)
     mtask = MTask(self.seqEdit.text())
     mtask.execute(M_CONDS)
     # self.connection.send(mtask)
     plots = [{'action': 'add_graph',
                         'a': mpot.a,
                         'b': mpot.b,
                         'length': mpot.length_of_a,
                         'gc%': mpot.gc_of_a,
                         't10': mpot.t10,
                         't90': mpot.t90,
                         'mpoints': mpot.mpoints_as_XY,
                         'color': 'rnd',
                         'marker': 'rnd',
                         }
              for mpot in mtask.melting_pots]
     messages = [yaml.dump({'plots':[plot]}) for plot in plots]
     self.connect_to_meltviewer()
     self.iface.sendPlot(messages[0])
Beispiel #2
0
 def onLoadButtonClicked(self):
     filename, filter = QtGui.QFileDialog.getOpenFileName(
         self, 'Load project', '/home/kablag/Документы/snpick')
     if filename != '':
         with open(filename, 'r') as f:
             dump = yaml.load(f.read())
             M_CONDS.fromYAML(dump['conditions'])
             self.name.setText(dump['name'])
             self.seqInput.setText(dump['task'])
             self.probeMin.setText(dump['probeMin'])
             self.probeMax.setText(dump['probeMax'])
             self.mtask = MTask(dump['task'], dump)
             self.add_data_to_tabs()
Beispiel #3
0
 def onCalcProbesClicked(self):
     mtask = '{sequence}{min_p}->{max_p}'.format(
         sequence=self.seqInput.text(),
         min_p=self.probeMin.text(),
         max_p=self.probeMax.text(),
     )
     self.mtask = MTask(mtask)
     self.seqInput.setText(self.mtask.task)
     self.mtask.meltingPotDone.connect(self.on_mpot_done)
     self.pd = QtGui.QProgressDialog('Melting probes', 'Cancel', 0,
                                     len(self.mtask.melting_pots))
     self.pd.setWindowModality(QtCore.Qt.WindowModal)
     self.calcProbes.setEnabled(False)
     self.pd.canceled.connect(self.cancel_melting)
     self.mtask.execute(M_CONDS)
     self.calcProbes.setEnabled(True)
     self.add_data_to_tabs()
Beispiel #4
0
 def onLoadButtonClicked(self):
     filename, filter = QtGui.QFileDialog.getOpenFileName(self,
                                                  'Load project',
                                                  '/home/kablag/Документы/snpick')
     if filename != '':
         with open(filename, 'r') as f:
             dump = yaml.load(f.read())
             M_CONDS.fromYAML(dump['conditions'])
             self.name.setText(dump['name'])
             self.seqInput.setText(dump['task'])
             self.probeMin.setText(dump['probeMin'])
             self.probeMax.setText(dump['probeMax'])
             self.mtask = MTask(dump['task'], dump)
             self.add_data_to_tabs()
Beispiel #5
0
 def onCalcProbesClicked(self):
     mtask = '{sequence}{min_p}->{max_p}'.format(
         sequence=self.seqInput.text(),
         min_p=self.probeMin.text(),
         max_p=self.probeMax.text(),
     )
     self.mtask = MTask(mtask)
     self.seqInput.setText(self.mtask.task)
     self.mtask.meltingPotDone.connect(self.on_mpot_done)
     self.pd = QtGui.QProgressDialog('Melting probes',
                                     'Cancel',
                                     0,
                                     len(self.mtask.melting_pots))
     self.pd.setWindowModality(QtCore.Qt.WindowModal)
     self.calcProbes.setEnabled(False)
     self.pd.canceled.connect(self.cancel_melting)
     self.mtask.execute(M_CONDS)
     self.calcProbes.setEnabled(True)
     self.add_data_to_tabs()
Beispiel #6
0
class Snpick(QtGui.QWidget):
    def __init__(self):
        super(Snpick, self).__init__()
        self.mtask = None
        self.init_ui()

    def init_ui(self):
        self.name = QtGui.QLineEdit()
        self.name.setText('Name')
        self.seqInput = QtGui.QLineEdit()
        self.seqInput.setText(
            'tcccctccaggccgtgcataaggctgtgctgaccatcgac(A>G)agaaagggactgaagctgctggggccatgtttttagaggc'
        )

        self.probeMin = QtGui.QLineEdit()
        self.probeMin.setText('15')

        self.probeMax = QtGui.QLineEdit()
        self.probeMax.setText('17')

        self.calcProbes = QtGui.QPushButton(text='Calc')
        self.calcProbes.clicked.connect(self.onCalcProbesClicked)

        self.saveBtn = QtGui.QPushButton(text='Save')
        self.saveBtn.clicked.connect(self.onSaveButtonClicked)
        self.loadBtn = QtGui.QPushButton(text='Load')
        self.loadBtn.clicked.connect(self.onLoadButtonClicked)
        self.batchCalcBtn = QtGui.QPushButton(text='Batch Calc')
        self.batchCalcBtn.clicked.connect(self.onBatchButtonClicked)

        self.tabs = QtGui.QTabWidget()
        self.tab_A = FilterTab('A')
        self.tab_B = FilterTab('B')
        self.tab_Am = FilterTab('Am')
        self.tab_Bm = FilterTab('Bm')

        self.tabs.addTab(self.tab_A, 'A')
        self.tabs.addTab(self.tab_B, 'B')
        self.tabs.addTab(self.tab_Am, 'Am')
        self.tabs.addTab(self.tab_Bm, 'Bm')

        vbox = QtGui.QVBoxLayout()
        vbox.addWidget(self.name)
        vbox.addWidget(self.seqInput)
        # vbox.addStretch(1)
        hbox = QtGui.QHBoxLayout()
        sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed,
                                       QtGui.QSizePolicy.Minimum)
        self.probeMin.setSizePolicy(sizePolicy)
        hbox.addWidget(self.probeMin)
        self.probeMax.setSizePolicy(sizePolicy)
        hbox.addWidget(self.probeMax)
        self.calcProbes.setSizePolicy(sizePolicy)
        hbox.addWidget(self.calcProbes)
        hbox.addStretch(1)
        hbox.addWidget(self.saveBtn)
        hbox.addWidget(self.loadBtn)
        hbox.addStretch(1)
        hbox.addWidget(self.batchCalcBtn)
        hbox.addStretch(1)
        rangeInputs = QtGui.QWidget()
        rangeInputs.setLayout(hbox)
        vbox.addWidget(rangeInputs)
        vbox.addWidget(self.tabs)

        self.setLayout(vbox)
        self.setGeometry(300, 300, 1000, 600)
        self.show()

    def resizeEvent(self, event):
        self.tabs.setBaseSize(self.tabs.width(), event.size().height() * 0.8)

    def add_data_to_tabs(self):
        if not self.mtask.canceled:
            self.tab_A.addData(self.mtask)
            self.tab_B.addData(self.mtask)
            self.tab_Am.addData(self.mtask)
            self.tab_Bm.addData(self.mtask)

    def onCalcProbesClicked(self):
        mtask = '{sequence}{min_p}->{max_p}'.format(
            sequence=self.seqInput.text(),
            min_p=self.probeMin.text(),
            max_p=self.probeMax.text(),
        )
        self.mtask = MTask(mtask)
        self.seqInput.setText(self.mtask.task)
        self.mtask.meltingPotDone.connect(self.on_mpot_done)
        self.pd = QtGui.QProgressDialog('Melting probes', 'Cancel', 0,
                                        len(self.mtask.melting_pots))
        self.pd.setWindowModality(QtCore.Qt.WindowModal)
        self.calcProbes.setEnabled(False)
        self.pd.canceled.connect(self.cancel_melting)
        self.mtask.execute(M_CONDS)
        self.calcProbes.setEnabled(True)
        self.add_data_to_tabs()

    def onSaveButtonClicked(self, filename=''):
        filename, filter = filename, '' if filename != '' else QtGui.QFileDialog.getSaveFileName(
            self, 'Save project', PROJECTS_FOLDER + self.name.text())
        if filename != '':
            with open(filename, 'w') as f:
                # print(yaml.dump(self.mtask.melting_pots), file=f)
                # pickle.dump(self.mtask, f)

                conditions = {
                    'unafold_path': M_CONDS.unafold_path,
                    'ram_disk': M_CONDS.ram_disk,
                    't_min': M_CONDS.t_min,
                    't_max': M_CONDS.t_max,
                    't_increment': M_CONDS.t_increment,
                    'a_conc': M_CONDS.a_conc,
                    'Na_conc': M_CONDS.Na_conc,
                    'Mg_conc': M_CONDS.Mg_conc,
                }
                mpots = [{
                    'A': mpot.a,
                    'B': mpot.b,
                    'Am': mpot.am,
                    'Bm': mpot.bm,
                    'position': mpot.position,
                    't10_AB': mpot.t10_AB,
                    't10_ABm': mpot.t10_ABm,
                    't10_AmBm': mpot.t10_AmBm,
                    't10_AmB': mpot.t10_AmB,
                    't90_AB': mpot.t90_AB,
                    't90_ABm': mpot.t90_ABm,
                    't90_AmBm': mpot.t90_AmBm,
                    't90_AmB': mpot.t90_AmB,
                } for mpot in self.mtask.melting_pots]
                dump = {
                    'name': self.name.text(),
                    'task': self.mtask.task,
                    'probeMin': self.probeMin.text(),
                    'probeMax': self.probeMax.text(),
                    'conditions': conditions,
                    'mpots': mpots,
                }
                print(yaml.dump(dump), file=f)

    def onLoadButtonClicked(self):
        filename, filter = QtGui.QFileDialog.getOpenFileName(
            self, 'Load project', '/home/kablag/Документы/snpick')
        if filename != '':
            with open(filename, 'r') as f:
                dump = yaml.load(f.read())
                M_CONDS.fromYAML(dump['conditions'])
                self.name.setText(dump['name'])
                self.seqInput.setText(dump['task'])
                self.probeMin.setText(dump['probeMin'])
                self.probeMax.setText(dump['probeMax'])
                self.mtask = MTask(dump['task'], dump)
                self.add_data_to_tabs()

    def onBatchButtonClicked(self):
        filename, filter = QtGui.QFileDialog.getOpenFileName(
            self, 'Load batch', PROJECTS_FOLDER)
        if filename != '':
            with open(filename, 'r') as f:
                tasks = f.readlines()
                for task in tasks:
                    name, sequence = task.split('\t')
                    self.name.setText(name)
                    self.seqInput.setText(sequence)
                    self.onCalcProbesClicked()
                    self.onSaveButtonClicked(PROJECTS_FOLDER + name)

    @QtCore.Slot()
    def cancel_melting(self):
        self.pd.close()
        self.mtask.cancel()

    @QtCore.Slot(int)
    def on_mpot_done(self, value):
        self.pd.setValue(value)
Beispiel #7
0
class Snpick(QtGui.QWidget):
    def __init__(self):
        super(Snpick, self).__init__()
        self.mtask = None
        self.init_ui()

    def init_ui(self):
        self.name = QtGui.QLineEdit()
        self.name.setText('Name')
        self.seqInput = QtGui.QLineEdit()
        self.seqInput.setText('tcccctccaggccgtgcataaggctgtgctgaccatcgac(A>G)agaaagggactgaagctgctggggccatgtttttagaggc')

        self.probeMin = QtGui.QLineEdit()
        self.probeMin.setText('15')

        self.probeMax = QtGui.QLineEdit()
        self.probeMax.setText('17')

        self.calcProbes = QtGui.QPushButton(text='Calc')
        self.calcProbes.clicked.connect(self.onCalcProbesClicked)

        self.saveBtn = QtGui.QPushButton(text='Save')
        self.saveBtn.clicked.connect(self.onSaveButtonClicked)
        self.loadBtn = QtGui.QPushButton(text='Load')
        self.loadBtn.clicked.connect(self.onLoadButtonClicked)
        self.batchCalcBtn = QtGui.QPushButton(text='Batch Calc')
        self.batchCalcBtn.clicked.connect(self.onBatchButtonClicked)

        self.tabs = QtGui.QTabWidget()
        self.tab_A = FilterTab('A')
        self.tab_B = FilterTab('B')
        self.tab_Am = FilterTab('Am')
        self.tab_Bm = FilterTab('Bm')

        self.tabs.addTab(self.tab_A, 'A')
        self.tabs.addTab(self.tab_B, 'B')
        self.tabs.addTab(self.tab_Am, 'Am')
        self.tabs.addTab(self.tab_Bm, 'Bm')

        vbox = QtGui.QVBoxLayout()
        vbox.addWidget(self.name)
        vbox.addWidget(self.seqInput)
        # vbox.addStretch(1)
        hbox = QtGui.QHBoxLayout()
        sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Minimum)
        self.probeMin.setSizePolicy(sizePolicy)
        hbox.addWidget(self.probeMin)
        self.probeMax.setSizePolicy(sizePolicy)
        hbox.addWidget(self.probeMax)
        self.calcProbes.setSizePolicy(sizePolicy)
        hbox.addWidget(self.calcProbes)
        hbox.addStretch(1)
        hbox.addWidget(self.saveBtn)
        hbox.addWidget(self.loadBtn)
        hbox.addStretch(1)
        hbox.addWidget(self.batchCalcBtn)
        hbox.addStretch(1)
        rangeInputs = QtGui.QWidget()
        rangeInputs.setLayout(hbox)
        vbox.addWidget(rangeInputs)
        vbox.addWidget(self.tabs)

        self.setLayout(vbox)
        self.setGeometry(300, 300, 1000, 600)
        self.show()

    def resizeEvent(self, event):
        self.tabs.setBaseSize(self.tabs.width(),
                              event.size().height() * 0.8)

    def add_data_to_tabs(self):
        if not self.mtask.canceled:
            self.tab_A.addData(self.mtask)
            self.tab_B.addData(self.mtask)
            self.tab_Am.addData(self.mtask)
            self.tab_Bm.addData(self.mtask)

    def onCalcProbesClicked(self):
        mtask = '{sequence}{min_p}->{max_p}'.format(
            sequence=self.seqInput.text(),
            min_p=self.probeMin.text(),
            max_p=self.probeMax.text(),
        )
        self.mtask = MTask(mtask)
        self.seqInput.setText(self.mtask.task)
        self.mtask.meltingPotDone.connect(self.on_mpot_done)
        self.pd = QtGui.QProgressDialog('Melting probes',
                                        'Cancel',
                                        0,
                                        len(self.mtask.melting_pots))
        self.pd.setWindowModality(QtCore.Qt.WindowModal)
        self.calcProbes.setEnabled(False)
        self.pd.canceled.connect(self.cancel_melting)
        self.mtask.execute(M_CONDS)
        self.calcProbes.setEnabled(True)
        self.add_data_to_tabs()

    def onSaveButtonClicked(self, filename=''):
        filename, filter = filename, '' if filename != '' else QtGui.QFileDialog.getSaveFileName(self,
                                                     'Save project',
                                                     PROJECTS_FOLDER+self.name.text())
        if filename != '':
            with open(filename, 'w') as f:
                # print(yaml.dump(self.mtask.melting_pots), file=f)
                # pickle.dump(self.mtask, f)

                conditions = {'unafold_path': M_CONDS.unafold_path,
                              'ram_disk': M_CONDS.ram_disk,
                              't_min': M_CONDS.t_min,
                              't_max': M_CONDS.t_max,
                              't_increment': M_CONDS.t_increment,
                              'a_conc': M_CONDS.a_conc,
                              'Na_conc': M_CONDS.Na_conc,
                              'Mg_conc': M_CONDS.Mg_conc,}
                mpots = [{'A':mpot.a,
                          'B':mpot.b,
                          'Am':mpot.am,
                          'Bm':mpot.bm,
                          'position':mpot.position,
                          't10_AB':mpot.t10_AB,
                          't10_ABm':mpot.t10_ABm,
                          't10_AmBm':mpot.t10_AmBm,
                          't10_AmB':mpot.t10_AmB,
                          't90_AB':mpot.t90_AB,
                          't90_ABm':mpot.t90_ABm,
                          't90_AmBm':mpot.t90_AmBm,
                          't90_AmB':mpot.t90_AmB,} for mpot in self.mtask.melting_pots]
                dump = {'name':self.name.text(),
                        'task':self.mtask.task,
                        'probeMin':self.probeMin.text(),
                        'probeMax':self.probeMax.text(),
                        'conditions': conditions,
                        'mpots': mpots,}
                print(yaml.dump(dump), file=f)


    def onLoadButtonClicked(self):
        filename, filter = QtGui.QFileDialog.getOpenFileName(self,
                                                     'Load project',
                                                     '/home/kablag/Документы/snpick')
        if filename != '':
            with open(filename, 'r') as f:
                dump = yaml.load(f.read())
                M_CONDS.fromYAML(dump['conditions'])
                self.name.setText(dump['name'])
                self.seqInput.setText(dump['task'])
                self.probeMin.setText(dump['probeMin'])
                self.probeMax.setText(dump['probeMax'])
                self.mtask = MTask(dump['task'], dump)
                self.add_data_to_tabs()

    def onBatchButtonClicked(self):
        filename, filter = QtGui.QFileDialog.getOpenFileName(self,
                                                     'Load batch',
                                                     PROJECTS_FOLDER)
        if filename != '':
            with open(filename, 'r') as f:
                tasks = f.readlines()
                for task in tasks:
                    name, sequence = task.split('\t')
                    self.name.setText(name)
                    self.seqInput.setText(sequence)
                    self.onCalcProbesClicked()
                    self.onSaveButtonClicked(PROJECTS_FOLDER + name)
    @QtCore.Slot()
    def cancel_melting(self):
        self.pd.close()
        self.mtask.cancel()


    @QtCore.Slot(int)
    def on_mpot_done(self, value):
        self.pd.setValue(value)