def initPreprocessOptionUI(self, frame):
options_frame = Frame(frame)
options_frame.pack(fill=X, expand=1, side=TOP)
label = Label(options_frame,
text=TS("GWAS File Options"),
relief=RIDGE)
label.pack(side=TOP, fill=X, expand=1)
file_options_frame = Frame(options_frame)
file_options_frame.pack(fill=X, expand=1, side=TOP)
controller = self.controller()
# compressed_on = controller.compressed_on
# self.compressed_check = Checkbutton(file_options_frame, text=TS('Compressed GWAS'), variable=compressed_on)
# self.compressed_check.grid(row=0, column=0, sticky=W+E)
# self.addToDisabable(self.compressed_check)
file_pattern_value = controller.gwas_file_pattern_value
file_pattern_label = Label(file_options_frame,
text=TS("GWAS Filename Pattern"))
file_pattern_label.grid(row=1, column=0, sticky=W)
self.file_pattern_entry = Entry(file_options_frame,
textvariable=file_pattern_value)
self.file_pattern_entry.grid(row=1, column=1, sticky=W + E)
self.addToDisabable(self.file_pattern_entry)
separator_value = controller.separator_value
separator_label = Label(file_options_frame, text=TS("separator"))
separator_label.grid(row=2, column=0, sticky=W)
self.separator_entry = Entry(file_options_frame,
textvariable=separator_value)
self.separator_entry.grid(row=2, column=1, sticky=W + E)
self.addToDisabable(self.separator_entry)
def checkGenerated(self):
clear = True
beta_empty = True
if os.path.exists(self.beta_folder):
beta_empty = len(os.listdir(self.beta_folder)) == 0
results_clear = not os.path.exists(self.output_path)
clean_up_beta = False
clean_up_results = False
message = None
if not beta_empty and not results_clear:
clear = False
clean_up_beta = True
clean_up_results = True
message = TS("Path for results already exists, and intermediate folder is already occupied."
"Should we delete them to move forward (potentially dangerous), or do you wish to cancel?")
elif not results_clear:
clear = False
clean_up_results = True
message = TS("Path for results already exists. Do you wish to cancel, or should we delete it to move forward (potentially dangerous)?")
elif not beta_empty:
clear = False
clean_up_beta = True
message = TS("Intermediate folder is already occupied. Should we delete it to move forward (potentially dangerous), or do you wish to cancel? (dangerous)")
return clear, message, clean_up_beta, clean_up_results
def initBottomUI(self):
b_container = Frame(self, relief=RAISED, borderwidth=1)
b_container.pack(fill=BOTH, expand=1)
controller = self.controller()
quit_button = Button(b_container, text=TS("QUIT"), command=controller.quitButtonPressed, style="Red.TButton")
quit_button.pack(side=RIGHT)
self.action_button = Button(b_container, text=TS("Run"), command=controller.actionButtonPressed)
self.action_button.pack(side = LEFT)
t_container = Frame(self, relief=RAISED, borderwidth=1)
t_container.pack(fill=BOTH, expand=1)
self.text = Text(t_container, height = 10)
self.text.pack(fill=BOTH, side=TOP)
def initGWASFolderUI(self, options_frame):
gwas_frame = Frame(options_frame)
gwas_frame.pack(fill=X, expand=1, side=TOP)
gwas_label = Label(gwas_frame, text=TS("GWAS data folder"), anchor=W)
gwas_label.pack(side=LEFT)
controller = self.controller()
self.gwas_button = Button(gwas_frame,
text=controller.gwas_folder,
command=controller.gwasFolderButtonPressed,
style="RHW.TButton")
self.gwas_button.pack(side=RIGHT, fill=X)
self.addToDisabable(self.gwas_button)
def initCovarianceUI(self, frame):
output_frame = Frame(frame)
output_frame.pack(fill=X, expand=1, side=TOP)
controller = self.controller()
label = Label(output_frame, text=TS("Covariance File"))
label.pack(side=LEFT)
self.covariance_file_button = Button(output_frame, text=controller.covariance_file,
command = controller.covarianceFileButtonPressed,
style = "RHW.TButton",
)
self.covariance_file_button.pack(side=RIGHT)
self.addToDisabable(self.covariance_file_button)
def checkClearToRun(self):
sane = checkSubdirectorySanity(self.cwd, self.beta_folder)
if not sane:
tkMessageBox.showwarning( "Beta Folder", "Beta folder cannot be current directory, or ancestor.")
return False
clear, message, clean_up_beta, clean_up_results = self.checkGenerated()
if not clear:
answer = tkMessageBox.askokcancel(TS("Warning!"), message, icon=tkMessageBox.ERROR)
if answer:
self.cleanUpGenerated(clean_up_beta, clean_up_results)
else:
return False
return True
def initWeightDBUI(self, frame):
w_frame = Frame(frame)
w_frame.pack(fill=X, expand=1, side=TOP)
controller = self.controller()
label = Label(w_frame, text=TS("Weight Model DB"))
label.pack(side=LEFT)
self.weight_db_button = Button(w_frame, text=controller.weight_db_path,
command=controller.weightDBButtonPressed,
style="RHW.TButton"
)
self.weight_db_button.pack(side=RIGHT)
self.addToDisabable(self.weight_db_button)
def initBetaFolderUI(self, options_frame):
output_frame = Frame(options_frame)
output_frame.pack(fill=X, expand=1, side=TOP)
controller = self.controller()
beta_label = Label(output_frame, text=TS("Processed beta folder"))
beta_label.pack(side=LEFT)
self.beta_folder_button = Button(output_frame, text=controller.beta_folder,
command=controller.betaFolderButtonPressed,
style="RHW.TButton"
)
self.beta_folder_button.pack(side=RIGHT)
self.addToDisabable(self.beta_folder_button)
def runMode(self):
text = TS("Stop")
self.action_button.config(text=text)
for control in self.disabable:
self.disabable_status[str(control)] = control.cget("state")
control.config(state=DISABLED)
def configureMode(self):
text = TS("Run")
self.action_button.config(text=text)
for control in self.disabable:
state = self.disabable_status[str(control)]
control.config(state=state)
def initPreprocessColumnUI(self, frame):
preprocess_frame = Frame(frame, relief=RAISED, borderwidth=1)
preprocess_frame.pack(fill=X, expand=1, side=TOP)
label = Label(preprocess_frame, text=TS("Data Columns"), relief=RIDGE)
label.pack(fill=X, expand=1, side=TOP)
column_frame = Frame(preprocess_frame)
column_frame.pack(fill=X, expand=1, side=TOP)
controller = self.controller()
#
snp_label = Label(column_frame, text=TS("SNP id"))
snp_label.grid(row=0, column=0, sticky=W)
self.snp_entry = Entry(column_frame, textvariable=controller.snp_value)
self.snp_entry.grid(row=0, column=1)
self.addToDisabable(self.snp_entry)
#
non_effect_allele_label = Label(column_frame,
text=TS("Non Effect Allele"))
non_effect_allele_label.grid(row=1, column=0, sticky=W)
self.non_effect_allele_entry = Entry(
column_frame, textvariable=controller.non_effect_allele_value)
self.non_effect_allele_entry.grid(row=1, column=1)
self.addToDisabable(self.non_effect_allele_entry)
#
effect_allele_label = Label(column_frame, text=TS("Effect Allele"))
effect_allele_label.grid(row=2, column=0, sticky=W)
self.effect_allele_entry = Entry(
column_frame, textvariable=controller.effect_allele_value)
self.effect_allele_entry.grid(row=2, column=1)
self.addToDisabable(self.effect_allele_entry)
# the following three are mutually exclusive
or_on = controller.or_on
or_value = controller.or_value
self.or_check = Checkbutton(column_frame,
text=TS('Odd Ratios'),
variable=or_on)
self.or_check.grid(row=0, column=3, sticky=W + E)
or_state = NORMAL if or_on.get() else DISABLED
self.or_entry = Entry(column_frame,
textvariable=or_value,
state=or_state)
self.or_entry.grid(row=0, column=4, sticky=W)
self.addToDisabable(self.or_check)
self.addToDisabable(self.or_entry)
beta_on = controller.beta_on
beta_value = controller.beta_value
self.beta_check = Checkbutton(column_frame,
text=TS('Beta'),
variable=beta_on)
self.beta_check.grid(row=1, column=3, sticky=W + E)
beta_state = NORMAL if beta_on.get() else DISABLED
self.beta_entry = Entry(column_frame,
textvariable=beta_value,
state=beta_state)
self.beta_entry.grid(row=1, column=4, sticky=W)
self.addToDisabable(self.beta_check)
self.addToDisabable(self.beta_entry)
beta_sign_on = controller.beta_sign_on
beta_sign_value = controller.beta_sign_value
self.beta_sign_check = Checkbutton(column_frame,
text=TS('Beta Sign'),
variable=beta_sign_on)
self.beta_sign_check.grid(row=2, column=3, sticky=W + E)
beta_sign_state = NORMAL if beta_sign_on.get() else DISABLED
self.beta_sign_entry = Entry(column_frame,
textvariable=beta_sign_value,
state=beta_sign_state)
self.beta_sign_entry.grid(row=2, column=4, sticky=W)
self.addToDisabable(self.beta_sign_check)
self.addToDisabable(self.beta_sign_entry)
or_cmd = lambda: controller.exclusiveToggle(or_on, self.or_entry, [
beta_on, beta_sign_on
], [self.beta_entry, self.beta_sign_entry])
self.or_check.config(command=or_cmd)
beta_lambda = lambda: controller.exclusiveToggle(
beta_on, self.beta_entry, [or_on, beta_sign_on],
[self.or_entry, self.beta_sign_entry])
self.beta_check.config(command=beta_lambda)
beta_sign_lambda = lambda: controller.exclusiveToggle(
beta_sign_on, self.beta_sign_entry, [beta_on, or_on],
[self.or_entry, self.beta_entry])
self.beta_sign_check.config(command=beta_sign_lambda)
#
self.p_check = Checkbutton(column_frame,
text=TS('P Value'),
variable=controller.p_on)
self.p_check.grid(row=0, column=5, sticky=W + E)
p_state = NORMAL if controller.p_on.get() else DISABLED
self.p_entry = Entry(column_frame,
textvariable=controller.p_value,
state=p_state)
self.p_entry.grid(row=0, column=6, sticky=W)
p_lambda = lambda: controller.toggleOption(controller.p_on, self.
p_entry)
self.p_check.config(command=p_lambda)
self.addToDisabable(self.p_check)
self.addToDisabable(self.p_entry)