Qt runs using run.py (for now)

gui/qt_window.py

@@ -3,16 +3,21 @@
 # PySide vs PyQT: https://www.pythonguis.com/faq/pyqt-vs-pyside/?gad_source=1&gclid=CjwKCAjwpbi4BhByEiwAMC8Jnfe7sYOqHjs5eOg_tYMD0iX3UDBduwykrF8qE5Y0IG66abhS6YXHvRoCg-kQAvD_BwE
 # (If using PyQT, see: https://www.gnu.org/licenses/license-list.en.html#GPLCompatibleLicenses)
 
+import re
 import sys
 import os
 from PySide6 import QtCore, QtWidgets, QtGui
 from PySide6.QtCore import QSize
 # Up to now needs (pip) installed PyPEF version
-from pypef import __version__
+#from pypef import __version__
 
 # https://stackoverflow.com/questions/67297494/redirect-console-output-to-pyqt5-gui-in-real-time
 # sudo apt-get install -y libxcb-cursor-dev
 pypef_root = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
+with open(os.path.join(pypef_root, 'pypef', '__init__.py')) as fh:
+    for line in fh:
+        if line.startswith('__version__'):
+            version = re.findall(r"[-+]?(?:\d*\.*\d.*\d+)", line)[0]
 #os.environ["PATH"] += os.pathsep + pypef_root
 
 
@@ -26,29 +31,43 @@ def __init__(
             self.pypef_root = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
         else:
             self.pypef_root = pypef_root
-
+        self.c = 0
         self.setMinimumSize(QSize(200, 100))
         self.setWindowTitle("PyPEF GUI")
 
         layout = QtWidgets.QVBoxLayout(self)
-        self.text = QtWidgets.QLabel(f"PyPEF v. {__version__}", alignment=QtCore.Qt.AlignRight)
+        self.text = QtWidgets.QLabel(f"PyPEF v. {version}", alignment=QtCore.Qt.AlignRight)
         self.textedit_out = QtWidgets.QTextEdit(readOnly=True)
+        self.textedit_out.setStyleSheet("font-family:DejaVu Sans Mono;font-size:12px;font-weight:normal;")
         self.button_mklsts = QtWidgets.QPushButton("Run MKLSTS")
         self.button_mklsts.setMinimumWidth(80)
         #self.button_mklsts.setMaximumWidth(80)        
         self.button_mklsts.setToolTip("Create files for training and testing from variant-fitness CSV data")
         self.button_mklsts.clicked.connect(self.pypef_mklsts)
 
-        self.button_dca_inference_gremlin = QtWidgets.QPushButton("Run GREMLIN")
+        self.button_dca_inference_gremlin = QtWidgets.QPushButton("GREMLIN (MSA optimization)")
         self.button_dca_inference_gremlin.setMinimumWidth(80)
-        self.button_dca_inference_gremlin.setToolTip("To be implemented")
+        self.button_dca_inference_gremlin.setToolTip(
+            "Generating DCA parameters using GREMLIN (\"MSA optimization\"), "
+            "you have to provide an MSA in FASTA or A2M format"
+        )
+        self.button_dca_inference_gremlin.clicked.connect(self.pypef_gremlin)
+
+        self.button_dca_predict_gremlin = QtWidgets.QPushButton("Predict GREMLIN")
+        self.button_dca_predict_gremlin.setMinimumWidth(80)
+        self.button_dca_predict_gremlin.setToolTip(
+            "Test performance on any test dataset using the MSA-optimized GREMLIN model"
+        )
+        self.button_dca_predict_gremlin.clicked.connect(self.pypef_gremlin_dca_test)
 
         self.setGeometry(100, 60, 1000, 800)
         layout.addWidget(self.text)
         layout.addWidget(self.button_mklsts)
         layout.addWidget(self.button_dca_inference_gremlin)
+        layout.addWidget(self.button_dca_predict_gremlin)
         layout.addWidget(self.textedit_out)
 
+
         self.process = QtCore.QProcess(self)
         #process_env = self.process.processEnvironment()
         #process_env.insert("PYTHONPATH", pypef_root) 
@@ -60,18 +79,35 @@ def __init__(
 
     def on_readyReadStandardOutput(self):
          text = self.process.readAllStandardOutput().data().decode()
+         self.c += 1
          self.textedit_out.append(text)
 
     @QtCore.Slot()
     def pypef_mklsts(self):
         self.text.setText("Running MKLSTS...")
         wt_fasta_file = QtWidgets.QFileDialog.getOpenFileName(self, "Select WT FASTA File")[0]
         csv_variant_file = QtWidgets.QFileDialog.getOpenFileName(self, "Select variant CSV File")[0]
-        self.exec_pypef(f'mklsts --wt {wt_fasta_file} --input {csv_variant_file}')       
+        self.exec_pypef(f'mklsts --wt {wt_fasta_file} --input {csv_variant_file}')
+
+    @QtCore.Slot()
+    def pypef_gremlin(self):
+        self.text.setText("Running GREMLIN (DCA) optimization on MSA...")
+        wt_fasta_file = QtWidgets.QFileDialog.getOpenFileName(self, "Select WT FASTA File")[0]
+        msa_file = QtWidgets.QFileDialog.getOpenFileName(self, "Select Multiple Sequence Alignment (MSA) file (in FASTA or A2M format)")[0]
+        self.exec_pypef(f'param_inference --wt {wt_fasta_file} --msa {msa_file}')  # --opt_iter 100
+
+    @QtCore.Slot()
+    def pypef_gremlin_dca_test(self):
+        self.text.setText("Testing GREMLIN (DCA) performance on provided test set...")
+        test_set_file = QtWidgets.QFileDialog.getOpenFileName(self, "Select Test Set File in \"FASL\" format")[0]
+        params_pkl_file = QtWidgets.QFileDialog.getOpenFileName(self, "GREMLIN parameter Pickle file")[0]
+        self.exec_pypef(f'hybrid --ts {test_set_file} -m {params_pkl_file} --params {params_pkl_file}')  # --opt_iter 100
 
     def exec_pypef(self, cmd):
-        self.process.start(f'python', ['-u', f'{self.pypef_root}/pypef/main.py'] + cmd.split(' '))
+        self.process.start(f'python', ['-u', f'{self.pypef_root}/run.py'] + cmd.split(' '))
         self.process.finished.connect(self.process_finished)
+        if self.c > 0:
+            self.textedit_out.append("=" * 104 + "\n")
 
     def process_finished(self):
         self.text.setText("Finished...") 

pypef/main.py

@@ -208,7 +208,7 @@
   -l --ls LEARNING_SET              Input learning set in .fasta format.
   -m --model MODEL                  Model (pickle file) for plotting of validation or for
                                     performing predictions.
-  --msa MSA_FILE                    Multiple sequence alignment (MSA) ins FASTA or A2M format for
+  --msa MSA_FILE                    Multiple sequence alignment (MSA) in FASTA or A2M format for
                                     inferring DCA parameters.
   --mutation_sep MUTATION_SEP       Mutation separator [default: /].
   --mutation_extrapolation          Mutation extrapolation [default: False].