def delete_template_clicked(self, template_index):
template_to_delete = self._templates[template_index]
alignments = db.get_alignments()
template_in_use = False
for alignment in alignments:
for library, template in alignment.library_templates.items():
if template == template_to_delete.id:
template_in_use = True
break
if template_to_delete.reverse_complement_template_id != None:
reverse_complement_template = db.get_template_by_id(\
template_to_delete.reverse_complement_template_id)
for alignment in alignments:
for library, template in alignment.library_templates.items():
if template == reverse_complement_template.id:
template_in_use = True
break
if template_in_use:
messagebox.showinfo("Error", "Template in use, cannot delete")
else:
db.delete_template(template_to_delete)
self.load_templates()
def add_update_clicked(self, template):
try:
if template == None:
template_name = self._template_edit_name.get()
template_sequence = self._template_edit_sequence.get()
reverse_complement_name = self._selected_reverse_complement.get()
if reverse_complement_name == "(None)":
reverse_complement_template_id = None
else:
reverse_complement_template = db.get_template_by_name(reverse_complement_name)
reverse_complement_template_id = reverse_complement_template.id
new_template = Template(template_sequence, template_name, \
reverse_complement_template_id = reverse_complement_template_id)
else:
template.name = self._template_edit_name.get()
template.sequence = self._template_edit_sequence.get()
reverse_complement_name = self._selected_reverse_complement.get()
if reverse_complement_name == "(None)":
reverse_complement_template_id = None
else:
reverse_complement_template = db.get_template_by_name(reverse_complement_name)
reverse_complement_template_id = reverse_complement_template.id
template.reverse_complement_template_id = reverse_complement_template_id
except Exception as exception:
messagebox.showinfo("Error", str(exception))
self._new_template_frame.destroy()
self.load_templates()
def load_samples(self):
if self._samples_frame != None:
self._samples_frame.destroy()
self._samples_frame = Frame(self._left_frame)
self._samples_frame.pack()
Label(self._samples_frame, text='Existing Samples')\
.pack(side=TOP)
self._samples_scroll_area = self.scroll_area(
self._samples_frame, height=self.winfo_toplevel().winfo_height())
self._samples = db.get_samples()
self._templates = db.get_templates()
self._template_options = ["(None)"]
self._template_options.extend(\
[template.name for template in self._templates])
sample_header = Label(self._samples_scroll_area, text="Sample", \
bg="white", relief="solid", bd="1")
sample_header.grid(row=0, column=0, sticky="news")
template_header = Label(self._samples_scroll_area, text="Template", \
bg="white", relief="solid", bd="1")
template_header.grid(row=0, column=1, sticky="news")
for sample_index, sample in enumerate(self._samples):
label = Label(self._samples_scroll_area, text=sample.name, \
bg="white", relief="solid", bd=1)
label.grid(row=sample_index + 1, column=0, sticky="news")
label.bind("<Button-4>", self.scroll)
label.bind("<Button-5>", self.scroll)
associated_template_var = StringVar()
associated_template_var.set(self._template_options[0])
template_selected_command = partial(self.template_selected, \
sample_index)
dropdown_frame = Frame(self._samples_scroll_area, bg="white", \
relief="solid", bd=1)
dropdown_frame.grid(row = sample_index + 1, column = 1, \
sticky = "news")
dropdown_frame.bind("<Button-4>", self.scroll)
dropdown_frame.bind("<Button-5>", self.scroll)
template_dropdown = OptionMenu(dropdown_frame, \
associated_template_var, *self._template_options, \
command=template_selected_command)
template_dropdown.pack()
template_dropdown.bind("<Button-4>", self.scroll)
template_dropdown.bind("<Button-5>", self.scroll)
def delete_sample_clicked(self, sample_index):
db.delete_sample(self._samples[sample_index])
for dropdown in self._sample_dropdowns:
dropdown["menu"].delete(sample_index + 1)
self._sample_labels[sample_index].destroy()
self._sample_rename_buttons[sample_index].destroy()
self._sample_delete_buttons[sample_index].destroy()
del self._sample_labels[sample_index]
def update_lists(self):
self.library_lines = []
self.alignment_lines = []
self.methods = [alignment.name for alignment in db.get_alignments()]
for child in self.library_wrapper.winfo_children():
child.destroy()
for child in self.alignment_wrapper.winfo_children():
child.destroy()
i = 0
for library in db.get_libraries():
line = Frame(self.library_wrapper)
line.id = library.id
line.name = library.name
line.var = StringVar()
line.var.set('0')
line.ch_btn = Checkbutton(line, text=line.name, variable=line.var)
line.ch_btn.pack(side=LEFT, fill=BOTH)
line.ch_btn['command'] = lambda index=i: \
self.add_library_to_comparison(index)
btn = Button(line, text='Files')
btn.bind("<Button-1>", self.view_files)
btn.pack(side=RIGHT, pady=2, padx=2)
line.pack(side=TOP, fill=BOTH)
self.library_lines.append(line)
line.bind("<Button-4>", self.scroll)
line.bind("<Button-5>", self.scroll)
line.ch_btn.bind("<Button-4>", self.scroll)
line.ch_btn.bind("<Button-5>", self.scroll)
btn.bind("<Button-4>", self.scroll)
btn.bind("<Button-5>", self.scroll)
i += 1
i = 0
for alignment in db.get_alignments():
line = Frame(self.alignment_wrapper)
line.id = alignment.id
line.name = alignment.name
line.var = StringVar()
line.var.set('0')
line.ch_btn = Checkbutton(line, text=line.name, variable=line.var)
line.ch_btn.pack(side=LEFT, fill=BOTH)
line.ch_btn['command'] = \
lambda index=i: self.add_alignment_to_comparison(index)
btn = Button(line, text='Parameters')
btn.bind("<Button-1>", lambda e: self.view_parameters(e))
btn.pack(side=RIGHT, pady=2, padx=2)
line.pack(side=TOP, fill=BOTH)
self.alignment_lines.append(line)
i += 1
def view_parameters(self, event):
parent = event.widget.master
grid_kwargs = {
'padx': 1,
'pady': 1,
'sticky': 'news',
'ipadx': 5,
'ipady': 5
}
if hasattr(self, 'parameter_viewer'):
self.parameter_viewer.destroy()
self.parameter_viewer = Toplevel(padx=10, pady=10)
self.parameter_viewer.title('Parameters for ' + parent.name)
Label(self.parameter_viewer, text = 'Parameter', bg = 'white')\
.grid(row=0, column=0, **grid_kwargs)
Label(self.parameter_viewer, text = 'Value', bg = 'white')\
.grid(row=0, column=1, **grid_kwargs)
i = 1
for parameter, value in db.get_alignment_by_id(str(parent.id))\
.parameters.items():
Label(self.parameter_viewer, text = parameter, bg = 'white',
anchor='e')\
.grid(row=i, column=0, **grid_kwargs)
Label(self.parameter_viewer, text = value, bg = 'white')\
.grid(row=i, column=1, **grid_kwargs)
i += 1
def sample_selected(self, FASTQ_file_index, selected_value):
FASTQ_file = self._FASTQ_files[FASTQ_file_index]
current_sample = db.get_associated_library(FASTQ_file.name)
if current_sample != None:
if current_sample.name == selected_value:
return
else:
current_sample.remove_file(FASTQ_file.name)
if selected_value == self._sample_options[0]:
return
new_sample = db.get_library(selected_value)
new_sample.add_file(FASTQ_file.name)
def load_templates(self):
self._templates = db.get_templates()
if self._existing_templates_table != None:
self._existing_templates_table.destroy()
self._existing_templates_table = Frame(self._existing_templates_frame)
self._existing_templates_table.pack()
Label(self._existing_templates_table, text="Name")\
.grid(row = 0, column = 0)
Label(self._existing_templates_table, text="Sequence")\
.grid(row = 0, column = 1)
Label(self._existing_templates_table, text="Reverse complement")\
.grid(row = 0, column = 2)
i = 1
for template in self._templates:
Label(self._existing_templates_table, text=template.name, bd=1, \
relief="solid")\
.grid(row = i, column=0, sticky="news")
Label(self._existing_templates_table, text=template.sequence, bd=1,\
relief="solid")\
.grid(row = i, column=1, sticky="news")
if template.reverse_complement_template_id != None:
reverse_complement_name = db.get_template_by_id(\
template.reverse_complement_template_id).name
else:
reverse_complement_name = ""
Label(self._existing_templates_table, text=reverse_complement_name,\
bd=1, relief="solid")\
.grid(row = i, column=2, sticky="news")
Button(self._existing_templates_table, text="Edit", \
command=lambda index=i-1: self.edit_template_clicked(index))\
.grid(row = i, column=3, sticky="news")
Button(self._existing_templates_table, text="Delete", \
command=lambda index=i-1: self.delete_template_clicked(index))\
.grid(row = i, column=4, sticky="news")
i += 1
def view_files(self, event):
parent = event.widget.master
grid_kwargs = {'padx': 1, 'pady': 1, 'sticky': 'news', 'column': 0}
if hasattr(self, 'file_viewer'):
self.file_viewer.destroy()
self.file_viewer = Toplevel(padx=10, pady=10)
self.file_viewer.title('Files in ' + str(parent.id))
Label(self.file_viewer, text = 'FASTQ file', bg='white')\
.grid(**grid_kwargs)
i = 1
files = db.get_library_by_id(str(parent.id)).fastq_files
for file in files:
Label(self.file_viewer, text=str(file), bg='white')\
.grid(row=i, **grid_kwargs)
i += 1
def load_samples(self):
self._samples = db.get_samples()
if self._sample_list_frame != None:
self._sample_list_frame.destroy()
self._sample_list_frame = Frame(self._existing_samples_frame)
self._sample_list_frame.pack()
self._sample_scroll_area = self.scroll_area(self._sample_list_frame, \
height=self.winfo_toplevel().winfo_height() - 200)
sample_index = 0
self._sample_labels = []
self._sample_rename_buttons = []
self._sample_delete_buttons = []
for sample in self._samples:
label = Label(self._sample_scroll_area, text=sample.name)
label.grid(row=sample_index, column=0)
rename_button = Button(self._sample_scroll_area, text="Rename", \
command=lambda index=sample_index: \
self.rename_sample_clicked(index))
rename_button.grid(row=sample_index, column=1, sticky="news")
delete_button = Button(self._sample_scroll_area, text="Delete", \
command=lambda index=sample_index: \
self.delete_sample_clicked(index))
delete_button.grid(row=sample_index, column=2, sticky="news")
self._sample_labels.append(label)
self._sample_rename_buttons.append(rename_button)
self._sample_delete_buttons.append(delete_button)
sample_index += 1
def load_FASTQ_files(self):
self._FASTQ_files = db.get_FASTQ_files()
if self._FASTQ_list_frame != None:
self._FASTQ_list_frame.destroy()
self._FASTQ_list_frame = Frame(self._FASTQ_frame)
self._FASTQ_list_frame.pack(fill=BOTH)
self._FASTQ_scroll_area = self.scroll_area(self._FASTQ_list_frame, \
height=self.winfo_toplevel().winfo_height())
FASTQ_file_index = 0
self._sample_options = ["(None)"]
self._sample_options.extend([sample.name for sample in self._samples])
self._sample_dropdowns = []
self._is_complement_vars = []
FASTQ_file_header = Label(self._FASTQ_scroll_area, text="FASTQ File", \
bg="white", relief="solid", bd="1")
FASTQ_file_header.grid(row=0, column=0, sticky="news")
sample_header = Label(self._FASTQ_scroll_area, text="Sample", \
bg="white", relief="solid", bd="1")
sample_header.grid(row=0, column=1, sticky="news")
reverse_complement_header = Label(self._FASTQ_scroll_area, \
text="Is Reverse Complement", bg="white", relief="solid", bd="1")
reverse_complement_header.grid(row=0, column=2, sticky="news")
for FASTQ_file_index, FASTQ_file in enumerate(self._FASTQ_files):
label = Label(self._FASTQ_scroll_area, text=FASTQ_file.name, \
bg="white", relief="solid", bd="1")
label.grid(row=FASTQ_file_index + 1, column=0, sticky="news")
label.bind("<Button-4>", self.scroll)
label.bind("<Button-5>", self.scroll)
associated_sample_var = StringVar()
associated_sample = db.get_associated_library(FASTQ_file.name)
if associated_sample == None:
associated_sample_var.set(self._sample_options[0])
else:
associated_sample_var.set(associated_sample.name)
sample_selected_command = partial(self.sample_selected, \
FASTQ_file_index)
dropdown_frame = Frame(self._FASTQ_scroll_area, bg="white", \
relief="solid", bd="1")
dropdown_frame.grid(row = FASTQ_file_index + 1, column = 1, \
sticky="news")
dropdown_frame.bind("<Button-4>", self.scroll)
dropdown_frame.bind("<Button-5>", self.scroll)
sample_dropdown = OptionMenu(dropdown_frame, \
associated_sample_var, command=sample_selected_command, \
*self._sample_options)
sample_dropdown.pack()
sample_dropdown.bind("<Button-4>", self.scroll)
sample_dropdown.bind("<Button-5>", self.scroll)
self._sample_dropdowns.append(sample_dropdown)
is_complement_var = IntVar()
if FASTQ_file.is_reverse_complement:
is_complement_var.set(1)
else:
is_complement_var.set(0)
complement_checkbox_command = partial(self.complement_selected, \
FASTQ_file_index)
is_complement_checkbox = Checkbutton(self._FASTQ_scroll_area, \
variable = is_complement_var, bg="white", relief="solid", \
bd="1", command=complement_checkbox_command)
is_complement_checkbox.grid(row = FASTQ_file_index + 1, \
column = 2, sticky="news")
is_complement_checkbox.bind("<Button-4>", self.scroll)
is_complement_checkbox.bind("<Button-5>", self.scroll)
self._is_complement_vars.append(is_complement_var)
def add_edit_template(self, template = None):
if self._new_template_frame != None:
self._new_template_frame.destroy()
self._editing_template = template
self._new_template_frame = Frame(self._templates_frame)
self._new_template_frame.pack(side=TOP)
new_template_fields_frame = Frame(self._new_template_frame)
new_template_fields_frame.pack(side=TOP)
Label(new_template_fields_frame, text="Name")\
.grid(row=0, column=0, sticky="e")
Label(new_template_fields_frame, text="Sequence")\
.grid(row=1, column=0, sticky="e")
Label(new_template_fields_frame, text="Reverse Complement Sequence")\
.grid(row=2, column=0, sticky="e")
self._template_edit_name = StringVar()
Entry(new_template_fields_frame, textvariable=self._template_edit_name)\
.grid(row=0, column=1, sticky="w")
if template != None:
self._template_edit_name.set(template.name)
self._template_edit_sequence = StringVar()
Entry(new_template_fields_frame, width=150, \
textvariable=self._template_edit_sequence)\
.grid(row=1, column=1, sticky="w")
if template != None:
self._template_edit_sequence.set(template.sequence)
templates = db.get_templates()
self._selected_reverse_complement = StringVar()
template_names = ["(None)"]
if template != None and template.reverse_complement_template_id != None:
self._selected_reverse_complement.set(db.get_template_by_id(\
template.reverse_complement_template_id).name)
else:
self._selected_reverse_complement.set(template_names[0])
template_names.extend([template.name for template in templates])
reverse_complement_dropdown = OptionMenu(new_template_fields_frame,\
self._selected_reverse_complement, *template_names)
reverse_complement_dropdown.grid(row=2, column=1, sticky="w")
if template != None:
done_button_text = "Update"
else:
done_button_text = "Add"
done_close_frame = Frame(self._new_template_frame)
done_close_frame.pack(side=TOP)
Button(done_close_frame, text=done_button_text,
command=lambda template=template: self.add_update_clicked(template))\
.grid(row=0,column=0)
Button(done_close_frame, text="Cancel",
command=self._new_template_frame.destroy)\
.grid(row=0,column=1)
def display_table(self):
for child in self.table_frame.winfo_children():
child.destroy()
libraries = self.selected_libraries[:]
aligns = self.selected_alignments[:]
self.columns = []
h1_font = font.Font(weight=font.BOLD)
# If table is to be sorted by alignment
if self.by_alignment:
# Loop through alignments to create labels
for i, alignment in enumerate(aligns):
align_name = alignment.name
index = i * (len(libraries)) + i + 1
method_label = Label(self.table_frame,
text=align_name,
padx=1,
pady=1,
bg='white',
font=h1_font)
method_label.grid(column=0,
row=index,
sticky='news',
columnspan=2,
pady=2,
padx=2)
alignment_id = alignment.id
getcontext().prec = 4
# Loop through libraries for data rows in table
for j, library in enumerate(libraries):
name = library.name
offset = index + j + 1
Label(self.table_frame,
text=name,
padx=1,
pady=1,
bg='white').grid(column=1,
row=offset,
sticky='news',
pady=2,
padx=2)
library_id = library.id
try:
stats = db.get_alignment_by_id(alignment_id).statistics
stats = stats[library_id]
# Loop through statistics for to put in table
for stat, value in stats.items():
# If stat has not yet been displayed, add a column
if stat not in self.columns:
self.columns.append(stat)
col_num = len(self.columns) - 1 + 2
Label(self.table_frame, text = stat,
bg='white')\
.grid(row = 0, column = col_num,
sticky ='news', pady = 2, padx = 2)
Grid.columnconfigure(self.table_frame,
col_num,
weight=1)
if (int(value) != float(value)
and float(value) != 0.0):
value = \
str(Decimal(float(value))/Decimal(0.01)) \
+ '%'
k = self.columns.index(stat)
label = Label(self.table_frame,
text=str(value),
bg='white')
label.grid(row=offset,
column=k + 2,
pady=2,
padx=2,
sticky='news')
label.bind('<Button-4>', lambda e: self.scroll(e))
label.bind('<Button-5>', lambda e: self.scroll(e))
except:
pass
# If the table is to be sorted by library
else:
for i, library in enumerate(libraries):
lib_name = library.name
index = i * (len(aligns)) + i + 1
lib_label = Label(self.table_frame,
text=lib_name,
padx=1,
pady=1,
bg='white',
font=h1_font)
lib_label.grid(column=0,
row=index,
sticky='news',
columnspan=2,
padx=2,
pady=2)
library_id = library.id
for j, alignment in enumerate(aligns):
name = alignment.name
offset = index + j + 1
Label(self.table_frame,
text=name,
padx=1,
pady=1,
bg='white').grid(column=1,
row=offset,
sticky='news',
pady=2,
padx=2)
alignment_id = alignment.id
try:
stats = db.get_alignment_by_id(alignment_id).statistics
stats = stats[library_id]
for stat, value in stats.items():
if stat not in self.columns:
self.columns.append(stat)
col_num = len(self.columns) - 1 + 2
Label(self.table_frame, text = stat,
bg='white')\
.grid(row = 0, column = col_num,
sticky ='news', pady = 2, padx = 2)
Grid.columnconfigure(self.table_frame,
col_num,
weight=1)
if (int(value) != float(value)
and float(value) != 0.0):
value = \
str(Decimal(float(value))/Decimal(0.01)) \
+ '%'
k = self.columns.index(stat)
label = Label(self.table_frame,
text=value,
bg='white')
label.grid(row=offset,
column=k + 2,
pady=2,
padx=2,
sticky='news')
label.bind('<Button-4>', lambda e: self.scroll(e))
label.bind('<Button-5>', lambda e: self.scroll(e))
except:
pass
def method_selected(self, selected_method_name):
alignment = db.get_alignment(selected_method_name)
ws.set_active_alignment(alignment)