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])
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 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 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 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()
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)
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)
