fixup! implemented Filter.filter_biotype_from_gtf() and Filter.biotyp…

…es_from_gtf(); refactored Filter.biotypes() into Filter.biotypes_from_ref_table() and Filter.filter_biotype() into Filter.filter_biotype_from_ref_table(); moved functions from the generic and fastq modules into the io module.

rnalysis/gui/gui.py

@@ -20,7 +20,6 @@
 from PyQt5 import QtCore, QtWidgets, QtGui
 from joblib.externals.loky import get_reusable_executor
 
-import utils.io
 from rnalysis import fastq, filtering, enrichment, __version__
 from rnalysis.gui import gui_style, gui_widgets, gui_windows, gui_graphics, gui_tutorial
 from rnalysis.utils import io, validation, generic, parsing, settings, enrichment_runner, clustering
@@ -40,7 +39,7 @@ def __init__(self, func_name: str, func: Callable, excluded_params: set, parent=
         self.func_name = func_name
         self.func = func
         self.signature = generic.get_method_signature(self.func)
-        self.desc, self.param_desc = utils.io.get_method_docstring(self.func)
+        self.desc, self.param_desc = io.get_method_docstring(self.func)
         self.excluded_params = excluded_params.copy()
 
         self.widgets = {}
@@ -496,7 +495,7 @@ def update_uis(self):
         analysis_type = self.get_current_analysis_type()
         chosen_func = self.get_current_func()
         signature = generic.get_method_signature(chosen_func)
-        func_desc, param_desc = utils.io.get_method_docstring(chosen_func)
+        func_desc, param_desc = io.get_method_docstring(chosen_func)
         for name, param in signature.items():
             this_desc = param_desc.get(name, '')
             if name in self.EXCLUDED_PARAMS:
@@ -1413,7 +1412,7 @@ def update_parameter_ui(self):
             self.funcSelected.emit(False)
             return
         signature = generic.get_method_signature(chosen_func_name, self.filter_obj)
-        desc, param_desc = utils.io.get_method_docstring(chosen_func_name, self.filter_obj)
+        desc, param_desc = io.get_method_docstring(chosen_func_name, self.filter_obj)
         self.func_combo.setToolTip(desc)
         self.func_help_button.connect_param_help(chosen_func_name, desc)
 
@@ -1622,7 +1621,7 @@ def update_basic_ui(self):
         func_name = '__init__'
         filter_obj_type = FILTER_OBJ_TYPES[self.basic_widgets['table_type_combo'].currentText()]
         signature = generic.get_method_signature(func_name, filter_obj_type)
-        desc, param_desc = utils.io.get_method_docstring(func_name, filter_obj_type)
+        desc, param_desc = io.get_method_docstring(func_name, filter_obj_type)
         self.basic_widgets['table_type_combo'].setToolTip(desc)
         i = 1
         for name, param in signature.items():
@@ -2202,7 +2201,7 @@ def update_args_ui(self, file: str):
         func_name = '__init__'
         filter_obj_type = FILTER_OBJ_TYPES[self.table_types[file].currentText()]
         signature = generic.get_method_signature(func_name, filter_obj_type)
-        desc, param_desc = utils.io.get_method_docstring(func_name, filter_obj_type)
+        desc, param_desc = io.get_method_docstring(func_name, filter_obj_type)
         self.table_types[file].setToolTip(desc)
         i = 1
         for name, param in signature.items():