def _build_state_display(self, position):
state_field = LabelFrame(self,
text=s.language.cards,
relief=RAISED,
width=self.master.width - 31)
state_slots_per_row = int((self.master.width - 31) / 32)
state_slot_height = 24 + (
(int(len(self._current_player.states) / state_slots_per_row) + 1) *
32)
if self._current_player.states:
for index, state in enumerate(self._current_player.states):
if state not in self._main_window.engine.nemKartyaStatusz:
if state in self._main_window.engine.eventszotar.keys():
origin = self._main_window.engine.eventszotar
prefix = "event"
else:
origin = self._main_window.engine.kincsszotar
prefix = "treasure"
icon = f"{prefix}_{self._main_window.engine.eventszotar[state].kep}_i"
icon = icon[(icon.find('_') + 1):]
button = Button(
state_field,
image=Gallery.get(icon),
command=lambda s=state: origin[s].megjelenik(1))
button.grid(row=int(index / state_slots_per_row),
column=index % state_slots_per_row)
state_field.config(height=state_slot_height)
if state_field.winfo_children():
state_field.grid(row=position, column=0)
state_field.grid_propagate(False)
def popup_window(self, text, filename):
top = Toplevel()
info = LabelFrame(top, text=text) #"Group Information")
info_text = Text(
info,
width=50,
height=8,
#bg=projectBgColor,
#fg=projectFgColor,
font=("nimbus mono bold", "11"))
def savefunc():
self.writepaste(filename, info_text)
def loadfunc():
self.readpaste(filename, info_text)
info_save_button = Button(info, text="Save", command=savefunc)
info_load_button = Button(info, text="Load", command=loadfunc)
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
info_load_button.grid(row=5, column=5, padx=10, pady=5)
info_save_button.grid(row=5, column=6, padx=10, pady=5)
info_text.grid(row=1,
rowspan=3,
column=1,
columnspan=7,
padx=5,
pady=5)
info.grid(row=7, column=0, columnspan=6, sticky=W, padx=20, pady=10)
top.focus_force()
def showMainValues():
global tkroot
global labels
global mframe
global values
from tkinter import Tk, N, W
from tkinter.ttk import LabelFrame, Label
# first run, set up the thingy
print("Setting up Main Values...")
init_parse(getMainValues, _parse_main_values_xml, values)
sleep(0.5)
print("Setting up Advanced Values...")
init_parse(getAdvancedValues, _parse_adv_values_xml, values)
print("initializing tkinter interface...")
tkroot = Tk()
mframe = LabelFrame(tkroot, text="Main Frame")
labels = {}
for group in values:
lframe = LabelFrame(mframe, text=group)
labels[group] = OrderedDict()
labels[group]['frame'] = lframe
for param, pv in values[group].items():
labels[group][param] = {}
plabel = Label(lframe, text=param)
vlabel = Label(lframe, text=pv)
labels[group][param]['plabel'] = plabel
labels[group][param]['vlabel'] = vlabel
mframe.grid()
for i, group in enumerate(labels):
for param in labels[group]:
if param == 'frame':
labels[group][param].grid(column=i, row=0, sticky=N)
else:
labels[group][param]['plabel'].grid(sticky=W)
labels[group][param]['vlabel'].grid(sticky=W)
tkroot.grid()
print('setting up polling intervals')
tkroot.after(500, poll_main_values)
tkroot.after(750, poll_adv_values)
print('Ready')
tkroot.mainloop()
print("afterloop")
def serverpanel(server):
''' Draws the top panel with the server information '''
serverpanel = LabelFrame(win, text = "Server Details")
serverpanel.grid(column = 0, row = 0, padx = 5, pady = 5, sticky = W+E)
Label(serverpanel, text = "Server Name: ").grid(column = 0, row = 0, sticky = W)
Label(serverpanel, text = "Server Type: ").grid(column = 0, row = 1, sticky = W)
Label(serverpanel, text = "Load Balancer Status: ").grid(column = 0, row = 2, sticky = W)
Label(serverpanel, textvariable = snv).grid(column = 1, row = 0, sticky = W)
Label(serverpanel, textvariable = stv ).grid(column = 1, row = 1, sticky = W)
Label(serverpanel, textvariable = lbv).grid(column = 1, row = 2, sticky = W)
serverstatus(server)
class StatsTabFrame(Frame):
def __init__(self, win, tabs):
super().__init__(tabs)
self.win = win
self.tabs = tabs
self.tabs.add(self, text="Stats")
self.stats: StatsCollection = None
self.selection: StatsCollection = None
self._body = Frame(self)
self._body.grid(row=0, column=0, sticky=EW, padx=PAD_X, pady=PAD_Y)
# Load
self._load_stats = LoadStatsFrame(self._body, self.set_stats)
self._load_stats.grid(row=0, column=0, padx=PAD_X, pady=PAD_Y, sticky=EW)
# Summary
self._summary = LabelFrame(self._body, text=" Records ")
self._summary.grid(row=1, column=0, sticky=EW)
self._all_counters = CountersFrame(self._summary, text=" All ")
self._all_counters.grid(row=0, column=0, padx=2 * PAD_X, pady=2 * PAD_Y, sticky=EW)
self._selection_counters = CountersFrame(self._summary, text=" Selection ")
self._selection_counters.grid(column=1, row=0, padx=2 * PAD_X, pady=2 * PAD_Y, sticky=EW)
# Filter
self._filters = FilterSelectionFrame(self._body, self.get_all, self.get_selection, self.set_selection)
self._filters.grid(row=2, column=0, sticky=EW)
# Reports
self._reports = ReportsFrame(self._body, self.get_selection)
self._reports.grid(row=3, column=0, sticky=EW)
def get_all(self) -> StatsCollection:
return self.stats
def get_selection(self) -> StatsCollection:
return self.selection
def set_stats(self, stats: StatsCollection):
self.stats = stats
self._all_counters.set_stats(stats.get_counters())
self._filters.set_countries(stats.unique_countries)
self.set_selection(stats)
def set_selection(self, stats: StatsCollection):
self.selection = stats
self._selection_counters.set_stats(stats.get_counters())
self._filters.set_tournaments(stats.unique_tournaments)
def buttonpanel():
''' Draws the panel with the buttons at the bottom '''
butpanel = LabelFrame(win, text = "")
butpanel.grid(column = 0, row = 2, padx = 5, pady = 5, sticky = W+E)
Button(butpanel, text = "Stop Services", command = onStop).grid(column = 0, row = 0)
Button(butpanel, text = "Start Services", command = onStart).grid(column = 1, row = 0)
Button(butpanel, text = "Refresh List", command = onStatus).grid(column = 2, row = 0)
if server.lbalanced.upper() == "YES":
# lbutpanel = LabelFrame(win, text = "")
# lbutpanel.grid(column = 0, row = 3, padx = 5, pady = 5, sticky = W+E)
Button(butpanel, text = "Stop Load Balancer", command = lbStop).grid(column = 0, row = 1)
Button(butpanel, text = "Start Load Balancer", command = lbStart).grid(column = 1, row = 1)
def _build_inventory_display(self, position):
gold_frame = LabelFrame(self._inventory_display,
text=s.language.treasure)
Label(gold_frame, image=Gallery.get("penz-d2")).grid(row=0, column=0)
Label(gold_frame,
textvariable=self._current_player.gold).grid(row=0, column=1)
gold_frame.grid(row=0, column=0, sticky=N + E + W + S, padx=5)
crew_frame = LabelFrame(self._inventory_display, text=s.language.crew)
Label(crew_frame, image=Gallery.get("crew")).grid(row=0, column=0)
Label(crew_frame,
textvariable=self._current_player.crew).grid(row=0, column=1)
crew_frame.grid(row=0, column=1, sticky=N + E + W + S, padx=5)
self._inventory_display.grid(row=position, column=0)
self._inventory_display.columnconfigure(
ALL, minsize=(self.master.width - 20) / 2)
def create_widgets(self):
''' creates GUI for app '''
# expand widget to fill the grid
# self.columnconfigure(1, weight=1, pad=100)
# self.rowconfigure(1, weight=1, pad=20)
lframe = LabelFrame(self, text="Combobox", width=100, height=100)
lframe.grid(row=1, column=1, sticky=N + S + E + W)
self.cbov = StringVar()
cbox = Combobox(lframe, textvariable=self.cbov)
cbox['values'] = ('value1', 'value2', 'value3')
# COMBO.bind('<<ComboboxSelected>>', self.ONCOMBOSELECT)
cbox.current(0)
cbox.grid(row=1, column=1, sticky=E + W, padx=10, pady=20)
def create_widgets(self):
''' Creates all widgets.
'''
self.columnconfigure(0, weight=1)
self.rowconfigure(1, weight=1)
validate_btn = Button(self,
text='Validate weight restrictions',
command=self.on_validate_weights)
validate_btn.grid(row=0, column=0, padx=10, pady=5, sticky=N + W)
panel = LabelFrame(self, text='Weight restrictions')
panel.columnconfigure(0, weight=1)
panel.rowconfigure(0, weight=1)
panel.grid(row=1, column=0, padx=5, pady=5, sticky=E + W + S + N)
weight_tab_main = VerticalScrolledFrame(panel)
weight_tab_main.grid(row=0, column=0, sticky=E + W + S + N)
weights_tab = weight_tab_main.interior
self.abs_weights = TextForWeights(weights_tab, 'absolute',
'Input1 <= 0.02',
self.current_categories, self.params,
'ABS_WEIGHT_RESTRICTIONS')
self.abs_weights.grid(row=0, column=0, padx=10, pady=5, sticky=N + W)
self.virtual_weights = TextForWeights(weights_tab, 'virtual',
'Input1 >= 0.34',
self.current_categories,
self.params,
'VIRTUAL_WEIGHT_RESTRICTIONS')
self.virtual_weights.grid(row=1,
column=0,
padx=10,
pady=5,
sticky=N + W)
self.price_ratio_weights = TextForWeights(weights_tab, 'price ratio',
'Input1/Input2 <= 5',
self.current_categories,
self.params,
'PRICE_RATIO_RESTRICTIONS',
True)
self.price_ratio_weights.grid(row=2,
column=0,
padx=10,
pady=5,
sticky=N + W)
def servicepanel(server):
''' Draws the panel with the service information '''
global servv, spanel
servicepanel = LabelFrame(win, text = "Service Details")
servicepanel.grid(column = 0, row = 1, padx = 5, pady = 5, sticky = W+E)
services = server.getservices()
scount = 0
for service in services:
servv[service] = StringVar()
Label(servicepanel, text = service + ": ").grid(column = 0, row = scount, sticky = W)
Label(servicepanel, textvariable = servv[service]).grid(column = 1, row = scount, sticky = W)
servicestatus(server, service)
scount += 1
spanel = Label(servicepanel, textvariable = status).grid(column = 0, row = scount + 1, columnspan = 2, sticky = W)
status.set("")
def add_model_component(self, sherpa_model_component):
'''Create UI elements for model component.
Each component is a separate LabelFrame. Each
model parameter is a row within that frame.
'''
self.sherpa_model = sherpa_model_component
lfrm = LabelFrame(self.get_win(),
text=sherpa_model_component.name)
lfrm.grid(row=self.get_row(), column=0, columnspan=1,
padx=(10, 10), pady=(10, 10))
self.next_row()
# Repeat column headers in each model component
self.add_column_headers(lfrm)
for par in self.sherpa_model.pars:
mod_par = DaxModelParameter(self, lfrm, par)
self.model_parameters.append(mod_par)
self.next_row()
def __init__(self, master):
top = self.top = Toplevel(master)
top.title("Parameters")
top.attributes("-topmost", True)
width = str(26 * (len(model_dict) + 4))
top.geometry("310x" + width)
top.grid()
top.resizable(0, 0)
frame = LabelFrame(top,
text=model_name,
relief=RIDGE,
width=260)
frame.grid(row=0,
column=0,
columnspan=2,
sticky="EWNS",
padx=15,
pady=15)
self.values = list()
line = 1
for k, v in model_dict.items():
Label(frame, text=k, width=20) \
.grid(row=line, column=0, columnspan=1, sticky='W', padx=4, pady=1)
e = Entry(frame, width=10)
e.insert(END, str(v))
e.grid(row=line,
column=1,
columnspan=1,
sticky='E',
padx=6,
pady=1)
self.values.append(e)
line += 1
Button(frame, text=' Help ', command=self.help) \
.grid(row=line+2, column=0, columnspan=1, sticky='W', padx=4, pady=4)
Button(frame, text=' Ok ', command=self.cleanup) \
.grid(row=line+2, column=1, columnspan=1, sticky='E', padx=4, pady=4)
top.bind('<Return>', self.cleanup)
def create_widgets(self):
''' Creates all widgets.
'''
self.columnconfigure(0, weight=1)
self.rowconfigure(1, weight=1)
validate_btn = Button(self, text='Validate weight restrictions',
command=self.on_validate_weights)
validate_btn.grid(row=0, column=0, padx=10, pady=5, sticky=N+W)
panel = LabelFrame(self, text='Weight restrictions')
panel.columnconfigure(0, weight=1)
panel.rowconfigure(0, weight=1)
panel.grid(row=1, column=0,
padx=5, pady=5, sticky=E+W+S+N)
weight_tab_main = VerticalScrolledFrame(panel)
weight_tab_main.grid(row=0, column=0, sticky=E+W+S+N)
weights_tab = weight_tab_main.interior
self.abs_weights = TextForWeights(weights_tab, 'absolute',
'Input1 <= 0.02',
self.current_categories, self.params,
'ABS_WEIGHT_RESTRICTIONS')
self.abs_weights.grid(row=0, column=0, padx=10, pady=5, sticky=N+W)
self.virtual_weights = TextForWeights(weights_tab, 'virtual',
'Input1 >= 0.34',
self.current_categories,
self.params,
'VIRTUAL_WEIGHT_RESTRICTIONS')
self.virtual_weights.grid(row=1, column=0, padx=10, pady=5, sticky=N+W)
self.price_ratio_weights = TextForWeights(weights_tab, 'price ratio',
'Input1/Input2 <= 5',
self.current_categories,
self.params,
'PRICE_RATIO_RESTRICTIONS',
True)
self.price_ratio_weights.grid(row=2, column=0, padx=10, pady=5,
sticky=N+W)
def add(self, widget, load=None):
#print("Add New :",widget)
# Widget Container
wid_frame = LabelFrame(self.cont, text="Note {}\n".format(widget))
# Text Widget Creation
#TextBox = tk.Text(wid_frame, width=w, height=h, undo=True)
TextBox = scrolledtext.ScrolledText(wid_frame,
width=w,
height=h,
undo=True)
TextBox.config(wrap="word")
TextBox.setvar("NAME", value=widget)
if load is None:
#TextBox.insert(tk.INSERT, "Note {}\n".format(widget))
pass
else:
TextBox.insert(INSERT, load)
TextBox.pack()
# BackUp
self.widgets[widget] = [wid_frame, TextBox]
# Place Widget Frame[container]
wid_frame.grid(row=0, column=0)
self.show(widget)
def popup_window( self, text, filename ) :
top = Toplevel()
info = LabelFrame(top, text=text )#"Group Information")
info_text = Text(info,
width=50,
height=8,
#bg=projectBgColor,
#fg=projectFgColor,
font=("nimbus mono bold","11")
)
def savefunc() :
self.writepaste( filename, info_text )
def loadfunc() :
self.readpaste( filename, info_text )
info_save_button = Button(info,
text="Save",
command = savefunc )
info_load_button = Button(info,
text="Load",
command = loadfunc )
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
info_load_button.grid( row=5, column=5, padx=10, pady=5 )
info_save_button.grid( row=5, column=6, padx=10, pady=5 )
info_text.grid(row=1, rowspan=3,
column=1, columnspan=7,
padx=5, pady=5 )
info.grid(row=7,column=0, columnspan=6, sticky=W, padx=20, pady=10 )
top.focus_force()
def build(self):
"""widget construction"""
fr4 = LabelFrame(self.fr0, text='yiq')
fr4.grid(column=2, row=0)
vcmdyiq = root.register(yiq_okay)
self.cans = []
sboxes = []
comps = ['y', 'i', 'q']
names = ['luma', 'i hue', 'q hue']
tkvars = [self.yvar, self.ivar, self.qvar]
froms = [0, -100, -100]
ticks = [10, 20, 20]
for ix, comp in enumerate(comps):
Label(fr4, text=names[ix]).grid(row=3 * ix, column=0)
Label(fr4, height=1).grid(row=2 + 3 * ix, column=2)
self.cans.append(
Canvas(fr4,
width=self.canvas_w,
height=self.canvas_h,
bd=0,
highlightthickness=0))
self.cans[ix].grid(row=3 * ix, column=1)
TtkScale(fr4,
from_=froms[ix],
to=100,
variable=tkvars[ix],
orient='horizontal',
length=self.scale_l,
command=self.yiqhandle,
tickinterval=ticks[ix]).grid(row=1 + 3 * ix,
column=1,
sticky='nw')
sboxes.append(
Spinbox(fr4,
from_=froms[ix],
to=100,
textvariable=tkvars[ix],
validatecommand=(vcmdyiq, '%d', '%P', '%S', froms[ix],
100),
validate='key',
command=self.yiqhandle,
width=5,
increment=1))
sboxes[ix].grid(row=1 + 3 * ix, column=2, sticky='nw')
sboxes[ix].bind('<KeyRelease>', self.checksyiq)
# assume initial setting 0,100,100 hsv
to_colour = yiq_to_rgb(*(30, 100.0, 40.56))
# print(self.canvas_w)
draw_gradient(self.cans[0],
yiq_to_rgb(0.0, 100.0, 40.56),
yiq_to_rgb(100, 100, 40.56),
width=self.canvas_w)
draw_gradient(self.cans[1],
yiq_to_rgb(30, -100.0, 40.56),
to_colour,
width=self.canvas_w)
draw_gradient(self.cans[2],
yiq_to_rgb(30, 100, -100),
yiq_to_rgb(30, 100, 100),
width=self.canvas_w)
self.can_yiq = can_yiq = Canvas(fr4,
width=self.space,
height=self.space)
can_yiq.grid(column=1, row=9, pady=25, sticky='n')
self.yiqGamut = PhotoImage(file='../../figures/colour_space.png')
can_yiq.create_image(0, 0, anchor='nw', image=self.yiqGamut)
self.ring = circle(can_yiq,
300.0,
210.84,
self.ring_radius,
width=self.ring_width,
activeoutline='#555555',
tags='ring') # 240, 181
can_yiq.bind('<Button-1>', self.move_ring)
can_yiq.tag_bind('ring', '<B1-Motion>', self.move_ring)
h = value.lstrip('#')
tvalue = tuple(int(h[i:i + 2], 16) for i in (0, 2, 4))
if contrast(tvalue) < 0.5:
lbl2["foreground"] = 'white'
lbl2["text"] = tvalue
lbl2["background"] = value
root = Tk()
fr = Frame(root)
fr.grid(column=0, row=0)
fr2 = Frame(root)
fr2.grid(column=1, row=0)
lbl = Label(fr,
text='Enter colour code\n use no quotes\n code can be r,g,b\n \
hash #rrggbb\n or name')
lbl.grid(column=0, row=0, padx=5, pady=10)
ey = Entry(fr2)
ey.grid(column=0, row=0, padx=5, pady=10)
out = StringVar(ey.get())
lf = LabelFrame(fr, text='Colour')
lf.grid(column=0, row=1)
lbl2 = Label(lf, text='waiting')
lbl2.grid(column=0, row=1)
but1 = Button(fr2, text='Make Colour', command=getit)
but1.grid(column=0, row=1, padx=5, pady=5)
root.mainloop()
def popup_window_contrast(self) :
text = "Comparing ChIP-seq Peaks"
contrast_fn = join(self.workpath.get(),self.contrast_fn)
peakinfo_fn = join(self.workpath.get(),self.peakinfo_fn)
NA='N/A'
try :
groups = list(set([l.split('\t')[-1].strip() for l in open(peakinfo_fn) if l.split('\t')[-1].strip()]))
if len(groups) < 2 :
showwarning( 'WARNING!', "More than one groups need to be fefined in Peak Information File!" )
print( 'groups:', groups )
return
except IOError :
showerror( 'Error', "Did you set peak information?" )
print('Error:', 'Cannot process peakcall.tab file:')
return
top = Toplevel()
info = LabelFrame(top, text=text )#"Group Information")
print( groups )
contrast_vars = []
contrast_menus = []
n = 0
groups.insert(0, NA)
for i in range( int((len(groups)-1)*(len(groups)-2)/2) ):
n = n + 1
v1, v2 = StringVar(), StringVar()
contrast_vars.append( [v1, v2] )
o1, o2 = OptionMenu(info, v1, *groups), OptionMenu(info, v2, *groups)
contrast_menus.append( [o1, o2] )
v1.set(NA)
v2.set(NA)
vslabel = Label(info, text=" VS ")
o1.grid( row=n, column=0, padx=4, pady=1 )
o2.grid( row=n, column=2, padx=4, pady=1 )
vslabel.grid( row=n, column=1, padx=4, pady=1 )
def savefunc() :
info_text = StringIO()
for v1, v2 in contrast_vars :
v1 = v1.get() if v1.get() != NA else ""
v2 = v2.get() if v2.get() != NA else ""
if v1 and v2 :
pass
elif v1 or v2 :
showerror( 'Error', "None or Both columns should be selected!" )
return
else:
continue
print( v1, v2, file=info_text, sep="\t" )
fp = open( contrast_fn, 'w' )
fp.write( info_text.getvalue() )
fp.close()
def loadfunc() :
#self.readpaste( filename, info_text )
for i, l in enumerate(open( contrast_fn )) :
v1, v2 = l.split('\t')
v1 = v1.strip()
v2 = v2.strip()
if v1 :
try : assert v1 in groups
except :
showwarning('WARNING', 'Group name is not in the selection list!' )
print( 'v1:',v1 )
print( 'group:', groups )
continue
if v2 :
try: assert v2 in groups
except :
showwarning('WARNING', 'Group name is not in the selection list!' )
print( 'v2:',v2 )
print( 'group:', groups )
continue
contrast_vars[i][0].set(v1)
contrast_vars[i][1].set(v2)
def clearfunc() :
for v1, v2 in contrast_vars :
v1.set(NA)
v2.set(NA)
info_clear_button = Button(top,
text="Clear",
command = clearfunc )
info_save_button = Button(top,
text="Save",
command = savefunc )
info_load_button = Button(top,
text="Load",
command = loadfunc )
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
info_clear_button.grid( row=5, column=3, padx=10, pady=5 )
info_load_button.grid( row=5, column=4, padx=10, pady=5 )
info_save_button.grid( row=5, column=5, padx=10, pady=5 )
info.grid(row=7,column=0, columnspan=6, sticky=W, padx=20, pady=10 )
top.focus_force()
class GenomeSeqFrame( PipelineFrame ) :
def __init__(self, pipepanel, pipeline_name, *args, **kwargs) :
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.pairs = None
eframe = self.eframe = LabelFrame(self,text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid( row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5 )
label = Label(eframe,text="Pipeline")#,fg=textLightColor,bg=baseColor)
label.grid(row=3,column=0,sticky=W,padx=10,pady=5)
PipelineLabels = ['Initial QC',
'Germline',
'Somatic Tumor-Normal',
'Somatic Tumor-Only']
Pipelines=["initialqcgenomeseq",
"wgslow",
'wgs-somatic',
'wgs-somatic-tumoronly']
self.label2pipeline = { k:v for k,v in zip(PipelineLabels, Pipelines)}
PipelineLabel = self.PipelineLabel = StringVar()
Pipeline = self.Pipeline = StringVar()
PipelineLabel.set(PipelineLabels[0])
#om = OptionMenu(eframe, Pipeline, *Pipelines, command=self.option_controller)
om = OptionMenu(eframe, PipelineLabel, *PipelineLabels, command=self.option_controller)
om.config()#bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config()#bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3,column=1,sticky=W,padx=10,pady=5)
def option_controller( self, *args, **kwargs ) :
PipelineFrame.option_controller( self )
self.Pipeline.set( self.label2pipeline[self.PipelineLabel.get()] )
print( self.Pipeline.get() )
if self.Pipeline.get() == 'wgs-somatic' :
self.add_pairs( self.eframe )
#self.dry_button.config( state="disabled" )
elif self.Pipeline.get() != 'wgs-somatic' :
self.del_pairs( self.eframe )
#if self.workpath.get() :
# self.dry_button.config( state='active' )
def add_pairs( self, parent ) :
if not self.pairs :
self.pairs = LabelFrame(parent, text='Pairs')
self.pairs_text = Text( self.pairs,
width=50,
height=8,
#bg=projectBgColor,
#fg=projectFgColor,
font=("nimbus mono bold","11")
)
self.pairs_save_button = Button(self.pairs,
text="Save",
command = self.writepair )
self.pairs_load_button = Button(self.pairs,
text="Load",
command = self.readpair )
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
self.pairs_load_button.grid( row=5, column=5, padx=10, pady=5 )
self.pairs_save_button.grid( row=5, column=6, padx=10, pady=5 )
self.pairs_text.grid( row=1, rowspan=3,
column=1, columnspan=7,
padx=5, pady=5 )
self.pairs.grid(row=7,column=0, columnspan=6, sticky=W, padx=20, pady=10 )
def del_pairs( self, parent ) :
if self.pairs :
self.pairs.grid_forget()
def writepair( self ) :
self.writepaste( 'pairs', self.pairs_text )
#self.dry_button.config( state='active' )
def readpair( self ) :
self.readpaste( 'pairs', self.pairs_text )
def build(self):
"""widget construction
Parameters
----------
None
Results
-------
None
"""
fr1 = LabelFrame(self.fr0, text='rgb')
fr1.grid(column=0, row=0, sticky='news')
rl0 = Label(fr1, text='red ')
rl0.grid(column=0, row=0, sticky='s')
self.rcan = Canvas(fr1, width=self.canvas_w, height=self.canvas_h, bd=0,
highlightthickness=0)
self.rcan.grid(column=1, row=0, sticky='s')
rsc = TtkScale(fr1, from_=0, to=255, variable=self.rvar, orient='horizontal',
length=self.scale_l, command=self.rhandle, tickinterval=20)
rsc.grid(column=1, row=1, sticky='news')
rsb = Spinbox(fr1, from_=0, to=255, textvariable=self.rvar,
command=self.rhandle, width=5)
rsb.grid(column=2, row=1, sticky='nw')
rel = Label(fr1, height=1)
rel.grid(column=2, row=2)
gl0 = Label(fr1, text='green')
gl0.grid(column=0, row=3)
self.gcan = Canvas(fr1, width=self.canvas_w, height=self.canvas_h, bd=0,
highlightthickness=0)
self.gcan.grid(column=1, row=3, sticky='s')
gsc = TtkScale(fr1, from_=0, to=255, variable=self.gvar, orient='horizontal',
length=self.scale_l, command=self.ghandle, tickinterval=20)
gsc.grid(column=1, row=4, sticky='news')
gsb = Spinbox(fr1, from_=0, to=255, textvariable=self.gvar,
command=self.ghandle, width=5)
gsb.grid(column=2, row=4, sticky='nw')
gel = Label(fr1, height=1)
gel.grid(column=2, row=5)
bl0 = Label(fr1, text='blue ')
bl0.grid(column=0, row=6, sticky='s')
self.bcan = Canvas(fr1, width=self.canvas_w, height=self.canvas_h, bd=0,
highlightthickness=0)
self.bcan.grid(column=1, row=6, sticky='n')
bsc = TtkScale(fr1, from_=0, to=255, variable=self.bvar, orient='horizontal',
length=self.scale_l, command=self.bhandle, tickinterval=20)
bsc.grid(column=1, row=7, sticky='news')
bsb = Spinbox(fr1, from_=0, to=255, textvariable=self.bvar,
command=self.bhandle, width=5)
bsb.grid(column=2, row=7, sticky='nw')
bel = Label(fr1, height=1)
bel.grid(column=2, row=8)
fr3 = LabelFrame(self.fr0, text='colour mix')
fr3.grid(column=1, row=0, sticky='nw')
self.cmcan = cmcan = Canvas(fr3, width=30, height=30, bd=0,
highlightthickness=0)
cmcan.grid(column=0, row=0, sticky='n', columnspan=2)
cmcan.grid_propagate(0)
vdraw_gradient(self.cmcan, (255, 0, 0), alpha=255)
cml = Label(fr3, text='hash\nvalue')
cml.grid(column=0, row=1)
ent0 = Entry(fr3, width=8, textvariable=self.evar)
ent0.grid(column=1, row=1)
fr2 = LabelFrame(self.fr0, text='opacity')
fr2.grid(column=0, row=1, sticky='news')
al0 = Label(fr2, text='alpha')
al0.grid(column=0, row=0, sticky='s')
self.acan = Canvas(fr2, width=self.canvas_w, height=self.canvas_h, bd=0,
highlightthickness=0)
self.acan.grid(column=1, row=0, sticky='n')
asc = TtkScale(fr2, from_=0, to=255, variable=self.avar, orient='horizontal',
length=self.scale_l, command=self.ahandle, tickinterval=20)
asc.grid(column=1, row=1, sticky='news')
asb = Spinbox(fr2, from_=0, to=255, textvariable=self.avar,
command=self.ahandle, width=5)
asb.grid(column=2, row=1, sticky='nw')
ael = Label(fr2, text=' ', height=1)
ael.grid(column=2, row=2, sticky='s')
draw_gradient(self.rcan, (0, 0, 0), (255, 0, 0), width=self.canvas_w)
draw_gradient(self.gcan, (255, 0, 0),
(255, 255, 0), width=self.canvas_w)
draw_gradient(self.bcan, (255, 0, 0),
(255, 0, 255), width=self.canvas_w)
draw_agradient(self.acan, (127, 127, 127),
(255, 0, 0), width=self.canvas_w)
class ExomeSeqFrame( PipelineFrame ) :
def __init__(self, pipepanel, pipeline_name, *args, **kwargs) :
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.pairs = None
eframe = self.eframe = LabelFrame(self,text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid( row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5 )
label = Label(eframe,text="Pipeline")#,fg=textLightColor,bg=baseColor)
label.grid(row=3,column=0,sticky=W,padx=10,pady=5)
Pipelines=["initialqc","exomeseq-somatic","exomeseq-germline"]
Pipeline = self.Pipeline = StringVar()
Pipeline.set(Pipelines[0])
om = OptionMenu(eframe, Pipeline, *Pipelines, command=self.option_controller)
#om.config()#bg = widgetBgColor,fg=widgetFgColor)
#om["menu"].config()#bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3,column=1,sticky=W,padx=10,pady=5)
targetsL=Label(eframe,
text="Target Capture Kit")
#,fg=textLightColor,bg=baseColor)
targetsL.grid(row=5,column=0,sticky=W,padx=10,pady=5)
targetsE = Entry(eframe,textvariable=self.targetspath, width=50)
if self.genome=="hg19":
self.targetspath.set(
"/data/CCBR_Pipeliner/db/PipeDB/lib/SS_v5_UTRs_hg19.bed" )
else:
self.targetspath.set(
"/data/CCBR_Pipeliner/db/PipeDB/lib/SureSelect_mm10.bed")
targetsE.grid(row=5,column=1,columnspan=6,sticky=W,padx=10,pady=5)
self.targetspath.trace('w', lambda a,b,c,x="targetspath":self.makejson(x))
label = Label (eframe,
text =
"By default, the path to the Agilent V5+UTR targets file is filled in here" )
label.grid(row=6, column=0, columnspan=5, sticky=W, padx=10, pady=5)
def option_controller( self, *args, **kwargs ) :
PipelineFrame.option_controller( self )
if self.Pipeline.get() == 'exomeseq-somatic' :
self.add_pairs( self.eframe )
#self.dry_button.config( state="disabled" )
elif self.Pipeline.get() != 'exomeseq-somatic' :
self.del_pairs( self.eframe )
#if self.workpath.get() :
# self.dry_button.config( state='active' )
def add_pairs( self, parent ) :
if not self.pairs :
self.pairs = LabelFrame(parent, text='Pairs')
self.pairs_text = Text( self.pairs,
width=50,
height=8,
#bg=projectBgColor,
#fg=projectFgColor,
font=("nimbus mono bold","11")
)
self.pairs_save_button = Button(self.pairs,
text="Save",
command = self.writepair )
self.pairs_load_button = Button(self.pairs,
text="Load",
command = self.readpair )
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
self.pairs_load_button.grid( row=5, column=5, padx=10, pady=5 )
self.pairs_save_button.grid( row=5, column=6, padx=10, pady=5 )
self.pairs_text.grid( row=1, rowspan=3,
column=1, columnspan=7,
padx=5, pady=5 )
self.pairs.grid(row=7,column=0, columnspan=6, sticky=W, padx=20, pady=10 )
def del_pairs( self, parent ) :
if self.pairs :
self.pairs.grid_forget()
def writepair( self ) :
self.writepaste( 'pairs', self.pairs_text )
#self.dry_button.config( state='active' )
def readpair( self ) :
self.readpaste( 'pairs', self.pairs_text )
class Assist_Serial_Port():
def __init__(self):
self.BTL = [110, 300, 600, 1200, 2400, 4800, 9600, 14400, 19200, 38400, 56000, 57600, 115200, 128000, 256000] # 波特率下拉列表框内容
self.JYW = ['NONE', 'ODD', 'EVEN', 'MARK', 'SPACE'] # 校验位下拉列表框内容
self.SJW = [5, 6, 7, 8] # 数据位下拉列表内容
self.TZW = [1, 1.5, 2] # 停止位下拉列表内容
self.CKXX = self.read_serial_info()
self.PZMC = ['串口号','波特率','校验位','数据位','停止位']
self.serial_res_hex_bzw = False # 接收数据框内容显示hex标志位
self.serial_sen_hex_bzw = False # 发送数据框内容显示hex标志位
self.radiobutton_sen_ascii_click_count = 1 # 设置发送ASCII单选框点击次数为0
self.radiobutton_sen_hex_click_count = 0 # 设置发送HEX单选框点击次数为0
self.root = Tk(className='串口调试助手') # 创建一个主窗体，并命名为‘串口调试助手’
self.root.protocol('WM_DELETE_WINDOW',self.close_window) # 实现点击窗口关闭按钮，调用self.close_window方法，关闭已经打开的串口，销毁窗口
self.root.geometry('630x580') # 设置窗体大小
self.root.minsize(width=630, height=435) # 这两句语言限制窗口不能随意变化
self.root.maxsize(width=630, height=435)
self.lf = LabelFrame(self.root, text='串口设置') # 创建标签容器，并且命名为‘串口设置’
self.lf.grid(padx=8, pady=10,ipadx=3, ipady=5,row=1,column=1,sticky='n') # 设置标签容器在窗口中的位置
self.text_res_con = LabelFrame(master=self.root,text='接收设置') # 创建标签容器，并命名为接收设置
self.text_res_con.grid(row=1,column=1,sticky='s') # 设置标签容器在窗口中的位置
self.text_sen_con = LabelFrame(master=self.root,text='发送设置') # 创建标签容器，并命名为接收设置
self.text_sen_con.grid(padx=8, pady=10,row=2,column=1,sticky='nesw') # 设置标签容器在窗口中的位置
self.data_rec = LabelFrame(self.root, text='数据日志') # 创建标签容器，并且命名为‘数据日志’
self.data_rec.grid(ipadx=3, ipady=5,row=1, column=2, sticky='e') # 设置标签容器在窗口中的位置
self.y_scroll = Scrollbar(self.data_rec) # 创建接收文本框的Y轴下拉框
self.y_scroll.pack(side=RIGHT,fill=Y) # 确定位置
self.result_text = Text(master=self.data_rec,height=22,width=66,yscrollcommand=self.y_scroll.set) # 创建一个多文本组件，用来显示接收的串口信息，并且配置关联滚轴
self.result_text.pack(side=RIGHT,fill=Y) # 设置多文本组件在窗口中的位置
self.y_scroll.config(command=self.result_text.yview) # 让文本框和滚轴关联起来
self.data_sen = LabelFrame(self.root, text='数据发送') # 创建标签容器，并且命名为‘数据日志’
self.data_sen.grid(ipadx=3, ipady=5,row=2, column=2, sticky='w') # 设置标签容器在窗口中的位置
self.send_text = Text(master=self.data_sen,height=6,width=60) # 创建一个发送文本框
self.send_text.grid(row=1,column=1,sticky='n') # 设置标签容器在窗口中的位置
self.button_send = Button(self.data_sen,text='发送消息',command=self.button_send_serial_click,width=7) # 创建一个发送文本框
self.button_send.grid(row=1,column=2,sticky='NSEW') # 设置串口打开按钮的位置
'''关闭串口工具窗口触发的函数'''
def close_window(self):
ans = messagebox.askyesno('警告',message='确定关闭窗口？')
print(ans,'ans')
if ans:
try:
self.thd.stop() # 停止读取串口线程
'''确保串口会被关掉，修复关掉串口立马更改波特率，显示错误的问题'''
while self.ser.isOpen():
self.ser.close() # 将串口实例关闭
except:
print('关闭窗口')
self.root.destroy()
else:
return
'''创建串口配置框架'''
def serial_config_frame(self):
for temp in enumerate(self.PZMC):
'''生成标签组'''
label_name = Label(self.lf, text=temp[1]) # 创建串口标签
label_name.grid(padx=5,pady=6,column=1,row=temp[0] + 1) # 设置标签在标签容器中的位置
'''生成下拉列表框组'''
if temp[0] == 0:
self.combobox0 = Combobox(master=self.lf, values=self.CKXX, width=6, height=3,state='readonly') # 创建下拉列表框
self.combobox0.current(0) # 设置下拉列表当前选中项
self.combobox0.grid(column=2, row=1, sticky='e') # 设置下拉列表框在标签容器中的位置
self.combobox0.bind('<Button-1>',self.update_serial_info)
elif temp[0] == 1:
self.combobox1 = Combobox(master=self.lf, values=self.BTL, width=6, height=3,state='readonly') # 创建下拉列表框
self.combobox1.current(6) # 设置下拉列表当前选中项
self.combobox1.grid(column=2, row=2, sticky='e') # 设置下拉列表框在标签容器中的位置
elif temp[0] == 2:
self.combobox2 = Combobox(master=self.lf, values=self.JYW, width=6, height=3,state='readonly') # 创建下拉列表框
self.combobox2.current(0) # 设置下拉列表当前选中项
self.combobox2.grid(column=2, row=3, sticky='e') # 设置下拉列表框在标签容器中的位置
elif temp[0] == 3:
self.combobox3 = Combobox(master=self.lf, values=self.SJW, width=6, height=3,state='readonly') # 创建下拉列表框
self.combobox3.current(3) # 设置下拉列表当前选中项
self.combobox3.grid(column=2, row=4, sticky='e') # 设置下拉列表框在标签容器中的位置
else:
self.combobox4 = Combobox(master=self.lf, values=self.TZW, width=6, height=3,state='readonly') # 创建下拉列表框
self.combobox4.current(0) # 设置下拉列表当前选中项
self.combobox4.grid(column=2, row=5, sticky='e') # 设置下拉列表框在标签容器中的位置
self.button_open_serial = Button(self.lf,text='打开串口',command=self.button_open_serial_click) # 创建串口打开按钮
self.button_open_serial.grid(row=6,columnspan=5,sticky='s') # 设置串口打开按钮的位置
'''串口单击按钮函数'''
def button_open_serial_click(self):
if self.button_open_serial['text'] == '打开串口':
'''下面的try...except...else操作确定当串口被占用报错后，无法在重新打开串口'''
try:
self.open_serial_and_config() # 打开串口
self.thd = Thread_myself(target=self.serial_read_content) # 新建线程对象，并且传入串口对象
self.thd.start() # 启动串口助手
except Exception:
self.button_open_serial['text'] = '打开串口'
self.result_text.config(state=NORMAL)
self.result_text.tag_config('text_error_tag', foreground='red') # 设置插入文本样式
self.result_text.insert('end','\r\n无法打开串口，请检查串口连接或者是否被占用...\r\n','text_error_tag')
self.result_text.config(state=DISABLED)
self.result_text.see(END) # 文本框总是显示最新内容
else:
self.button_open_serial['text'] = '关闭串口'
self.combobox0.config(state='disabled') # 打开之后将所有下拉列表框禁用防止误操作
self.combobox1.config(state='disabled')
self.combobox2.config(state='disabled')
self.combobox3.config(state='disabled')
self.combobox4.config(state='disabled')
else:
self.button_open_serial['text'] = '打开串口'
self.combobox0.config(state='readonly')
self.combobox1.config(state='readonly')
self.combobox2.config(state='readonly')
self.combobox3.config(state='readonly')
self.combobox4.config(state='readonly')
try:
self.thd.stop() # 停止读取串口线程
'''确保串口会被关掉，修复关掉串口立马更改波特率，显示错误的问题'''
while self.ser.isOpen():
self.ser.close() # 将串口实例关闭
except:
print('无聊')
'''打开串口并配置'''
def open_serial_and_config(self,timeout=5):
if self.combobox2.get() == 'NONE': # 判断校验位方式
parity = 'N'
elif self.combobox2.get() == 'ODD':
parity = 'O'
elif self.combobox2.get() == 'EVEN':
parity = 'E'
elif self.combobox2.get() == 'MARK':
parity = 'M'
else:
parity = 'S'
if self.combobox3.get() == '5': # 判断数据然后配数据位
bytesize = 5
elif self.combobox3.get() == '6':
bytesize = 6
elif self.combobox3.get() == '7':
bytesize = 7
else:
bytesize = 8
if self.combobox4.get() == '1': # 判断串口停止位
stopbits = 1
elif self.combobox4.get() == '1.5':
stopbits = 1.5
else:
stopbits = 2
'''创建一个串口实例'''
self.ser = Serial(port=self.combobox0.get(),baudrate=self.combobox1.get(),parity=parity,bytesize=bytesize,stopbits=stopbits,timeout=timeout)
self.ser.set_buffer_size(rx_size=4096) # 设置输入缓存去为4096个字节
self.ser.flushInput() # 将输入缓存去清空
print('波特率为%s' %self.ser.baudrate)
'''读取设备串口信息，并返回串口列表'''
def read_serial_info(self):
serial_info = [temp.__getitem__(0) for temp in list_ports.comports()]
print(serial_info)
if serial_info:
return serial_info
else:
serial_info = ['No Port!']
return serial_info
'''当下拉框被选中时更新串口列表信息'''
def update_serial_info(self,*args):
self.combobox0['values'] = self.read_serial_info()
'''将发送文本框中的内容发送出去'''
def button_send_serial_click(self):
'''if逻辑是判断串口有没有打开，如果打开在发送数据，如果没有打开提示打开串口'''
if self.button_open_serial['text'] == '打开串口':
messagebox.showwarning('警告','请先打开串口！')
else:
try:
'''判断发送的内容是HEX还是ASCII，根据方式的不同发送方式也不同'''
if self.serial_sen_hex_bzw: # HEX方式发送
content = self.send_text.get(1.0, 'end').strip()
self.ser.write(bytes.fromhex(content)) # HEX方式发送串口数据
else: # ASCII方式发送
content = self.send_text.get(1.0, 'end').strip().encode().hex()
self.ser.write(bytes.fromhex(content)) # ASCII方式发送串口数据
if content.encode() == b'':
messagebox.showwarning('警告', '发送内容不能为空...')
except Exception:
messagebox.showerror('错误','请先打开串口...')
'''串口接收设置'''
def text_res_config(self):
'''创建单选框ASCII并配置单选框'''
self.radiobutton_res_variable = IntVar() # 设置单选框variable变量，作用是规定value的数值类型
self.radiobutton_res_dx_acci = Radiobutton(master=self.text_res_con)
self.radiobutton_res_dx_acci.config(
text = 'ASCII', # 单选框名字
variable = self.radiobutton_res_variable, # 设置数值类型
value = 1, # 设置value数值，同一组单选框中数值必须不一样
command = self.res_ascii_set # 绑定单选框单击之后调用的函数
)
'''创建单选框HEX并配置单选框'''
self.radiobutton_res_dx_hex = Radiobutton(master=self.text_res_con)
self.radiobutton_res_dx_hex.config(
text = 'HEX', # 单选框名字
variable = self.radiobutton_res_variable, # 设置数值类型
value = 2, # 设置value数值，同一组单选框中数值必须不一样
command = self.res_hex_set # 绑定单选框单击之后调用的函数
)
self.radiobutton_res_variable.set(1) # 设置那个单选框初始的时候为选中状态
self.radiobutton_res_dx_acci.grid(padx=5,row=1, column=1, sticky='w') # 封装ASCII单选框
self.radiobutton_res_dx_hex.grid(padx=5,row=1,column=2,sticky='e') # 封装HEX单选框
self.button_clear_res = Button(master=self.text_res_con,text='清空接收',command=lambda:self.clear_text(self.result_text)) # 添加清空接手区按键
self.button_clear_res.grid(row=2,sticky='s',columnspan=5,pady=7) # 将清空按键打包
'''串口发送设置'''
def text_sen_config(self):
'''创建单选框ASCII并配置单选框'''
self.radiobutton_sen_variable = IntVar() # 设置单选框variable变量，作用是规定value的数值类型
self.button_sen_dx_acci = Radiobutton(master=self.text_sen_con)
self.button_sen_dx_acci.config(
text = 'ASCII', # 单选框名字
variable = self.radiobutton_sen_variable, # 设置数值类型
value = 1, # 设置value数值，同一组单选框中数值必须不一样
command = self.sen_ascii_set # 绑定单选框单击之后调用的函数
)
'''创建单选框HEX并配置单选框'''
self.button_sen_dx_hex = Radiobutton(master=self.text_sen_con)
self.button_sen_dx_hex.config(
text = 'HEX', # 单选框名字
variable = self.radiobutton_sen_variable, # 设置数值类型
value = 2, # 设置value数值，同一组单选框中数值必须不一样
command = self.sen_hex_set # 绑定单选框单击之后调用的函数
)
self.radiobutton_sen_variable.set(1) # 设置那个单选框初始的时候为选中状态
self.button_sen_dx_acci.grid(padx=5,row=1, column=1, sticky='w') # 封装ASCII单选框
self.button_sen_dx_hex.grid(padx=5,row=1,column=2,sticky='e') # 封装HEX单选框
self.button_sen_clear_res = Button(master=self.text_sen_con,text='清空发送',command=lambda:self.clear_text(self.send_text)) # 添加清空接手区按键
self.button_sen_clear_res.grid(row=2,sticky='s',columnspan=5,pady=7) # 将清空按键打包
'''清空文本空间内容'''
def clear_text(self,object):
print('清除')
object.config(state=NORMAL) # 设置text对象可以操作
object.delete(1.0,'end') # 清空text对象内容
# object.config(state=DISABLED) # 设置text对象不可用
'''设置接收框ASCII转换标志位'''
def res_ascii_set(self):
self.serial_res_hex_bzw = False
'''设置接收框HEX转换标志位'''
def res_hex_set(self):
self.serial_res_hex_bzw = True
'''将发送文本框中的内容以ASCII方式显示'''
def sen_ascii_set(self):
self.radiobutton_sen_hex_click_count = 0 # 清零
self.radiobutton_sen_ascii_click_count += 1 # 单击一次次数+1
self.serial_sen_hex_bzw = False # 设置HEX标志位为False
if not self.serial_sen_hex_bzw and self.radiobutton_sen_ascii_click_count == 1:
self.send_text.unbind('<Key>')
self.send_text.unbind('<BackSpace>')
self.send_text.unbind('<Control--V>')
self.send_text.unbind('<Control--v>')
self.send_text.unbind('<Control--C>')
self.send_text.unbind('<Control--c>')
self.send_text.config(state=NORMAL)
send_content = self.send_text.get(1.0,'end').strip() # 读取输入文本框中的内容
send_content = ''.join(send_content.split()) # 将16进制的文本去掉空格
'''实现输入的数据个数不是偶数时，对不成对的数据用0进行补位'''
if len(send_content) % 2 == 0:
send_content = [send_content[x * 2:x * 2 + 2] for x in range(len(send_content)//2)] # 将内容分成2个字符的数组，如：['01','02']
else:
temp = send_content
send_content = [send_content[x * 2:x * 2 + 2] for x in range(len(send_content) // 2)]
send_content.append(temp[-1].zfill(2)) # 在最后一位前面补0
send_content = ''.join(send_content)
send_content = [send_content[x * 2:x * 2 + 2] for x in range(len(send_content) // 2)] # 将内容分成2个字符的数组，如：['01','02']
print(send_content, 'send_content')
send_content = ''.join([chr(int(x,16)) for x in send_content]) # 将上面的数组中的每个元素转换成ASCII格式
self.clear_text(self.send_text) # 清空输入文本框内容
self.send_text.insert('end',send_content.encode()) # 将转换好的内容插入到文本框中
'''将发送文本框中的内容以HEX方式显示'''
def sen_hex_set(self):
self.radiobutton_sen_ascii_click_count = 0 # 清零
self.radiobutton_sen_hex_click_count += 1 # 单击一次次数+1
self.serial_sen_hex_bzw = True # 设置HEX标志位为True
if self.serial_sen_hex_bzw and self.radiobutton_sen_hex_click_count == 1:
self.send_text.bind('<Key>',self.key_callback)
self.send_text.bind('<BackSpace>',self.key_backspace_control_v_callback)
self.send_text.bind('<Control--V>',self.key_backspace_control_v_callback)
self.send_text.bind('<Control--v>', self.key_backspace_control_v_callback)
self.send_text.bind('<Control--C>',self.key_backspace_control_v_callback)
self.send_text.bind('<Control--c>', self.key_backspace_control_v_callback)
send_content = self.send_text.get(1.0, 'end').strip() # 读取输入文本框中的内容
# send_content = ''.join(send_content.split()) # 将16进制的文本去掉空格
send_content = send_content.encode().hex() # 将输入框中的内容转换成16进制
send_content = ''.join([send_content[x * 2:x * 2 + 2] for x in range(len(send_content) // 2)]) # 转换成16进制的数据进行格式化
print(send_content, '+++++++++++++++')
self.clear_text(self.send_text) # 清空原来的输入框内容
self.send_text.insert('end', send_content.encode().upper()) # 将转换好的内容插入到文本框中
'''backspace、control-v、control-c键盘事件回调函数'''
def key_backspace_control_v_callback(self,event):
self.send_text.config(state=NORMAL)
'''发送框绑定键盘事件回调函数'''
def key_callback(self,event):
if event.char not in 'abcdefABCDEF0123456789 ':
self.send_text.config(state=DISABLED)
else:
self.send_text.config(state=NORMAL)
'''类方法：读取串口内容'''
def serial_read_content(self):
try:
'''判断显示方式，self.serial_hex_bzw = True时为16进制显示，self.serial_hex_bzw=False时为ascii显示'''
if self.serial_res_hex_bzw:
time_str = time.strftime('[%Y-%m-%d %H:%M:%S]') + '-->HEX\r\n'
data_res_sum = self.ser.inWaiting() # 读取输入缓存中有多少个字节数据
if data_res_sum:
text_content = self.ser.read(data_res_sum).hex() # 将缓存中的数据读取出来
text_content = ' '.join([text_content[x*2:x*2+2] for x in range(len(text_content)//2)]).upper() # 转换成16进制的数据进行格式化,带空格
print(text_content,'转换格式之后的文本')
else:
time_str = time.strftime('[%Y-%m-%d %H:%M:%S]') + '-->ASCII\r\n'
data_res_sum = self.ser.inWaiting() # 读取输入缓存中有多少个字节数据
if data_res_sum:
text_content = self.ser.read(data_res_sum).decode(encoding='utf-8',
errors='replace') # 将缓存中的数据读取出来
print('---------------------{}'.format(data_res_sum), text_content)
time.sleep(0.5)
if text_content:
# print('sssssss')
self.result_text.config(state=NORMAL) # 打开文本框输入
self.result_text.tag_config('text_head_tag', foreground='blue') # 设置插入文本样式
self.result_text.tag_config('text_tag',foreground='green') # 设置插入文本样式
self.result_text.insert('end','\r\n' + time_str + '\r\n','text_head_tag') # 在文本框中插入数据
self.result_text.insert('end',text_content + '\r\n','text_tag') # 在文本框中插入数据
self.result_text.config(state=DISABLED) # 禁止文本框输入
self.result_text.see(END) # 文本框总是显示最新内容
text_content = ''
except Exception:
print('F**k you!')
'''运行软件'''
def run(self):
self.serial_config_frame()
self.text_res_config()
self.text_sen_config()
self.root.mainloop()
class App:
def __init__(self):
self.root = Tk()
self.s = Style()
self.fr = Frame(self.root)
self.fr.grid(sticky='nsew')
self.img = PhotoImage("frameBorder", data="""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""")
self.img1 = PhotoImage("frameFocusBorder", data="""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""")
self.s.element_create("RoundedFrame", "image", "frameBorder",
("focus", "frameFocusBorder"), border=16, sticky="nsew")
self.s.layout("RoundedFrame", [("RoundedFrame", {"sticky": "nsew"})])
self.build()
def build(self):
self.rbs = []
self.rbs1 = []
self.lF0 = lF0 = LabelFrame(self.fr, text='Widget and Themes')
lF0.grid(row=0, column=0, sticky='nw')
self.fr1 = fr1 = Frame(lF0)
fr1.grid(row=0, column=0, sticky='nw')
# create check box to select reverse selection order
self.lF12 = lF12 = LabelFrame(fr1, text='Select Widget before Theme')
lF12.grid(row=0, column=0, sticky='nw')
self.ord = ord = IntVar()
ord.set(0)
cbut3 = Checkbutton(lF12, text='Reverse selection order', variable=ord,
command=self.selord)
cbut3.grid(row=0, column=0, padx=5, pady=5)
cbut3.state(['!selected'])
# create a Combobox to choose widgets
widget_sel = ['Button', 'Checkbutton', 'Combobox', 'Entry', 'Frame',
'Label', 'LabelFrame', 'Menubutton', 'Notebook',
'PanedWindow', 'Progressbar', 'Radiobutton', 'Scale',
'Scrollbar', 'Separator', 'Sizegrip', 'Treeview']
ord = self.ord
self.lf6 = LabelFrame(self.fr1, text='Select Widget', style="RoundedFrame",
padding=(10,1,10,10))
self.lf6.grid(row=1, column=0, sticky='nw')
self.lf6.state([("focus" if self.ord.get() == 0 else "!focus")])
self.widget_value = StringVar()
self.cb = Combobox(self.lf6, values=widget_sel,
textvariable=self.widget_value,
state= ('disabled' if self.ord.get()==1 else 'active'))
self.cb.grid(row=0, column=0, padx=5, pady=5, sticky='nw')
self.cb.bind('<<ComboboxSelected>>', self.enabled)
# create a Radio Buttons to choose orientation
fr2 = Frame(self.lF0)
fr2.grid(row=0, column=1, sticky='nw')
self.lF5 = lF5 = LabelFrame(fr2, style="RoundedFrame", padding=(10,1,10,10),
text='Orientation of \nProgressbar \nScale \nScrollbar')
lF5.grid(row=0, column=0, padx=5, pady=5, sticky='nw')
self.orient = StringVar()
orientT = ['Horizontal', 'Vertical']
for ix, val in enumerate(orientT):
rb = Radiobutton(lF5, text=val, value=val, command=self.orient_command,
variable=self.orient, state='disabled')
rb.grid(row=ix, column=0, sticky='w')
self.rbs.append(rb)
# create Radio Buttons to choose themes
themes = {"alt": "alt - standard",
"clam": "clam - standard", "classic": "classic - standard",
"default": "default - standard"}
self.lF1 = LabelFrame(self.fr1, text='Select Theme', style="RoundedFrame",
padding=(10,1,10,10))
self.lF1.grid(row=2, column=0, sticky='n')
self.theme_value = StringVar()
for ix, val in enumerate(themes):
rb1 = Radiobutton(self.lF1, text=themes[val], value=val,
state='disabled', variable=self.theme_value, command=self.theme_command)
rb1.grid(row=ix, column=0, padx=10, sticky='nw')
self.rbs1.append(rb1)
def enabled(self, event):
# from widget selection
self.lf6.state(["!focus"])
if self.ord.get() == 0:
if self.widget_value.get() in ('Progressbar', 'Scale', 'Scrollbar'):
self.lF5.state(["focus"])
for opt in self.rbs:
opt.state(['!disabled'])
for opt in self.rbs1:
opt.state(['disabled'])
else:
for opt in self.rbs1:
opt.state(['!disabled'])
self.lF1.state(["focus"])
self.lF1['text'] = 'Select Theme'
self.theme_value.set(None)
if self.ord.get() == 1:
self.lf6['text'] = 'Widget'
if self.widget_value.get() in ('Progressbar', 'Scale', 'Scrollbar'):
self.lF5.state(["focus"])
for opt in self.rbs:
opt.state(['!disabled'])
def orient_command(self):
# from orient selection
self.lF5.state(["!focus"])
if self.ord.get() == 0:
try:
for opt in self.rbs1:
opt.state(['!disabled'])
self.lF1.state(["focus"])
self.theme_value.set(None)
self.lF1['text'] = 'Select Theme'
except (NameError, AttributeError):
pass
def theme_command(self):
# from theme selection
self.s.theme_use(self.theme_value.get())
self.lF1.state(["!focus"])
if self.ord.get() == 0:
self.lF1['text'] = 'Theme'
if self.ord.get() == 1:
self.cb.state(['!disabled'])
self.lF1['text'] = 'Theme'
self.lf6.state(["focus"])
def selord(self):
# from select ord
if self.ord.get() == 0:
self.lf6.state(["focus"])
self.lF12['text'] = 'Select widget before theme'
self.theme_value.set(None)
self.orient.set(None)
self.cb.set('')
self.lF1.state(["!focus"])
self.lF5.state(["!focus"])
if self.ord.get() == 1:
self.lF12['text'] = 'Select theme before widget'
self.cb.state(['disabled'])
for opt in self.rbs1:
opt.state(['!disabled'])
self.lF1.state(["focus"])
self.theme_value.set(None)
self.orient.set(None)
self.cb.set('')
self.lf6.state(["!focus"])
self.lF5.state(["!focus"])
class DatabaseContent:
def __init__(self, root):
self.master = Frame(master=root)
self.labelframe = None
self.btn = None
self.db_max = None
self.db_min = None
self.db_current = None
self.text_field = None
self.field_width = 40
self.field_height = 10
self.data_ing = DataProcessing()
self.db = DB()
self.config_file = './res/config/dbconfig.ini'
def on_create_labelframe(self, name, col, row, px, py, pos):
self.labelframe = LabelFrame(master=self.master, text=name)
self.labelframe.grid(column=col, row=row, padx=px, pady=py, sticky=pos)
def add_btn(self, col, row, colpad, rowpad):
self.btn = sbutton(root=self.labelframe).get_btn()
self.btn.configure(text='Load Content')
self.btn.configure(command=self.on_writing_in_the_field)
MessageTip(gui=self.btn, msg='Click here to pull the db')
self.btn.grid(column=col, row=row, padx=rowpad, pady=colpad, sticky='W')
def on_create_label(self, label_name, col, row, colpad, rowpad, pos):
lab = Label(master=self.labelframe, text=label_name)
lab.grid(column=col, row=row, padx=colpad, pady=rowpad, sticky=pos)
def on_create_field(self, col, row, px, py, cspan):
self.text_field = scrollT(master=self.labelframe, width=self.field_width, height=self.field_height, wrap=WORD)
self.text_field.grid(column=col, row=row, padx=px, pady=py, columnspan=cspan)
def on_writing_in_the_field(self):
if self.btn['text'] == 'Load Content':
self.btn.configure(text='Loading...')
self.btn.configure(bg='#ffa500')
print(self.btn['text'], self.btn['state'])
self.write_all()
time.sleep(.5)
self.btn.configure(text='Load Content')
self.btn.configure(bg='#00bfff')
def format_date(self, d):
return d.strftime('%Y %b %d')
def write_all(self):
print('Inhalt der Datenbank( aktuell ): \n')
self.text_field.get(1.0, END)
print('Inhalt nicht leer, wird gelöscht...')
self.text_field.delete(1.0, END)
connection = self.db.in_connecting(self.config_file)
df = self.db.read_db_content(connection)
id = df['id'].values
strom = df['strom'].values
datum = df['datum'].values
m = df.min()
print("MIN IN DF: ", m['strom'], " date: ", m['datum'])
print("STATISTIK:")
self.print_db_stats(df)
for i, s, d in zip(id, strom, datum):
self.text_field.insert(INSERT, ' ' + str(i) + '\t\t' + str(s) + "\t " + str(
self.format_date(d)) + '\n')
print(i, "\t", s, "\t", d)
time.sleep(.2)
def print_db_stats(self, df):
new_df = self.data_ing.on_getting_data_from_server(df)
min, max, current = new_df.min(), new_df.max(), self.data_ing.select_current_value(new_df)
df_min = new_df[new_df['strom'] == min['strom']]
df_max = new_df[new_df['strom'] == max['strom']]
text1 = ' {} Watt \t\t Datum: {}, den {} {} {}'.format(df_min['strom'][0], df_min['wochentag'][0],
df_min['tag'][0], df_min.index[0].strftime('%b'),
df_min['jahr'][0])
text2 = ' {} Watt \t\t Datum: {}, den {} {} {}'.format(df_max['strom'][0], df_max['wochentag'][0],
df_max['tag'][0], df_max.index[0].strftime('%b'),
df_max['jahr'][0])
text3 = ' {} Watt \t\t Datum: {}, den {} {} {}'.format(current['strom'][0], current['wochentag'][0],
current['tag'][0], current.index[0].strftime('%b'),
current['jahr'][0])
self.db_min = Label(master=self.labelframe, text=text1)
self.db_min.grid(column=3, row=0, padx=8, pady=8, sticky='N', columnspan=3)
self.db_max = Label(master=self.labelframe, text=text2)
self.db_max.grid(column=3, row=1, padx=8, pady=8, sticky='N', columnspan=3)
self.db_current = Label(master=self.labelframe, text=text3)
self.db_current.grid(column=3, row=2, padx=8, pady=8, sticky='N', columnspan=3)
add_item_btn.grid(row=0, column=0, sticky="we", padx=10, pady=5)
remove_item_btn = Button(button_frame, text="Remove item", command=remove_item)
remove_item_btn.grid(row=0, column=1, sticky="we", padx=10, pady=5)
update_item_btn = Button(button_frame, text="Update item", command=update_item)
update_item_btn.grid(row=0, column=2, sticky="we", padx=10, pady=5)
clear_item_btn = Button(button_frame, text="Clear Input", command=clear_input)
clear_item_btn.grid(row=0, column=3, sticky="we", padx=10, pady=5)
export_to_excel_btn = Button(
button_frame, text="Export To Excel", command=export_to_excel
)
export_to_excel_btn.grid(row=0, column=4, sticky="we", padx=10, pady=5)
entry_frame.grid(row=0, column=0, sticky="we", padx=10, pady=5)
button_frame.grid(row=1, column=0, sticky="we", padx=10, pady=5)
button_frame.grid_columnconfigure(0, weight=1)
button_frame.grid_columnconfigure(1, weight=1)
button_frame.grid_columnconfigure(2, weight=1)
button_frame.grid_columnconfigure(3, weight=1)
button_frame.grid_columnconfigure(4, weight=1)
listing_frame.grid(row=2, column=0, sticky="we", padx=10)
listing_frame.grid_columnconfigure(0, weight=2)
populate_list()
root.mainloop()
def build(self):
"""widget construction"""
lf1 = LabelFrame(self.fr0, text='rgb')
lf1.grid(column=0, row=0, sticky='new')
lf1.columnconfigure(1, weight=1)
vcmdsb = root.register(sb_okay)
self.rgbcans = []
rgbsboxes = []
rgbcomps = ['r', 'g', 'b', 'a']
rgbnames = ['red ', 'green', 'blue ', 'alpha']
rgbvars = [self.rvar, self.gvar, self.bvar, self.avar]
rgbhandles = [
self.rgbhandle, self.rgbhandle, self.rgbhandle, self.ahandle
]
binds = [self.checksb, self.checksb, self.checksb, self.checksba]
for ix, comp in enumerate(rgbcomps):
Label(lf1, text=rgbnames[ix]).grid(row=3 * ix, column=0)
Label(lf1).grid(row=2 + 3 * ix, column=2)
self.rgbcans.append(
Canvas(lf1,
height=self.canvas_h,
width=self.canvas_w,
bd=0,
highlightthickness=0))
self.rgbcans[ix].grid(row=3 * ix,
column=1,
sticky='ew',
padx=self.sliderlength // 2)
self.rgbcans[ix].bind("<Configure>",
partial(self.resize, can=self.rgbcans[ix]))
TtkScale(lf1,
self.scale_l,
from_=0,
to=255,
variable=rgbvars[ix],
orient='horizontal',
command=rgbhandles[ix],
tickinterval=20).grid(row=1 + 3 * ix,
column=1,
sticky='new')
rgbsboxes.append(
Spinbox(lf1,
from_=0,
to=255,
textvariable=rgbvars[ix],
validate='key',
validatecommand=(vcmdsb, '%d', '%P', '%S', 0, 255),
command=rgbhandles[ix],
width=5))
rgbsboxes[ix].grid(row=1 + 3 * ix, column=2, sticky='nw')
rgbsboxes[ix].bind('<KeyRelease>', binds[ix])
lf3 = LabelFrame(self.fr0, text='colour mix')
lf3.grid(column=1, row=0, sticky='nw')
self.cmcan = cmcan = Canvas(lf3,
width=30,
height=30,
bd=0,
highlightthickness=0)
cmcan.grid(column=0, row=0, sticky='n', columnspan=2)
cmcan.grid_propagate(0)
vdraw_gradient(self.cmcan, (255, 0, 0), alpha=255)
cml = Label(lf3, text='hash\nvalue')
cml.grid(column=0, row=1)
vcmd = root.register(is_okay)
self.en = en = Entry(lf3,
width=8,
validate='key',
validatecommand=(vcmd, '%i', '%P', '%S'),
textvariable=self.evar)
en.grid(column=1, row=1)
en.bind('<KeyRelease>', self.checkhash)
lf5 = LabelFrame(lf3,
text='related colours') # style='Width.Tlabelframe'
lf5.grid(column=0, row=2, sticky='nw', columnspan=2)
self.rcls = []
self.rccans = []
relateds = [0, 20, 40, 60, 80, 100]
rtexts = ['0% Y', '20% Y', '40% Y', '60% Y', '80% Y', '100% Y']
for ix, rel in enumerate(relateds):
Label(lf5, text=rtexts[ix]).grid(row=1 + 2 * ix,
column=0,
sticky='n')
self.rcls.append(Label(lf5))
self.rcls[ix].grid(row=1 + 2 * ix, column=1, sticky='n')
self.rccans.append(
Canvas(lf5, width=30, height=30, bd=0, highlightthickness=0))
self.rccans[ix].grid(row=2 * ix,
column=0,
sticky='n',
columnspan=2)
self.cccan = Canvas(lf5,
width=30,
height=30,
bd=0,
highlightthickness=0)
self.cccan.grid(column=0, row=12, sticky='n', columnspan=2)
self.ccla = Label(lf5, text="comp'y")
self.ccla.grid(column=0, row=13, sticky='n')
self.ccl = Label(lf5, text="")
self.ccl.grid(column=1, row=13, sticky='n')
draw_gradient(self.rgbcans[0], (0, 0, 0), (255, 0, 0),
width=self.canvas_w)
draw_gradient(self.rgbcans[1], (255, 0, 0), (255, 255, 0),
width=self.canvas_w)
draw_gradient(self.rgbcans[2], (255, 0, 0), (255, 0, 255),
width=self.canvas_w)
draw_agradient(self.rgbcans[3], (127, 127, 127), (255, 0, 0),
width=self.canvas_w)
lf4 = LabelFrame(self.fr0, text='yiq')
lf4.grid(column=2, row=0, sticky='ew')
lf4.columnconfigure(1, weight=1)
vcmdyiq = root.register(yiq_okay)
self.cans = []
sboxes = []
comps = ['y', 'i', 'q']
names = ['luma', 'i hue', 'q hue']
tkvars = [self.yvar, self.ivar, self.qvar]
handles = [self.yhandle, self.iqhandle, self.iqhandle]
froms = [0, -100, -100]
ticks = [10, 20, 20]
for ix, comp in enumerate(comps):
Label(lf4, text=names[ix]).grid(row=3 * ix, column=0)
Label(lf4).grid(row=2 + 3 * ix, column=2)
self.cans.append(
Canvas(lf4,
width=self.canvas_w,
height=self.canvas_h,
bd=0,
highlightthickness=0))
self.cans[ix].grid(row=3 * ix,
column=1,
sticky='ew',
padx=self.sliderlength // 2)
self.cans[ix].bind("<Configure>",
partial(self.resize_yiq, can=self.cans[ix]))
TtkScale(lf4,
from_=froms[ix],
to=100,
variable=tkvars[ix],
orient='horizontal',
length=self.scale_l,
command=handles[ix],
tickinterval=ticks[ix]).grid(row=1 + 3 * ix,
column=1,
sticky='new')
sboxes.append(
Spinbox(lf4,
from_=froms[ix],
to=100,
textvariable=tkvars[ix],
validatecommand=(vcmdyiq, '%d', '%P', '%S', froms[ix],
100),
validate='key',
command=handles[ix],
width=5,
increment=1))
sboxes[ix].grid(row=1 + 3 * ix, column=2, sticky='nw')
sboxes[ix].bind('<KeyRelease>', self.checksyiq)
# assume initial setting 30,100.0,40.56 yiq
to_colour = yiq_to_rgb(*(30, 100.0, 40.56))
# print(self.canvas_w)
draw_gradient(self.cans[0],
yiq_to_rgb(0.0, 100.0, 40.56),
yiq_to_rgb(100, 100, 40.56),
width=self.canvas_w)
draw_gradient(self.cans[1],
yiq_to_rgb(30, -100.0, 40.56),
to_colour,
width=self.canvas_w)
draw_gradient(self.cans[2],
yiq_to_rgb(30, 100, -100),
yiq_to_rgb(30, 100, 100),
width=self.canvas_w)
self.related(30, 100.0, 40.56)
self.canYiq = canYiq = Canvas(lf4, width=self.space, height=self.space)
canYiq.grid(column=0, row=9, columnspan=3, pady=25, sticky='n')
self.yiqGamut = PhotoImage(file='../../figures/colour_space.png')
canYiq.create_image(0, 0, anchor='nw', image=self.yiqGamut)
self.ring = circle(canYiq,
300.0,
210.84,
self.ring_radius,
width=self.ring_width,
activeoutline='#555555',
tags='ring')
canYiq.bind('<Button-1>', self.move_ring)
canYiq.tag_bind('ring', '<B1-Motion>', self.move_ring)
def create_main_frame(self):
"""
Large function creating all the basic elements of the main app frame.
Creates the treeview and associated buttons, the scoring plugin frame
and the go button.
"""
# Frame for the Treeview and New/Edit/Delete buttons
main = Frame(self, padding=(3, 3, 12, 12))
main.rowconfigure(0, weight=1)
main.columnconfigure(0, weight=1)
main.columnconfigure(1, weight=0)
main.grid(row=0, column=0, sticky="nsew")
# ------------------------------------------------------- #
# Frame for the Treeview and its scrollbars
tree_frame = Frame(main, padding=(3, 3, 12, 12))
tree_frame.rowconfigure(0, weight=1)
tree_frame.rowconfigure(1, weight=0)
tree_frame.columnconfigure(0, weight=1)
tree_frame.columnconfigure(1, weight=0)
tree_frame.grid(row=0, column=0, sticky="nsew")
# ------------------------------------------------------- #
# Treeview with column headings
self.treeview = Treeview(tree_frame)
self.treeview["columns"] = ("class", "barcodes", "variants")
self.treeview.column("class", width=120)
self.treeview.heading("class", text="Type")
self.treeview.column("barcodes",
width=25,
stretch=tk.NO,
anchor=tk.CENTER)
self.treeview.heading("barcodes", text="BC")
self.treeview.column("variants",
width=25,
stretch=tk.NO,
anchor=tk.CENTER)
self.treeview.heading("variants", text="V")
self.treeview.grid(row=0, column=0, sticky="nsew")
# Treeview context menu bindings
self.treeview.bind("<Button-2>", self.treeview_context_menu)
# Treeview scrollbars
tree_ysb = tk.Scrollbar(tree_frame,
orient="vertical",
command=self.treeview.yview)
tree_xsb = tk.Scrollbar(tree_frame,
orient="horizontal",
command=self.treeview.xview)
tree_ysb.grid(row=0, column=1, sticky="nsw")
tree_xsb.grid(row=1, column=0, sticky="ewn")
self.treeview.config(yscroll=tree_ysb.set, xscroll=tree_xsb.set)
# ------------------------------------------------------- #
# Frame for New/Edit/Delete buttons
button_frame = Frame(main, padding=(3, 3, 12, 12))
button_frame.grid(row=1, column=0)
new_button = Button(button_frame,
text="New...",
command=self.new_button_press)
new_button.grid(row=0, column=0)
edit_button = Button(button_frame,
text="Edit...",
command=self.edit_button_press)
edit_button.grid(row=0, column=1)
delete_button = Button(button_frame,
text="Delete",
command=self.delete_button_press)
delete_button.grid(row=0, column=2)
self.treeview_buttons = [new_button, delete_button, edit_button]
# ------------------------------------------------------- #
# Frame for Plugin and Analysis Options
right_frame = Frame(main, padding=(3, 3, 12, 12))
right_frame.rowconfigure(0, weight=1)
right_frame.rowconfigure(1, weight=0)
right_frame.columnconfigure(0, weight=1)
right_frame.columnconfigure(1, weight=0)
right_frame.grid(row=0, column=1, sticky="new")
# ------------------------------------------------------- #
# LabelFrame for plugin and options
scoring_plugin = ScorerScriptsDropDown(right_frame,
text="Scoring Options",
padding=(3, 3, 12, 12))
scoring_plugin.grid(row=0, column=0, sticky="new")
self.scorer_widget = scoring_plugin
# ------------------------------------------------------- #
# LabelFrame for Analysis Options
row = 0
options_frame = LabelFrame(right_frame,
text="Analysis Options",
padding=(3, 3, 12, 12))
options_frame.grid(row=1, column=0, sticky="new", pady=4)
# force recalculate
force_recalculate = Checkbutton(options_frame,
text="Force Recalculation",
variable=self.force_recalculate)
force_recalculate.grid(column=0, row=row, sticky="w")
row += 1
# component outliers
component_outliers = Checkbutton(
options_frame,
text="Component Outlier Statistics",
variable=self.component_outliers,
)
component_outliers.grid(column=0, row=row, sticky="w")
row += 1
# write tsv
tsv_requested = Checkbutton(options_frame,
text="Write TSV Files",
variable=self.tsv_requested)
tsv_requested.grid(column=0, row=row, sticky="w")
tsv_requested.invoke()
row += 1
# ------------------------------------------------------- #
# Run Analysis button frame
go_button_frame = Frame(main, padding=(3, 3, 12, 12))
go_button_frame.grid(row=1, column=1)
go_button = Button(go_button_frame,
text="Run Analysis",
command=self.go_button_press)
go_button.grid(column=0, row=0)
self.go_button = go_button
class ChIPSeqFrame(PipelineFrame):
def __init__(self, pipepanel, pipeline_name, *args, **kwargs):
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.info = None
eframe = self.eframe = LabelFrame(self, text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid(row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5)
label = Label(eframe,
text="Pipeline") #,fg=textLightColor,bg=baseColor)
label.grid(row=3, column=0, sticky=W, padx=10, pady=5)
Pipelines = ["ChIPSeq"]
Pipeline = self.Pipeline = StringVar()
Pipeline.set(Pipelines[0])
om = OptionMenu(eframe,
Pipeline,
*Pipelines,
command=self.option_controller)
om.config() #bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config() #bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3, column=1, sticky=W, padx=10, pady=5)
label.grid(row=6, column=0, columnspan=5, sticky=W, padx=10, pady=5)
self.add_info(eframe)
'''
def set_data_directory( self ):
fname = askdirectory( initialdir = USER_HOME,
title="Select Data Directory")
self.datapath.set(fname)
#count number
self.data_count['text'] = str(
len([fn for fn in listdir(fname) if fn.endswith(filetype) or fn.endswith('.fastq')] )
)
print( "Found", self.data_count['text'], filetype, "files!" )
'''
def add_info(self, parent):
if not self.info:
self.info = LabelFrame(parent, text='Peak Call Info')
self.info_text = Text(
self.info,
width=50,
height=8,
#bg=projectBgColor,
#fg=projectFgColor,
font=("nimbus mono bold", "11"))
self.info_save_button = Button(self.info,
text="Save",
command=self.writeinfo)
self.info_load_button = Button(self.info,
text="Load",
command=self.readinfo)
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
self.info_load_button.grid(row=5, column=5, padx=10, pady=5)
self.info_save_button.grid(row=5, column=6, padx=10, pady=5)
self.info_text.grid(row=1,
rowspan=3,
column=1,
columnspan=7,
padx=5,
pady=5)
self.info.grid(row=7,
column=0,
columnspan=6,
sticky=W,
padx=20,
pady=10)
def writeinfo(self):
self.writepaste('peakcallinfo.csv', self.info_text)
def readinfo(self):
self.readpaste('peakcallinfo.csv', self.info_text)
def readData_createWindow(self):
try:
filename = filedialog.askopenfilename()
f = open(filename, "rb")
self.set_header(self.header_bool)
# f = 'http://archive.ics.uci.edu/ml/machine-learning-databases/iris/iris.data'
header = self.header_bool.get() == 1
self.data = pd.read_csv(f, header=0 if header else None, sep=',')
if not header:
self.data.columns = [
'var' + str(i) for i in range(len(self.data.columns))
]
except AttributeError:
pass
except Exception as e:
return showerror("Error", "Data could not be loaded! Make sure the data is " \
+ "formated in a similar way as the sample data: {}.".format(e))
self.cols = self.data.columns
self.setUpData()
self.bools = [
] # variables for columns: first axis: which col; second axis: what type
height = min(5, self.data.shape[0])
width = len(self.cols)
# data frame
data_frame = LabelFrame(self.master, text="Data Summary", relief=RIDGE)
data_frame.grid(row=0,
column=0,
columnspan=5,
sticky="EWNS",
padx=15,
pady=7.5)
data_size = "Data size is {} kilobytes. " \
.format(np.round(self.data.memory_usage(deep=False).sum() / 1000, 2))
cols_rows = "The number of columns is {} and the number of rows is {}. " \
.format(self.data.shape[1], self.data.shape[0])
miss_data = "The data does have missing values." if self.data.isnull().values.any() \
else "The data does not have missing values."
Message(data_frame, text=data_size + cols_rows + miss_data, width=335) \
.grid(row=0, column=0, columnspan=width-1, rowspan=3, sticky='NW')
Button(data_frame, text="Data", width=13, command=self.show_data) \
.grid(row=0, column=4, columnspan=1, padx=4, pady=4)
Button(data_frame, text="Description", width=13, command=self.show_description) \
.grid(row=1, column=4, columnspan=1, padx=4, pady=0)
Button(data_frame, text="Pair Plot", width=13, command=self.pair_plot) \
.grid(row=2, column=4, columnspan=1, padx=4, pady=4)
# head frame
head_frame = LabelFrame(self.master, text="Head of data", relief=RIDGE)
head_frame.grid(row=5,
column=0,
columnspan=5,
sticky="EWNS",
padx=15,
pady=7.5)
for i in range(len(self.cols)):
self.bools.append(
self.initBools(5, trues=[0, 3] if i < width - 1 else [1, 3]))
table = CustomTable(main_window=self,
parent=head_frame,
dataframe=self.data.head(),
editable=False,
width=1,
height=120)
config.apply_options({'fontsize': 10}, table)
table.show()
# modeling frame
model_frame = LabelFrame(self.master, text="Modeling", relief=RIDGE)
model_frame.grid(row=height + 11,
column=0,
columnspan=5,
sticky="EWNS",
padx=15,
pady=7.5)
# train / test ratio
self.train_test_ratio = 1 / 3
self.train_test_ratio_str = StringVar(
self.master, value=str(np.round(self.train_test_ratio, 2)))
Button(model_frame, text="Shuffle Data", width=13, command=self.shuffle_data) \
.grid(row=0, column=0, columnspan=1)
Button(model_frame, text="TrainTest Ratio", width=13, command=self.set_traintest) \
.grid(row=0, column=2, columnspan=1)
Label(model_frame, textvariable=self.train_test_ratio_str) \
.grid(row=0, column=3, columnspan=1, sticky="E")
# model selection
ttk.Style().configure("TMenubutton", background="#E1E1E1")
self.model_btn = Menubutton(model_frame, text="Model", width=9)
self.set_model(self.model_btn)
self.model_btn.grid(row=1, column=0, columnspan=1, padx=0, pady=4)
Button(model_frame, text="Parameters", width=13, command=self.set_model_parameters) \
.grid(row=1, column=1, columnspan=1, padx=0, pady=4)
self.metric_btn = Menubutton(model_frame, text="Metric", width=9)
self.set_metric(self.metric_btn)
self.metric_btn.grid(row=1, column=2, columnspan=1, padx=0, pady=4)
# model training
self.score = -1
self.score_str = StringVar(self.master, value="")
Button(model_frame, text="Train Model", width=13, command=self.startModel) \
.grid(row=1, column=3, columnspan=width-1)
Label(model_frame, textvariable=self.score_str) \
.grid(row=3, columnspan=width, sticky='W')
# Export Frame
export_frame = LabelFrame(self.master, text="Save", relief=RIDGE)
export_frame.grid(row=height + 15,
column=0,
columnspan=5,
sticky="EWNS",
padx=15,
pady=7.5)
Button(export_frame, text="Export Data", width=13, command=self.export_data) \
.grid(row=0, column=0, columnspan=1, padx=4, pady=4)
Button(export_frame, text="Export Model", width=13, command=self.export_model) \
.grid(row=0, column=1, columnspan=1, padx=0, pady=4)
class scRNASeqFrame(PipelineFrame):
def __init__(self, pipepanel, pipeline_name, *args, **kwargs):
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.info = None
eframe = self.eframe = LabelFrame(self, text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid(row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5)
label = Label(eframe,
text="Pipeline") #,fg=textLightColor,bg=baseColor)
label.grid(row=3, column=0, sticky=W, padx=10, pady=5)
PipelineLabels = ["Initial QC", "Differential Expression"]
Pipelines = ["scrnaQC", "scrnaDE"]
self.label2pipeline = {k: v for k, v in zip(PipelineLabels, Pipelines)}
PipelineLabel = self.PipelineLabel = StringVar()
self.Pipeline = StringVar()
PipelineLabel.set(PipelineLabels[0])
om = OptionMenu(eframe,
PipelineLabel,
*PipelineLabels,
command=self.option_controller)
om.config() #bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config() #bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3, column=1, sticky=W, padx=10, pady=5)
######## QUALITY CONTROL/FILTERING/CLUSTERING ###############
self.qcOptions = qcOptions = LabelFrame(
eframe, text="QC, Filtering, and Initial Clustering")
#algorithm selection
self.clustAlg = clustAlg = StringVar()
clustAlgLabel = Label(qcOptions, text="Clustering Algorithm: ")
clustAlgDropdown = [
"SLM (Smart Local Moving)", "Louvain (Original)",
"Louvain (with Multilevel Refinement)"
]
clustAlg.set(clustAlgDropdown[0])
clustAlgOptMenu = OptionMenu(qcOptions, clustAlg, *clustAlgDropdown)
clustAlgLabel.grid(row=8, column=1, sticky=W, padx=10, pady=5)
clustAlgOptMenu.grid(row=8, column=2, sticky=W, padx=0, pady=5)
#clustering resolutions
self.resolution = resolution = StringVar()
resolution.set("0.4,0.6,0.8,1.0,1.2")
resolutionLabel = Label(
qcOptions, text="Clustering Resolution(s): \nSeparate with commas")
resolutionEntry = Entry(qcOptions,
bd=2,
width=25,
textvariable=resolution)
resolutionLabel.grid(row=9, column=1, sticky=W, padx=10, pady=5)
resolutionEntry.grid(row=9, column=2, sticky=W, padx=0, pady=5)
#annotation db: human: HPCA/BP Encode; mouse: immgen/mouseRNAseq
self.annotDB = annotDB = StringVar()
annotLabel = Label(qcOptions, text="Annotation database: ")
annotHuman = [
"Human Primary Cell Atlas", "Blueprint/ENCODE", "Monaco Immune",
"Database of Immune Cell Expression (DICE)"
]
annotMouse = ["ImmGen", "Mouse RNASeq"]
annotDropdown = []
genome = self.global_info.annotation.get()
if (genome == "GRCh38"):
annotDropdown = annotHuman.copy()
elif (genome == "mm10"):
annotDropdown = annotMouse.copy()
else:
annotDropdown.append("No genome selected")
annotDB.set(annotDropdown[0])
annotDB_om = OptionMenu(qcOptions, annotDB, *annotDropdown)
annotLabel.grid(row=10, column=1, sticky=W, padx=10, pady=5)
annotDB_om.grid(row=10, column=2, sticky=W, padx=0, pady=5)
self.citeseq = citeseq = StringVar()
citeseqLabel = Label(qcOptions, text="CITESeq Included: ")
citeseqDropdown = ["Yes", "No"]
citeseq.set(citeseqDropdown[1])
citeseqOptMenu = OptionMenu(qcOptions, citeseq, *citeseqDropdown)
citeseqLabel.grid(row=11, column=1, sticky=W, padx=10, pady=5)
citeseqOptMenu.grid(row=11, column=2, sticky=W, padx=0, pady=5)
#set groups, mostly for relabeling purposes
self.add_info(qcOptions) #Position 13
# self.option_controller()
# groups_buttonL = Label(qcOptions, text="Sample Information: ")
# groups_button = Button(qcOptions,
# text="Set Groups",
# command = self.popup_groups )
# groups_buttonL.grid(row=12,column=1,sticky=W,padx=10,pady=5)
# groups_button.grid(row=12,column=2,sticky=W,padx=0,pady=5)
#
#
######### DIFFERENTIAL EXPRESSION #########
self.deOptions = deOptions = LabelFrame(
eframe, text="Differential Gene Expression")
#option for which object to run DE on
self.rdsObject = rdsObject = StringVar()
rdsLabel = Label(deOptions,
text="Use the pre- or post-batch corrected data:")
rdsDropdown = [
"Merged (Pre-batch correction)",
"Integrated (Post-batch correction)", "Both"
]
rdsObject.set(rdsDropdown[2])
rdsOptMenu = OptionMenu(deOptions, rdsObject, *rdsDropdown)
rdsLabel.grid(row=8, column=1, sticky=W, padx=10, pady=5)
rdsOptMenu.grid(row=8, column=2, sticky=W, padx=0, pady=5)
#option for cluster resolution for DE
self.resolutionDE = resolutionDE = StringVar()
resolutionDE.set("0.4,0.6,0.8,1.0,1.2")
resolutionDELabel = Label(
deOptions,
text=
"Clustering Resolution: \nChoose a previous resolution or \nselect a new resolution to run"
)
resolutionDEEntry = Entry(deOptions,
bd=2,
width=25,
textvariable=resolutionDE)
resolutionDELabel.grid(row=9, column=1, sticky=W, padx=10, pady=5)
resolutionDEEntry.grid(row=9, column=2, sticky=W, padx=0, pady=5)
#options for difftest
self.testDE = testDE = StringVar()
testDELabel = Label(
deOptions, text="Statistical test for differential expression:")
testDEDropdown = [
"MAST", "DESeq2", "Likelihood Ratio", "Logistic regression",
"Negative Binomial", "Wilcoxon", "Student's T"
]
testDE.set(testDEDropdown[0])
testDEMenu = OptionMenu(deOptions, testDE, *testDEDropdown)
testDELabel.grid(row=10, column=1, sticky=W, padx=10, pady=5)
testDEMenu.grid(row=10, column=2, sticky=W, padx=0, pady=5)
#options for filters
self.deMinPct = deMinPct = StringVar()
deMinPctLabel = Label(
deOptions, text="Minimum fraction of cells expressing DE genes:")
deMinPct.set("0.1")
deMinPctEntry = Entry(deOptions, bd=2, width=10, textvariable=deMinPct)
deMinPctLabel.grid(row=11, column=1, sticky=W, padx=10, pady=5)
deMinPctEntry.grid(row=11, column=2, sticky=W, padx=0, pady=5)
self.deMinFC = deMinFC = StringVar()
deMinFCLabel = Label(deOptions,
text="Minimum fold change to report DE genes:")
deMinFC.set("0.25")
deMinFCEntry = Entry(deOptions, bd=2, width=10, textvariable=deMinFC)
deMinFCLabel.grid(row=12, column=1, sticky=W, padx=10, pady=5)
deMinFCEntry.grid(row=12, column=2, sticky=W, padx=0, pady=5)
#use groups and contrasts for differential expression, have options to create new groups
self.om_groups = LabelFrame(deOptions, text="Sample Information")
self.groups_button = Button(self.om_groups,
text="Set Groups",
command=self.popup_groups)
self.groups_button.grid(row=5, column=5, padx=10, pady=5)
self.contrasts_button = Button(self.om_groups,
text="Set Contrasts",
command=self.popup_groups)
self.contrasts_button.grid(row=5, column=6, padx=10, pady=5)
self.om_groups.grid(row=13,
column=0,
columnspan=6,
sticky=W,
padx=20,
pady=10)
#option for merged/integrated object
# self.integrateOption = integrateOption = StringVar()
# integrateLabel = Label(deOptions, text="Merged or Integrated (batch corrected): ")
# integrateDropdown = ["Merged","Integrated"]
# integrateOption.set(integrateDropdown[0])
# integrateOptMenu = OptionMenu(deOptions, integrateOption, *integrateDropdown)
# integrateLabel.grid(row=9,column=1,sticky=W,padx=10,pady=5)
# integrateOptMenu.grid(row=9,column=2,sticky=W,padx=0,pady=5)
self.option_controller()
### SUBFUNCTION FOR CREATING GROUPS.TAB AND CLUSTERS.TAB WINDOW ######
def add_info(self, parent):
if not self.info:
self.info = LabelFrame(parent, text="Sample Information")
self.groups_button = Button(self.info,
text="Set Groups",
command=self.popup_groups)
self.contrasts_button = Button(self.info,
text="Set Contrasts",
command=self.popup_contrasts)
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
self.groups_button.grid(row=5, column=5, padx=10, pady=5)
self.contrasts_button.grid(row=5, column=6, padx=10, pady=5)
self.info.grid(row=13,
column=0,
columnspan=6,
sticky=W,
padx=20,
pady=10)
def popup_groups(self):
self.popup_window("Groups Information", "groups.tab")
def popup_contrasts(self):
self.popup_window("Contrasts Information", "contrasts.tab")
def popup_window(self, text, filename):
top = Toplevel()
info = LabelFrame(top, text=text) #"Group Information")
info_text = Text(
info,
width=50,
height=8,
#bg=projectBgColor,
#fg=projectFgColor,
font=("nimbus mono bold", "11"))
def savefunc():
self.writepaste(filename, info_text)
def loadfunc():
self.readpaste(filename, info_text)
info_save_button = Button(info, text="Save", command=savefunc)
info_load_button = Button(info, text="Load", command=loadfunc)
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
info_load_button.grid(row=5, column=5, padx=10, pady=5)
info_save_button.grid(row=5, column=6, padx=10, pady=5)
info_text.grid(row=1,
rowspan=3,
column=1,
columnspan=7,
padx=5,
pady=5)
info.grid(row=7, column=0, columnspan=6, sticky=W, padx=20, pady=10)
top.focus_force()
def set_count_directory(self):
fname = askdirectory(initialdir=USER_HOME,
title="Select Data Directory")
self.countpath.set(fname)
def option_controller(self, *args, **kwargs):
PipelineFrame.option_controller(self)
self.Pipeline.set(self.label2pipeline[self.PipelineLabel.get()])
print(self.Pipeline.get())
if self.Pipeline.get() == 'scrnaQC':
self.deOptions.grid_forget()
self.qcOptions.grid(row=8,
column=0,
columnspan=6,
sticky=W,
padx=20,
pady=10)
elif self.Pipeline.get() == 'scrnaDE':
self.deOptions.grid(row=8,
column=0,
columnspan=4,
sticky=W,
padx=20,
pady=10)
self.qcOptions.grid_forget()
def makejson_wrapper(self, *args, **kwargs):
self.makejson(*args, **kwargs)
def makejson(self, *args):
###################################################### FROM RNASEQ.PY, NOT SURE WHAT ALL THIS DOES #############################3
#print(args[0])
caller = args[0]
#global PD
#global UnitsBak
#global RGbak
D = dict()
try:
F = open(self.workpath.get() + "/samples", "r")
f = F.read().split("\n")
F.close()
for line in f:
L = line.split()
a = L.pop(0)
D[a] = L
samples = D
except:
samples = {"na": "na"}
D = dict()
try:
F = open(self.workpath.get() + "/pairs", "r")
f = F.read().split()
F.close()
for i in range(0, len(f), 2):
# a=f[i].split(".")[0]
# b=f[i+1].split(".")[0]
a = f[i]
b = f[i + 1]
D[a + "+" + b] = [a, b]
pairs = D
except:
pairs = {"na": "na"}
D = dict()
try:
F = open(self.workpath.get() + "/contrasts.tab", "r")
# f=F.read().split('\n')
# F.close()
# D["rsamps"]=f[0].split()
# D["rgroups"]=f[1].split()
# D["rcontrasts"]=f[2].split()
# D["rlabels"]=f[3].split()
f = F.readlines()
F.close()
## sampl=[]
## grp=[]
cont = []
## lbl=[]
for x in f:
if len(x.split()) == 2:
cont.append(x.split()[0])
cont.append(x.split()[1])
D["rcontrasts"] = cont
# contrasts["rcontrasts"]=cont
contrasts = D
except:
contrasts = {"rcontrasts": "na"}
## contrasts={"rsamps":"na","rgroups":"na","rcontrasts":"na","rlabels":"na"}
##------
D = dict()
try:
F = open(self.workpath.get() + "/groups.tab", "r")
f = F.readlines()
F.close()
sampl = []
grp = []
# cont=[]
lbl = []
for x in f:
# if len(x.split()) == 4 or len(x.split()) == 3:
if len(x.split()) == 3:
sampl.append(x.split()[0])
grp.append(x.split()[1])
lbl.append(x.split()[2])
D["rsamps"] = sampl
D["rgroups"] = grp
D["rlabels"] = lbl
# D["rcontrasts"]="na"
# contrasts=D
groups = D
except:
# contrasts={"rsamps":"na","rgroups":"na","rcontrasts":"na","rlabels":"na"}
groups = {"rsamps": "na", "rgroups": "na", "rlabels": "na"}
##------
D = dict()
FT = filetype #.get()
# p = Popen("ls "+workpath.get()+"/*."+FT, shell=True, stdin=PIPE, stdout=PIPE, stderr=DEVNULL, close_fds=True)
p = Popen("find " + self.workpath.get() +
" -maxdepth 1 -type l -printf '%f\n' ",
shell=True,
stdin=PIPE,
stdout=PIPE,
stderr=DEVNULL,
close_fds=True)
a = p.stdout.read().decode(encoding='UTF-8').split("\n")
RG = dict()
b = a.pop()
# tkinter.messagebox.showerror("",a)
# if freezeunits.get()=="no":
for i in a:
key = re.sub(".realign", "", i.split("/")[-1])
key = re.sub(".bai", "", key)
key = re.sub(".bam", "", key)
key = re.sub(".sam", "", key)
key = re.sub(".recal", "", key)
key = re.sub(".dedup", "", key)
key = re.sub(".sorted", "", key)
key = re.sub(".fin", "", key)
key = re.sub("\.R[12]", "", key)
key = re.sub("_R[12]", "", key)
key = re.sub(".fastq", "", key)
key = re.sub(".gz", "", key)
# key=re.sub("[\._](R[12]\.)*"+FT+"$","",i.split("/")[-1])
# key=re.sub(".R[12]."+FT+"$","",i.split("/")[-1])
# key=re.sub("([._]R[12][._])*([fin|sorted|dedup|recal|realign])*\.{0}$".format(FT),"",i.split("/")[-1])
D[key] = key
RG[key] = {
'rgsm': key,
'rglb': 'na',
'rgpu': 'na',
'rgpl': 'ILLUMINA',
'rgcn': 'na'
}
units = D
UnitsBak = D
try:
F = open(self.workpath.get() + "/rg.tab", "r")
f = F.read().splitlines()
F.close()
for theLine in f:
if not re.match("^ID", theLine):
(rgid, rgsm, rglb, rgpl, rgpu, rgcn) = theLine.split("\t")
RG[rgid] = {
'rgsm': rgsm,
'rglb': rglb,
'rgpu': rgpu,
'rgpl': rgpl,
'rgcn': rgcn
}
except:
pass
RGbak = RG
# else:
# units=UnitsBak
# RG=RGbak
# ###########################################################################################################################
PD = dict()
smparams = []
algorithmDict = {
"Louvain (Original)": 1,
"Louvain (with Multilevel Refinement)": 2,
"SLM (Smart Local Moving)": 3
}
algorithm = algorithmDict[self.clustAlg.get()]
annotationDict = {
"Human Primary Cell Atlas": "HPCA",
"Blueprint/ENCODE": "BP_encode",
"Monaco Immune": "monaco",
"Database of Immune Cell Expression (DICE)": "dice",
"ImmGen": "immgen",
"Mouse RNASeq": "mouseRNAseq"
}
annotation = annotationDict[self.annotDB.get()]
resolutionStr = self.resolution.get()
resolutionStr = re.sub("\s", ",", resolutionStr) #remove whitespaces
resolutionStr = re.sub("[,]+", ",",
resolutionStr) #remove multiple commas
rdsDict = {
"Merged (Pre-batch correction)": "merged",
"Integrated (Post-batch correction)": "integrated",
"Both": "both"
}
rdsSelect = rdsDict[self.rdsObject.get()]
deResolutionStr = self.resolutionDE.get()
deResolutionStr = re.sub("\s", ",",
deResolutionStr) #remove whitespace
deResolutionStr = re.sub("[,]+", ",",
deResolutionStr) #remove multiple commas
deTestDict = {
"MAST": "MAST",
"DESeq2": "DESeq2",
"Likelihood Ratio": "bimod",
"Logistic regression": "LR",
"Negative Binomial": "negbinom",
"Wilcoxon": "wilcox",
"Student's T": "t"
}
testDESelect = deTestDict[self.testDE.get()]
for i in range(len(self.parameters)):
if cp[i].var.get() == "1":
smparams.append(parameters[i])
AD = eval(
open(join(PIPELINER_HOME,
self.annotation.get() + ".json"), "r").read())
gi = self.global_info
species = ""
if gi.annotation.get() == "GRCh38":
species = "human"
elif gi.annotation.get() == "mm10":
species = "mouse"
PD = {
'project': {
'pfamily': gi.pfamily.get(),
'units': units,
'samples': samples,
'pairs': pairs,
'id': gi.eprojectid.get(),
'pi': gi.epi.get(),
'organism': gi.eorganism.get(),
'analyst': gi.eanalyst.get(),
'poc': gi.epoc.get(),
'pipeline': self.Pipeline.get(),
'version': "4.0",
'annotation': gi.annotation.get(),
'datapath': self.datapath.get(),
'targetspath': self.targetspath.get(),
'filetype': filetype,
'binset': "standard-bin",
'username': gi.euser.get(),
'flowcellid': gi.eflowcell.get(),
'platform': gi.eplatform.get(),
'custom': customRules,
'efiletype': efiletype,
'workpath': self.workpath.get(),
'batchsize': batchsize,
"smparams": smparams,
"rgid": RG,
"cluster": "cluster_medium.json",
"description": gi.description.get('1.0', END),
"technique": gi.technique.get(),
"CLUSTALG": algorithm,
"ANNOTDB": annotation,
"CLUSTRESOLUTION": resolutionStr,
# "INTEGRATEDE": self.integrateOption.get(),
"SPECIES": species,
"CITESEQ": self.citeseq.get(),
# "CRID": self.scrCRID.get(),
# "EXPECTED": self.scrExpected.get(),
# "COUNTSPATH": self.countpath.get(),
# "MATTYPE": self.mattype.get(),
# "DOCYCLEREGRESS": self.docycleregress.get(),
# "RESOLUTION": self.scrRes.get(),
# "PCS": self.scrPCs.get(),
"FILEDE": rdsSelect,
"CLUSTERDE": deResolutionStr,
"TESTDE": testDESelect,
"DEMINPCT": self.deMinPct.get(),
"DEMINFC": self.deMinFC.get(),
"contrasts": contrasts,
"groups": groups
}
}
J = json.dumps(PD, sort_keys=True, indent=4, ensure_ascii=True)
gi.jsonconf.delete("1.0", END)
gi.jsonconf.insert(INSERT, J)
self.saveproject(gi.jsonconf.get("1.0", END))
class ExomeSeqFrame(PipelineFrame):
def __init__(self, pipepanel, pipeline_name, *args, **kwargs):
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.pairs = None
eframe = self.eframe = LabelFrame(self, text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid(row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5)
label = Label(eframe,
text="Pipeline") #,fg=textLightColor,bg=baseColor)
label.grid(row=3, column=0, sticky=W, padx=10, pady=5)
PipelineLabels = [
"Initial QC", "Germline", 'Somatic Tumor-Normal',
'Somatic Tumor-Only'
]
Pipelines = [
"initialqc", "exomeseq-germline", "exomeseq-somatic",
"exomeseq-somatic-tumoronly"
]
self.label2pipeline = {k: v for k, v in zip(PipelineLabels, Pipelines)}
Pipeline = self.Pipeline = StringVar()
PipelineLabel = self.PipelineLabel = StringVar()
self.Pipeline = StringVar()
PipelineLabel.set(PipelineLabels[0])
om = OptionMenu(eframe,
PipelineLabel,
*PipelineLabels,
command=self.option_controller)
#om.config()#bg = widgetBgColor,fg=widgetFgColor)
#om["menu"].config()#bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3, column=1, sticky=W, padx=10, pady=5)
targetsL = Label(eframe, text="Target Capture Kit")
#,fg=textLightColor,bg=baseColor)
targetsL.grid(row=5, column=0, sticky=W, padx=10, pady=5)
targetsE = Entry(eframe, textvariable=self.targetspath, width=50)
label_ref_text = "By default, the path to the Agilent SureSelect V7 targets file is filled in here"
if self.genome == "hg19":
self.targetspath.set(
"/data/CCBR_Pipeliner/db/PipeDB/lib/Agilent_SSv7_allExons_hg19.bed"
)
elif self.genome == "hg38":
self.targetspath.set(
"/data/CCBR_Pipeliner/db/PipeDB/lib/Agilent_SSv7_allExons_hg38.bed"
)
else:
self.targetspath.set(
"/data/CCBR_Pipeliner/db/PipeDB/lib/SureSelect_mm10.bed")
label_ref_text = "By default, the path to the Agilent SureSelect Mouse All Exon V1 targets file is filled in here"
targetsE.grid(row=5, column=1, columnspan=6, sticky=W, padx=10, pady=5)
self.targetspath.trace(
'w', lambda a, b, c, x="targetspath": self.makejson(x))
label = Label(eframe, text=label_ref_text)
label.grid(row=6, column=0, columnspan=5, sticky=W, padx=10, pady=5)
def option_controller(self, *args, **kwargs):
PipelineFrame.option_controller(self)
self.Pipeline.set(self.label2pipeline[self.PipelineLabel.get()])
print(self.Pipeline.get())
if self.Pipeline.get() == 'exomeseq-somatic':
self.add_pairs(self.eframe)
#self.dry_button.config( state="disabled" )
elif self.Pipeline.get() != 'exomeseq-somatic':
self.del_pairs(self.eframe)
#if self.workpath.get() :
# self.dry_button.config( state='active' )
def add_pairs(self, parent):
if not self.pairs:
self.pairs = LabelFrame(parent, text='Pairs')
self.pairs_text = Text(
self.pairs,
width=50,
height=8,
#bg=projectBgColor,
#fg=projectFgColor,
font=("nimbus mono bold", "11"))
self.pairs_save_button = Button(self.pairs,
text="Save",
command=self.writepair)
self.pairs_load_button = Button(self.pairs,
text="Load",
command=self.readpair)
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
self.pairs_load_button.grid(row=5, column=5, padx=10, pady=5)
self.pairs_save_button.grid(row=5, column=6, padx=10, pady=5)
self.pairs_text.grid(row=1,
rowspan=3,
column=1,
columnspan=7,
padx=5,
pady=5)
self.pairs.grid(row=7,
column=0,
columnspan=6,
sticky=W,
padx=20,
pady=10)
def del_pairs(self, parent):
if self.pairs:
self.pairs.grid_forget()
def writepair(self):
self.writepaste('pairs', self.pairs_text)
#self.dry_button.config( state='active' )
def readpair(self):
self.readpaste('pairs', self.pairs_text)
class MiRSeqFrame( PipelineFrame ) :
def __init__(self, pipepanel, pipeline_name, *args, **kwargs) :
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.info = None
eframe = self.eframe = LabelFrame(self,text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid( row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5 )
label = Label(eframe,text="Pipeline")#,fg=textLightColor,bg=baseColor)
label.grid(row=3,column=0,sticky=W,padx=10,pady=5)
Pipelines=["CAPmirseq-plus"]
Pipeline = self.Pipeline = StringVar()
Pipeline.set(Pipelines[0])
om = OptionMenu(eframe, Pipeline, *Pipelines, command=self.option_controller)
om.config()#bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config()#bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3,column=1,sticky=W,padx=10,pady=5)
self.add_info( eframe )
def add_info( self, parent ) :
if not self.info :
self.info = LabelFrame(parent, text="Sample Information")
self.groups_button = Button(self.info,
text="Set Groups",
command = self.popup_groups )
self.contrasts_button = Button(self.info,
text="Set Contrasts",
command = self.popup_contrasts )
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
self.groups_button.grid( row=5, column=5, padx=10, pady=5 )
self.contrasts_button.grid( row=5, column=6, padx=10, pady=5 )
self.info.grid(row=10,column=0, columnspan=6, sticky=W, padx=20, pady=10 )
def popup_groups( self ) :
self.popup_window( "Groups Information", "groups.tab" )
def popup_contrasts( self ) :
self.popup_window( "Contrasts Information", "contrasts.tab" )
def popup_window( self, text, filename ) :
top = Toplevel()
info = LabelFrame(top, text=text )#"Group Information")
info_text = Text(info,
width=50,
height=8,
#bg=projectBgColor,
#fg=projectFgColor,
font=("nimbus mono bold","11")
)
def savefunc() :
self.writepaste( filename, info_text )
def loadfunc() :
self.readpaste( filename, info_text )
info_save_button = Button(info,
text="Save",
command = savefunc )
info_load_button = Button(info,
text="Load",
command = loadfunc )
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
info_load_button.grid( row=5, column=5, padx=10, pady=5 )
info_save_button.grid( row=5, column=6, padx=10, pady=5 )
info_text.grid(row=1, rowspan=3,
column=1, columnspan=7,
padx=5, pady=5 )
info.grid(row=7,column=0, columnspan=6, sticky=W, padx=20, pady=10 )
top.focus_force()
def makejson(self, *args):
#print(args[0])
caller=args[0]
#global PD
#global UnitsBak
#global RGbak
D=dict()
try:
F=open(self.workpath.get()+"/samples","r")
f=F.read().split("\n")
F.close()
for line in f:
L=line.split()
a=L.pop(0)
D[a]=L
samples=D
except:
samples={"na":"na"}
D=dict()
try:
F=open(self.workpath.get()+"/pairs","r")
f=F.read().split()
F.close()
for i in range(0,len(f),2):
# a=f[i].split(".")[0]
# b=f[i+1].split(".")[0]
a=f[i]
b=f[i+1]
D[a+"+"+b]=[a,b]
pairs=D
except:
pairs={"na":"na"}
D=dict()
try:
F=open(self.workpath.get()+"/contrasts.tab","r")
# f=F.read().split('\n')
# F.close()
# D["rsamps"]=f[0].split()
# D["rgroups"]=f[1].split()
# D["rcontrasts"]=f[2].split()
# D["rlabels"]=f[3].split()
f=F.readlines()
F.close()
## sampl=[]
## grp=[]
cont=[]
## lbl=[]
for x in f:
if len(x.split()) == 2:
cont.append(x.split()[0])
cont.append(x.split()[1])
D["rcontrasts"]=cont
# contrasts["rcontrasts"]=cont
contrasts=D
except:
contrasts={"rcontrasts":"na"}
## contrasts={"rsamps":"na","rgroups":"na","rcontrasts":"na","rlabels":"na"}
##------
D=dict()
try:
F=open(self.workpath.get()+"/groups.tab","r")
f=F.readlines()
F.close()
sampl=[]
grp=[]
# cont=[]
lbl=[]
for x in f:
# if len(x.split()) == 4 or len(x.split()) == 3:
if len(x.split()) == 3:
sampl.append(x.split()[0])
grp.append(x.split()[1])
lbl.append(x.split()[2])
D["rsamps"]=sampl
D["rgroups"]=grp
D["rlabels"]=lbl
# D["rcontrasts"]="na"
# contrasts=D
groups=D
except:
# contrasts={"rsamps":"na","rgroups":"na","rcontrasts":"na","rlabels":"na"}
groups={"rsamps":"na","rgroups":"na","rlabels":"na"}
##------
D=dict()
FT = filetype#.get()
# p = Popen("ls "+workpath.get()+"/*."+FT, shell=True, stdin=PIPE, stdout=PIPE, stderr=DEVNULL, close_fds=True)
p = Popen("find "+self.workpath.get()+" -maxdepth 1 -type l -printf '%f\n' ", shell=True, stdin=PIPE, stdout=PIPE, stderr=DEVNULL, close_fds=True)
a = p.stdout.read().decode(encoding='UTF-8').split("\n")
RG=dict()
b=a.pop()
# tkinter.messagebox.showerror("",a)
# if freezeunits.get()=="no":
for i in a:
key=re.sub(".realign","",i.split("/")[-1])
key=re.sub(".bai","",key)
key=re.sub(".bam","",key)
key=re.sub(".sam","",key)
key=re.sub(".recal","",key)
key=re.sub(".dedup","",key)
key=re.sub(".sorted","",key)
key=re.sub(".fin","",key)
key=re.sub(".R[12]","",key)
key=re.sub("_R[12]","",key)
key=re.sub(".fastq","",key)
key=re.sub(".gz","",key)
# key=re.sub("[\._](R[12]\.)*"+FT+"$","",i.split("/")[-1])
# key=re.sub(".R[12]."+FT+"$","",i.split("/")[-1])
# key=re.sub("([._]R[12][._])*([fin|sorted|dedup|recal|realign])*\.{0}$".format(FT),"",i.split("/")[-1])
D[key]=key
RG[key]={'rgsm':key,'rglb':'na','rgpu':'na','rgpl':'ILLUMINA','rgcn':'na'}
units=D
UnitsBak=D
try:
F=open(self.workpath.get()+"/rg.tab","r")
f=F.read().splitlines()
F.close()
for theLine in f:
if not re.match("^ID",theLine):
(rgid,rgsm,rglb,rgpl,rgpu,rgcn)=theLine.split("\t")
RG[rgid]={'rgsm':rgsm,'rglb':rglb,'rgpu':rgpu,'rgpl':rgpl,'rgcn':rgcn}
except:
pass
RGbak=RG
# else:
# units=UnitsBak
# RG=RGbak
#
PD=dict()
smparams=[]
for i in range(len(self.parameters)):
if cp[i].var.get()=="1":
smparams.append(parameters[i])
AD=eval( open( join(PIPELINER_HOME,
self.annotation.get()+".json"
), "r"
).read()
)
SD=AD['references']['rnaseq']['STARDIR']
# tkinter.messagebox.showinfo("initLock","SD={0}".format(SD))
gi = self.global_info
PD={
'project': {
'pfamily': gi.pfamily.get(),
'units': units,
'samples': samples,
'pairs': pairs,
'id': gi.eprojectid.get(),
'pi': gi.epi.get(),
'organism': gi.eorganism.get(),
'analyst': gi.eanalyst.get(),
'poc': gi.epoc.get(),
'pipeline': self.Pipeline.get(),
'version':"1.0",
'annotation': gi.annotation.get(),
'datapath': self.datapath.get(),
'targetspath': self.targetspath.get(),
'filetype': filetype ,
'binset': "standard-bin",
'username': gi.euser.get(),
'flowcellid': gi.eflowcell.get(),
'platform': gi.eplatform.get(),
'custom': customRules,
'efiletype': efiletype,
'workpath': self.workpath.get(),
'batchsize': batchsize,
"smparams": smparams,
"rgid": RG,
"cluster": "cluster_medium.json",
"description": gi.description.get('1.0',END),
"technique" : gi.technique.get(),
"TRIM": "yes",
"groups": groups,
"contrasts": contrasts,
}
}
J=json.dumps(PD, sort_keys = True, indent = 4, ensure_ascii=True)
gi.jsonconf.delete("1.0", END)
gi.jsonconf.insert(INSERT, J)
self.saveproject(gi.jsonconf.get("1.0",END))
def build(self):
"""widget construction
Parameters
----------
None
Results
-------
None
"""
fr4 = LabelFrame(self.fr0, text='hsv')
fr4.grid(column=2, row=0)
hl = Label(fr4, text='hue ')
hl.grid(column=0, row=0, sticky='s')
self.hcan = Canvas(fr4,
width=self.canvas_w,
height=self.canvas_h,
bd=0,
highlightthickness=0)
self.hcan.grid(column=1, row=0, sticky='s')
hsc = TtkScale(fr4,
from_=0,
to=360,
variable=self.hvar,
orient='horizontal',
length=self.scale_l,
command=self.hhandle,
tickinterval=30)
hsc.grid(column=1, row=1, sticky='nw')
vcmdsb = root.register(sb_okay)
hsb = Spinbox(fr4,
from_=0,
to=360,
textvariable=self.hvar,
validate='key',
validatecommand=(vcmdsb, '%P', '%S', 360),
command=self.hhandle,
width=5)
hsb.grid(column=2, row=1, sticky='nw')
hsb.bind('<KeyRelease>', self.checksbh)
hel = Label(fr4, height=1)
hel.grid(column=2, row=2)
sl = Label(fr4, text='sat ')
sl.grid(column=0, row=3)
self.scan = Canvas(fr4,
width=self.canvas_w,
height=self.canvas_h,
bd=0,
highlightthickness=0)
self.scan.grid(column=1, row=3, sticky='s')
ssc = TtkScale(fr4,
from_=0,
to=100,
variable=self.svar,
orient='horizontal',
length=self.scale_l,
command=self.shandle,
tickinterval=10)
ssc.grid(column=1, row=4, sticky='nw')
ssb = Spinbox(fr4,
from_=0,
to=100,
textvariable=self.svar,
validate='key',
validatecommand=(vcmdsb, '%P', '%S', 100),
command=self.shandle,
width=5)
ssb.grid(column=2, row=4, sticky='nw')
ssb.bind('<KeyRelease>', self.checksb100)
sel = Label(fr4, height=1)
sel.grid(column=2, row=5)
vl = Label(fr4, text='value')
vl.grid(column=0, row=6, sticky='s')
self.vcan = Canvas(fr4,
width=self.canvas_w,
height=self.canvas_h,
bd=0,
highlightthickness=0)
self.vcan.grid(column=1, row=6, sticky='n')
vsc = TtkScale(fr4,
from_=0,
to=100,
variable=self.vvar,
orient='horizontal',
length=self.scale_l,
command=self.vhandle,
tickinterval=10)
vsc.grid(column=1, row=7, sticky='nw')
vsb = Spinbox(fr4,
from_=0,
to=100,
textvariable=self.vvar,
validate='key',
validatecommand=(vcmdsb, '%P', '%S', 100),
command=self.vhandle,
width=5)
vsb.grid(column=2, row=7, sticky='nw')
vsb.bind('<KeyRelease>', self.checksb100)
vel = Label(fr4, height=1)
vel.grid(column=2, row=8)
# assume initial setting 0,100,100 hsv
to_colour = hsv_to_rgb(*(0, 100, 100))
hue_gradient(self.hcan, width=self.canvas_w)
draw_gradient(self.scan, (255, 255, 255),
to_colour,
width=self.canvas_w)
draw_gradient(self.vcan, (0, 0, 0), to_colour, width=self.canvas_w)
class MiRSeqFrame(PipelineFrame):
def __init__(self, pipepanel, pipeline_name, *args, **kwargs):
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.info = None
eframe = self.eframe = LabelFrame(self, text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid(row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5)
label = Label(eframe,
text="Pipeline") #,fg=textLightColor,bg=baseColor)
label.grid(row=3, column=0, sticky=W, padx=10, pady=5)
Pipelines = ["CAPmirseq-plus"]
Pipeline = self.Pipeline = StringVar()
Pipeline.set(Pipelines[0])
om = OptionMenu(eframe,
Pipeline,
*Pipelines,
command=self.option_controller)
om.config() #bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config() #bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3, column=1, sticky=W, padx=10, pady=5)
self.add_info(eframe)
def add_info(self, parent):
if not self.info:
self.info = LabelFrame(parent, text="Sample Information")
self.groups_button = Button(self.info,
text="Set Groups",
command=self.popup_groups)
self.contrasts_button = Button(self.info,
text="Set Contrasts",
command=self.popup_contrasts)
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
self.groups_button.grid(row=5, column=5, padx=10, pady=5)
self.contrasts_button.grid(row=5, column=6, padx=10, pady=5)
self.info.grid(row=10,
column=0,
columnspan=6,
sticky=W,
padx=20,
pady=10)
def popup_groups(self):
self.popup_window("Groups Information", "groups.tab")
def popup_contrasts(self):
self.popup_window("Contrasts Information", "contrasts.tab")
def popup_window(self, text, filename):
top = Toplevel()
info = LabelFrame(top, text=text) #"Group Information")
info_text = Text(
info,
width=50,
height=8,
#bg=projectBgColor,
#fg=projectFgColor,
font=("nimbus mono bold", "11"))
def savefunc():
self.writepaste(filename, info_text)
def loadfunc():
self.readpaste(filename, info_text)
info_save_button = Button(info, text="Save", command=savefunc)
info_load_button = Button(info, text="Load", command=loadfunc)
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
info_load_button.grid(row=5, column=5, padx=10, pady=5)
info_save_button.grid(row=5, column=6, padx=10, pady=5)
info_text.grid(row=1,
rowspan=3,
column=1,
columnspan=7,
padx=5,
pady=5)
info.grid(row=7, column=0, columnspan=6, sticky=W, padx=20, pady=10)
top.focus_force()
def makejson(self, *args):
#print(args[0])
caller = args[0]
#global PD
#global UnitsBak
#global RGbak
D = dict()
try:
F = open(self.workpath.get() + "/samples", "r")
f = F.read().split("\n")
F.close()
for line in f:
L = line.split()
a = L.pop(0)
D[a] = L
samples = D
except:
samples = {"na": "na"}
D = dict()
try:
F = open(self.workpath.get() + "/pairs", "r")
f = F.read().split()
F.close()
for i in range(0, len(f), 2):
# a=f[i].split(".")[0]
# b=f[i+1].split(".")[0]
a = f[i]
b = f[i + 1]
D[a + "+" + b] = [a, b]
pairs = D
except:
pairs = {"na": "na"}
D = dict()
try:
F = open(self.workpath.get() + "/contrasts.tab", "r")
# f=F.read().split('\n')
# F.close()
# D["rsamps"]=f[0].split()
# D["rgroups"]=f[1].split()
# D["rcontrasts"]=f[2].split()
# D["rlabels"]=f[3].split()
f = F.readlines()
F.close()
## sampl=[]
## grp=[]
cont = []
## lbl=[]
for x in f:
if len(x.split()) == 2:
cont.append(x.split()[0])
cont.append(x.split()[1])
D["rcontrasts"] = cont
# contrasts["rcontrasts"]=cont
contrasts = D
except:
contrasts = {"rcontrasts": "na"}
## contrasts={"rsamps":"na","rgroups":"na","rcontrasts":"na","rlabels":"na"}
##------
D = dict()
try:
F = open(self.workpath.get() + "/groups.tab", "r")
f = F.readlines()
F.close()
sampl = []
grp = []
# cont=[]
lbl = []
for x in f:
# if len(x.split()) == 4 or len(x.split()) == 3:
if len(x.split()) == 3:
sampl.append(x.split()[0])
grp.append(x.split()[1])
lbl.append(x.split()[2])
D["rsamps"] = sampl
D["rgroups"] = grp
D["rlabels"] = lbl
# D["rcontrasts"]="na"
# contrasts=D
groups = D
except:
# contrasts={"rsamps":"na","rgroups":"na","rcontrasts":"na","rlabels":"na"}
groups = {"rsamps": "na", "rgroups": "na", "rlabels": "na"}
##------
D = dict()
FT = filetype #.get()
# p = Popen("ls "+workpath.get()+"/*."+FT, shell=True, stdin=PIPE, stdout=PIPE, stderr=DEVNULL, close_fds=True)
p = Popen("find " + self.workpath.get() +
" -maxdepth 1 -type l -printf '%f\n' ",
shell=True,
stdin=PIPE,
stdout=PIPE,
stderr=DEVNULL,
close_fds=True)
a = p.stdout.read().decode(encoding='UTF-8').split("\n")
RG = dict()
b = a.pop()
# tkinter.messagebox.showerror("",a)
# if freezeunits.get()=="no":
for i in a:
key = re.sub(".realign", "", i.split("/")[-1])
key = re.sub(".bai", "", key)
key = re.sub(".bam", "", key)
key = re.sub(".sam", "", key)
key = re.sub(".recal", "", key)
key = re.sub(".dedup", "", key)
key = re.sub(".sorted", "", key)
key = re.sub(".fin", "", key)
key = re.sub("\.R[12]", "", key)
key = re.sub("_R[12]", "", key)
key = re.sub(".fastq", "", key)
key = re.sub(".gz", "", key)
# key=re.sub("[\._](R[12]\.)*"+FT+"$","",i.split("/")[-1])
# key=re.sub(".R[12]."+FT+"$","",i.split("/")[-1])
# key=re.sub("([._]R[12][._])*([fin|sorted|dedup|recal|realign])*\.{0}$".format(FT),"",i.split("/")[-1])
D[key] = key
RG[key] = {
'rgsm': key,
'rglb': 'na',
'rgpu': 'na',
'rgpl': 'ILLUMINA',
'rgcn': 'na'
}
units = D
UnitsBak = D
try:
F = open(self.workpath.get() + "/rg.tab", "r")
f = F.read().splitlines()
F.close()
for theLine in f:
if not re.match("^ID", theLine):
(rgid, rgsm, rglb, rgpl, rgpu, rgcn) = theLine.split("\t")
RG[rgid] = {
'rgsm': rgsm,
'rglb': rglb,
'rgpu': rgpu,
'rgpl': rgpl,
'rgcn': rgcn
}
except:
pass
RGbak = RG
# else:
# units=UnitsBak
# RG=RGbak
#
PD = dict()
smparams = []
for i in range(len(self.parameters)):
if cp[i].var.get() == "1":
smparams.append(parameters[i])
AD = eval(
open(join(PIPELINER_HOME,
self.annotation.get() + ".json"), "r").read())
SD = AD['references']['rnaseq']['STARDIR']
# tkinter.messagebox.showinfo("initLock","SD={0}".format(SD))
gi = self.global_info
PD = {
'project': {
'pfamily': gi.pfamily.get(),
'units': units,
'samples': samples,
'pairs': pairs,
'id': gi.eprojectid.get(),
'pi': gi.epi.get(),
'organism': gi.eorganism.get(),
'analyst': gi.eanalyst.get(),
'poc': gi.epoc.get(),
'pipeline': self.Pipeline.get(),
'version': "1.0",
'annotation': gi.annotation.get(),
'datapath': self.datapath.get(),
'targetspath': self.targetspath.get(),
'filetype': filetype,
'binset': "standard-bin",
'username': gi.euser.get(),
'flowcellid': gi.eflowcell.get(),
'platform': gi.eplatform.get(),
'custom': customRules,
'efiletype': efiletype,
'workpath': self.workpath.get(),
'batchsize': batchsize,
"smparams": smparams,
"rgid": RG,
"cluster": "cluster_medium.json",
"description": gi.description.get('1.0', END),
"technique": gi.technique.get(),
"TRIM": "yes",
"groups": groups,
"contrasts": contrasts,
}
}
J = json.dumps(PD, sort_keys=True, indent=4, ensure_ascii=True)
gi.jsonconf.delete("1.0", END)
gi.jsonconf.insert(INSERT, J)
self.saveproject(gi.jsonconf.get("1.0", END))
def popup_window_peakinfo( self, text, filename ) :
NA = 'N/A'
selections = [fn.split('.R1.fastq.gz')[0]
for fn in self.datafiles if fn.endswith( ".R1.fastq.gz" )]
################################
#check availablity of the files before moving on!
if not selections :
showerror( "No FASTQ files available matching the pattern *.R1.fastq.gz" )
return
################################
selections.insert(0, NA) #Adding N/A for the groups where no input is available
groups = ['Grp%d'%i for i in range(1, len(selections)+1)]
##checking for debugging purpose
print( selections )
assert len(selections) == len(set(selections))
##
top = Toplevel()
info = LabelFrame(top, text=text )#"Group Information")
chip_vars = [ StringVar() for s in selections[1:] ]
input_vars = [ StringVar() for s in selections[1:] ]
group_vars = [ StringVar() for s in selections[1:] ]
chip_menus = [OptionMenu(info,var,*selections) for var in chip_vars]
input_menus = [OptionMenu(info,var,*selections) for var in input_vars]
group_menus = [OptionMenu(info,var,*groups) for var in group_vars]
group_entries = [Entry(info, bd=2, width=8, textvariable=var) for var in group_vars]
chiplabel = Label(info, text= "ChIP Names")
inputlabel = Label(info, text="Input Names")
grouplabel = Label(info, text="Group Names")
chiplabel.grid( row = 0, column = 1, padx=4, pady=1)
inputlabel.grid( row = 0, column = 2, padx=4, pady=1)
grouplabel.grid( row = 0, column = 3, padx=4, pady=1 )
for i, (chvar, invar) in enumerate(zip(chip_vars, input_vars)) :
chvar.set(selections[0])
invar.set(selections[0])
chip_menus[i].grid( row = i+1, column = 1, padx=4, pady=1 )
input_menus[i].grid( row = i+1, column = 2, padx=4, pady=1 )
group_entries[i].grid( row = i+1, column = 3, padx=4, pady=1 )
group_menus[i].grid( row = i+1, column = 4, padx=4, pady=1 )
def savefunc() :
info_text = StringIO()
for v1, v2, v3 in zip( chip_vars, input_vars, group_vars ) :
v1 = v1.get().strip() if v1.get().strip() != NA else ""
if not v1 :
continue
v2 = v2.get().strip() if v2.get().strip() != NA else ""
v3 = v3.get().strip() if v3.get().strip() != NA else ""
if not v3 :
showerror( "Error", "Missing Replicate group name detected.\nReplicate group names should be given!" )
print( "Error", "Missing Replicate group name detected.\nReplicate group names should be given!" )
return
print( v1, v2, v3, file=info_text, sep="\t" )
fp = open( filename, 'w' )
fp.write( info_text.getvalue() )
fp.close()
def loadfunc() :
if not exists(filename) :
print( filename, 'does not exists!' )
return
for i, l in enumerate(open( filename )) :
v1, v2, v3 = l.split('\t')
if v1 :
try : assert v1 in selections
except :
showwarning('WARNING', 'ChIP name is not in the selection list!' )
print( 'v1:',v1 )
print( 'selection:', selection )
continue
if v2 :
try: assert v2 in selections
except :
showwarning('WARNING', 'Input name is not in the selection list!' )
print( 'v2:',v2 )
print( 'selection:', selection )
return
chip_vars[i].set(v1.strip())
input_vars[i].set(v2.strip())
group_vars[i].set(v3.strip())
def clearfunc() :
for i, (chvar, invar, grvar) in enumerate(zip(chip_vars, input_vars, group_vars)) :
chvar.set(selections[0])
invar.set(selections[0])
grvar.set('')
info_clear_button = Button(top,
text="Clear",
command = clearfunc )
info_save_button = Button(top,
text="Save",
command = savefunc )
info_load_button = Button(top,
text="Load",
command = loadfunc )
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
info_clear_button.grid( row=5, column=3, padx=10, pady=5 )
info_load_button.grid( row=5, column=4, padx=10, pady=5 )
info_save_button.grid( row=5, column=5, padx=10, pady=5 )
info.grid(row=7,column=0, columnspan=6, sticky=W, padx=20, pady=10 )
top.focus_force()
class MarkovDemo(Frame):
"MarkovDemo(master=None, **kw) -> MarkovDemo instance"
TEXT = dict(height=2, width=46, wrap=WORD) # Text Options
GRID = dict(padx=5, pady=5) # Grid Options
# Initialize a MarkovDemo instance with a GUI for interaction.
def __init__(self, master=None, **kw):
"Initialize the MarkovDemo instance's widgets and settings."
super().__init__(master, **kw)
self.build_widgets()
self.place_widgets()
self.setup_widgets()
self.grid_rowconfigure(2, weight=1)
self.grid_rowconfigure(3, weight=1)
self.grid_columnconfigure(0, weight=1)
self.key = self.primer = None
def build_widgets(self):
"Build the various widgets that will be used in the program."
# Create processing frame widgets.
self.processing_frame = LabelFrame(self, text='Processing Mode:')
self.mode_var = StringVar(self, 'encode')
self.decode_button = Radiobutton(self.processing_frame,
text='Decode Cipher-Text',
command=self.handle_radiobuttons,
value='decode',
variable=self.mode_var)
self.encode_button = Radiobutton(self.processing_frame,
text='Encode Plain-Text',
command=self.handle_radiobuttons,
value='encode',
variable=self.mode_var)
self.freeze_var = BooleanVar(self, False)
self.freeze_button = Checkbutton(self.processing_frame,
text='Freeze Key & Primer',
command=self.handle_checkbutton,
offvalue=False,
onvalue=True,
variable=self.freeze_var)
# Create encoding frame widgets.
self.encoding_frame = LabelFrame(self, text='Encoding Options:')
self.chain_size_label = Label(self.encoding_frame, text='Chain Size:')
self.chain_size_entry = Entry(self.encoding_frame)
self.plain_text_label = Label(self.encoding_frame, text='Plain-Text:')
self.plain_text_entry = Entry(self.encoding_frame)
# Create input frame widgets.
self.input_frame = LabelFrame(self, text='Input Area:')
self.input_text = ScrolledText(self.input_frame, **self.TEXT)
# Create output frame widgets.
self.output_frame = LabelFrame(self, text='Output Area:')
self.output_text = ScrolledText(self.output_frame, **self.TEXT)
def place_widgets(self):
"Place the widgets where they belong in the MarkovDemo frame."
# Locate processing frame widgets.
self.processing_frame.grid(sticky=EW, **self.GRID)
self.decode_button.grid(row=0, column=0, **self.GRID)
self.encode_button.grid(row=0, column=1, **self.GRID)
self.freeze_button.grid(row=0, column=2, **self.GRID)
# Locate encoding frame widgets.
self.encoding_frame.grid(sticky=EW, **self.GRID)
self.chain_size_label.grid(row=0, column=0, sticky=W, **self.GRID)
self.chain_size_entry.grid(row=0, column=1, sticky=EW, **self.GRID)
self.plain_text_label.grid(row=1, column=0, sticky=W, **self.GRID)
self.plain_text_entry.grid(row=1, column=1, sticky=EW, **self.GRID)
self.encoding_frame.grid_columnconfigure(1, weight=1)
# Locate input frame widgets.
self.input_frame.grid(sticky=NSEW, **self.GRID)
self.input_text.grid(sticky=NSEW, **self.GRID)
self.input_frame.grid_rowconfigure(0, weight=1)
self.input_frame.grid_columnconfigure(0, weight=1)
# Locate output frame widgets.
self.output_frame.grid(sticky=NSEW, **self.GRID)
self.output_text.grid(sticky=NSEW, **self.GRID)
self.output_frame.grid_rowconfigure(0, weight=1)
self.output_frame.grid_columnconfigure(0, weight=1)
def setup_widgets(self):
"Setup each widget's configuration for the events they handle."
self.input_text.bind('<Key>', self.handle_key_events)
self.input_text.bind('<Control-Key-a>', self.handle_control_a)
self.input_text.bind('<Control-Key-/>', lambda event: 'break')
self.output_text['state'] = DISABLED
self.output_text.bind('<Control-Key-a>', self.handle_control_a)
self.output_text.bind('<Control-Key-/>', lambda event: 'break')
########################################################################
# Take care of any special event needing dedicated processing.
def handle_radiobuttons(self):
"Change the interface based on the encoding / decoding setting."
if self.encrypting:
self.freeze_button.grid()
if not self.freeze_var.get():
self.encoding_frame.grid()
else:
self.freeze_button.grid_remove()
if not self.freeze_var.get():
self.encoding_frame.grid_remove()
self.handle_key_events(None)
def handle_checkbutton(self):
"Change the interface based on the key / primer freeze setting."
if self.freeze_var.get():
self.encoding_frame.grid_remove()
else:
self.encoding_frame.grid()
def handle_key_events(self, event):
"Schedule refreshing the output area after an input area event."
if event is None or event.char and event.state | 0o11 == 0o11:
self.after_idle(self.refresh)
@staticmethod
def handle_control_a(event):
"Select all text in the widget associated with the given event."
event.widget.tag_add(SEL, 1.0, END + '-1c')
return 'break'
########################################################################
# Handle interface's updates when either encoding or decoding.
def refresh(self):
"Refresh the output based on the value of the input."
text = self.input_text.get(1.0, END + '-1c')
if not text:
self.output = text
elif self.encrypting:
self.encode(text)
else:
self.decode(text)
def output(self, value):
"Set the text in the output area to the string value."
self.output_text['state'] = NORMAL
self.output_text.delete(1.0, END)
self.output_text.insert(END, value)
if self.encrypting and self.freeze_var.get():
self.output_text.see(END)
self.output_text['state'] = DISABLED
output = property(fset=output, doc='Output area property.')
@property
def chain_size(self):
"Chain size for the Markov chains used when encrypting."
try:
value = ast.literal_eval(self.chain_size_entry.get())
assert isinstance(value, int) and 2 <= value <= 256
return value
except:
self.chain_size_entry.delete(0, END)
self.chain_size_entry.insert(0, '2')
return 2
@property
def plain_text(self):
"Plain text or ignored characters in encryption process."
try:
value = self.repr_to_obj(self.plain_text_entry.get(), '')
assert isinstance(value, str)
return value
except:
self.plain_text_entry.delete(0, END)
return ''
########################################################################
# Encrypt a string for display in the interface's output area.
def encode(self, string):
"Encode the string and show the cipher-text in the output."
try:
cipher = self.build_cipher(string)
except ValueError:
self.output = ''
except:
self.output = traceback.format_exc()
else:
self.output = self.build_header() + '\n\n' + cipher
def build_cipher(self, string):
"Build cipher-text based on plain-text and return answer."
if self.key and self.freeze_var.get():
cipher, primer = me.encrypt_str(string, self.key, self.primer)
else:
args = string, self.chain_size, self.plain_text
cipher, self.key, self.primer = me.auto_encrypt_str(*args)
return cipher
def build_header(self):
"Build header from key and primer values in current use."
header = '\n'.join(map(self.bytes_to_repr, self.key.data))
header += '\n' + self.bytes_to_repr(self.primer.data)
return header
########################################################################
# Decrypt a string for display in the interface's output area.
def decode(self, string):
"Decode encrypted message and display plain-text in output."
try:
cipher = self.extract_keys(string)
text = self.extract_text(cipher)
except ValueError:
self.output = ''
except:
self.output = traceback.format_exc()
else:
self.output = text
def extract_keys(self, string):
"Extract keys to decryption and return the cipher-text area."
header, cipher = string.split('\n\n', 1)
*key, primer = map(self.repr_to_obj, header.split('\n'))
self.key, self.primer = me.Key(tuple(key)), me.Primer(primer)
return cipher
def extract_text(self, string):
"Extract text message from string using built key and primer."
text, primer = me.decrypt_str(string, self.key, self.primer)
return text
########################################################################
# Provide some special methods to simplify the program's code.
@property
def encrypting(self):
"Encrypting boolean stating current operations mode."
return {'encode': True, 'decode': False}[self.mode_var.get()]
@staticmethod
def bytes_to_repr(obj):
"Convert bytes object into suitable representation."
if not isinstance(obj, bytes):
raise TypeError('Object must be a bytes instance!')
return repr(obj)[2:-1]
@staticmethod
def repr_to_obj(string, prefix='b'):
"Convert representation into an equivalent object."
for template in '{}"{}"', "{}'{}'":
try:
return ast.literal_eval(template.format(prefix, string))
except:
pass
raise ValueError('Cannot convert {!r} to object!'.format(string))
@classmethod
def main(cls):
"Create context for demo and run a test instance."
NoDefaultRoot()
root = Tk()
root.minsize(420, 330)
root.title('Markov Demo 2')
test = cls(root)
test.grid(sticky=NSEW)
root.grid_rowconfigure(0, weight=1)
root.grid_columnconfigure(0, weight=1)
root.mainloop()
class MarkovDemo(Frame):
"MarkovDemo(master=None, **kw) -> MarkovDemo instance"
TEXT = dict(height=2, width=46, wrap=WORD) # Text Options
GRID = dict(padx=5, pady=5) # Grid Options
# Initialize a MarkovDemo instance with a GUI for interaction.
def __init__(self, master=None, **kw):
"Initialize the MarkovDemo instance's widgets and settings."
super().__init__(master, **kw)
self.build_widgets()
self.place_widgets()
self.setup_widgets()
self.grid_rowconfigure(2, weight=1)
self.grid_rowconfigure(3, weight=1)
self.grid_columnconfigure(0, weight=1)
self.key = self.primer = None
def build_widgets(self):
"Build the various widgets that will be used in the program."
# Create processing frame widgets.
self.processing_frame = LabelFrame(self, text='Processing Mode:')
self.mode_var = StringVar(self, 'encode')
self.decode_button = Radiobutton(self.processing_frame,
text='Decode Cipher-Text',
command=self.handle_radiobuttons,
value='decode',
variable=self.mode_var)
self.encode_button = Radiobutton(self.processing_frame,
text='Encode Plain-Text',
command=self.handle_radiobuttons,
value='encode',
variable=self.mode_var)
self.freeze_var = BooleanVar(self, False)
self.freeze_button = Checkbutton(self.processing_frame,
text='Freeze Key & Primer',
command=self.handle_checkbutton,
offvalue=False,
onvalue=True,
variable=self.freeze_var)
# Create encoding frame widgets.
self.encoding_frame = LabelFrame(self, text='Encoding Options:')
self.chain_size_label = Label(self.encoding_frame, text='Chain Size:')
self.chain_size_entry = Entry(self.encoding_frame)
self.plain_text_label = Label(self.encoding_frame, text='Plain-Text:')
self.plain_text_entry = Entry(self.encoding_frame)
# Create input frame widgets.
self.input_frame = LabelFrame(self, text='Input Area:')
self.input_text = ScrolledText(self.input_frame, **self.TEXT)
# Create output frame widgets.
self.output_frame = LabelFrame(self, text='Output Area:')
self.output_text = ScrolledText(self.output_frame, **self.TEXT)
def place_widgets(self):
"Place the widgets where they belong in the MarkovDemo frame."
# Locate processing frame widgets.
self.processing_frame.grid(sticky=EW, **self.GRID)
self.decode_button.grid(row=0, column=0, **self.GRID)
self.encode_button.grid(row=0, column=1, **self.GRID)
self.freeze_button.grid(row=0, column=2, **self.GRID)
# Locate encoding frame widgets.
self.encoding_frame.grid(sticky=EW, **self.GRID)
self.chain_size_label.grid(row=0, column=0, sticky=W, **self.GRID)
self.chain_size_entry.grid(row=0, column=1, sticky=EW, **self.GRID)
self.plain_text_label.grid(row=1, column=0, sticky=W, **self.GRID)
self.plain_text_entry.grid(row=1, column=1, sticky=EW, **self.GRID)
self.encoding_frame.grid_columnconfigure(1, weight=1)
# Locate input frame widgets.
self.input_frame.grid(sticky=NSEW, **self.GRID)
self.input_text.grid(sticky=NSEW, **self.GRID)
self.input_frame.grid_rowconfigure(0, weight=1)
self.input_frame.grid_columnconfigure(0, weight=1)
# Locate output frame widgets.
self.output_frame.grid(sticky=NSEW, **self.GRID)
self.output_text.grid(sticky=NSEW, **self.GRID)
self.output_frame.grid_rowconfigure(0, weight=1)
self.output_frame.grid_columnconfigure(0, weight=1)
def setup_widgets(self):
"Setup each widget's configuration for the events they handle."
self.input_text.bind('<Key>', self.handle_key_events)
self.input_text.bind('<Control-Key-a>', self.handle_control_a)
self.input_text.bind('<Control-Key-/>', lambda event: 'break')
self.output_text['state'] = DISABLED
self.output_text.bind('<Control-Key-a>', self.handle_control_a)
self.output_text.bind('<Control-Key-/>', lambda event: 'break')
########################################################################
# Take care of any special event needing dedicated processing.
def handle_radiobuttons(self):
"Change the interface based on the encoding / decoding setting."
if self.encrypting:
self.freeze_button.grid()
if not self.freeze_var.get():
self.encoding_frame.grid()
else:
self.freeze_button.grid_remove()
if not self.freeze_var.get():
self.encoding_frame.grid_remove()
self.handle_key_events(None)
def handle_checkbutton(self):
"Change the interface based on the key / primer freeze setting."
if self.freeze_var.get():
self.encoding_frame.grid_remove()
else:
self.encoding_frame.grid()
def handle_key_events(self, event):
"Schedule refreshing the output area after an input area event."
if event is None or event.char and event.state | 0o11 == 0o11:
self.after_idle(self.refresh)
@staticmethod
def handle_control_a(event):
"Select all text in the widget associated with the given event."
event.widget.tag_add(SEL, 1.0, END + '-1c')
return 'break'
########################################################################
# Handle interface's updates when either encoding or decoding.
def refresh(self):
"Refresh the output based on the value of the input."
text = self.input_text.get(1.0, END + '-1c')
if not text:
self.output = text
elif self.encrypting:
self.encode(text)
else:
self.decode(text)
def output(self, value):
"Set the text in the output area to the string value."
self.output_text['state'] = NORMAL
self.output_text.delete(1.0, END)
self.output_text.insert(END, value)
if self.encrypting and self.freeze_var.get():
self.output_text.see(END)
self.output_text['state'] = DISABLED
output = property(fset=output, doc='Output area property.')
@property
def chain_size(self):
"Chain size for the Markov chains used when encrypting."
try:
value = ast.literal_eval(self.chain_size_entry.get())
assert isinstance(value, int) and 2 <= value <= 256
return value
except:
self.chain_size_entry.delete(0, END)
self.chain_size_entry.insert(0, '2')
return 2
@property
def plain_text(self):
"Plain text or ignored characters in encryption process."
try:
value = self.repr_to_obj(self.plain_text_entry.get(), '')
assert isinstance(value, str)
return value
except:
self.plain_text_entry.delete(0, END)
return ''
########################################################################
# Encrypt a string for display in the interface's output area.
def encode(self, string):
"Encode the string and show the cipher-text in the output."
try:
cipher = self.build_cipher(string)
except ValueError:
self.output = ''
except:
self.output = traceback.format_exc()
else:
self.output = self.build_header() + '\n\n' + cipher
def build_cipher(self, string):
"Build cipher-text based on plain-text and return answer."
if self.key and self.freeze_var.get():
cipher, primer = me.encrypt_str(string, self.key, self.primer)
else:
args = string, self.chain_size, self.plain_text
cipher, self.key, self.primer = me.auto_encrypt_str(*args)
return cipher
def build_header(self):
"Build header from key and primer values in current use."
header = '\n'.join(map(self.bytes_to_repr, self.key.data))
header += '\n' + self.bytes_to_repr(self.primer.data)
return header
########################################################################
# Decrypt a string for display in the interface's output area.
def decode(self, string):
"Decode encrypted message and display plain-text in output."
try:
cipher = self.extract_keys(string)
text = self.extract_text(cipher)
except ValueError:
self.output = ''
except:
self.output = traceback.format_exc()
else:
self.output = text
def extract_keys(self, string):
"Extract keys to decryption and return the cipher-text area."
header, cipher = string.split('\n\n', 1)
*key, primer = map(self.repr_to_obj, header.split('\n'))
self.key, self.primer = me.Key(tuple(key)), me.Primer(primer)
return cipher
def extract_text(self, string):
"Extract text message from string using built key and primer."
text, primer = me.decrypt_str(string, self.key, self.primer)
return text
########################################################################
# Provide some special methods to simplify the program's code.
@property
def encrypting(self):
"Encrypting boolean stating current operations mode."
return {'encode': True, 'decode': False}[self.mode_var.get()]
@staticmethod
def bytes_to_repr(obj):
"Convert bytes object into suitable representation."
if not isinstance(obj, bytes):
raise TypeError('Object must be a bytes instance!')
return repr(obj)[2:-1]
@staticmethod
def repr_to_obj(string, prefix='b'):
"Convert representation into an equivalent object."
for template in '{}"{}"', "{}'{}'":
try:
return ast.literal_eval(template.format(prefix, string))
except:
pass
raise ValueError('Cannot convert {!r} to object!'.format(string))
@classmethod
def main(cls):
"Create context for demo and run a test instance."
NoDefaultRoot()
root = Tk()
root.minsize(420, 330)
root.title('Markov Demo 2')
test = cls(root)
test.grid(sticky=NSEW)
root.grid_rowconfigure(0, weight=1)
root.grid_columnconfigure(0, weight=1)
root.mainloop()
class RNASeqFrame(PipelineFrame):
def __init__(self, pipepanel, pipeline_name, *args, **kwargs):
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.info = None
eframe = self.eframe = LabelFrame(self, text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid(row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5)
label = Label(eframe,
text="Pipeline") #,fg=textLightColor,bg=baseColor)
label.grid(row=3, column=0, sticky=W, padx=10, pady=5)
Pipelines = ["initialqcrnaseq", "rnaseq"]
Pipeline = self.Pipeline = StringVar()
Pipeline.set(Pipelines[0])
om = OptionMenu(eframe,
Pipeline,
*Pipelines,
command=self.option_controller)
om.config() #bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config() #bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3, column=1, sticky=W, padx=10, pady=5)
rReadlens = [
'Read Length is 50', 'Read Length is 75', 'Read Length is 100',
'Read Length is 125', 'Read Length is 150', 'Read Length is 250'
]
self.rReadlen = rReadlen = StringVar()
rReadlen.set(rReadlens[2])
self.om2 = OptionMenu(eframe,
rReadlen,
*rReadlens,
command=self.option_controller)
#self.om2.grid(row=4,column=1,sticky=W,padx=10,pady=5)
rStrands = [
'0, Reads are Unstranded', '1, Reads are from Sense Strand',
'2, Reads are from Anti-Sense Strand'
]
self.rStrand = rStrand = StringVar()
rStrand.set(rStrands[0])
self.om3 = OptionMenu(eframe,
rStrand,
*rStrands,
command=self.option_controller)
#self.om3.grid(row=5,column=1,sticky=W,padx=10,pady=5)
rDegs = [
"no, Do not Report Differentially Expressed Genes",
"yes, Report Differentially Expressed Genes"
]
self.rDeg = rDeg = StringVar()
rDeg.set(rDegs[0])
self.om4 = OptionMenu(eframe,
rDeg,
*rDegs,
command=self.option_controller)
self.om4.grid(row=6, column=1, sticky=W, padx=10, pady=5)
#####################
#Sample Threshold
#####################
self.sampleLF = sampleLF = LabelFrame(
eframe, text="Low Abundance Gene Thresholds")
self.rMincount = rMincount = StringVar()
rMincount.set("5")
self.rMinsamples = rMinsamples = StringVar()
rMinsamples.set("2")
#rMincount.trace('w', lambda a,b,c,x="rmincount": makejson(x))
#Filter out genes < [5] read counts in < [2] samples
rminsamplesL = Label(sampleLF, text="Include genes with >=") # in")
rmincountE = Entry(sampleLF, bd=2, width=3, textvariable=rMincount)
rmincountL = Label(sampleLF, text="read counts in >=")
rminsamplesE = Entry(sampleLF, bd=2, width=3, textvariable=rMinsamples)
rminsamplesR = Label(sampleLF, text="samples")
rminsamplesL.grid(row=9, column=1, sticky=W, padx=10, pady=5)
rmincountE.grid(row=9, column=2, sticky=W, padx=0, pady=5)
rmincountL.grid(row=9, column=3, sticky=W, padx=5, pady=5)
rminsamplesE.grid(row=9, column=4, sticky=W, padx=0, pady=5)
rminsamplesR.grid(row=9, column=5, sticky=W, padx=10, pady=5)
#rMinsamples.trace('w', lambda a,b,c,x="rmincount": makejson(x))
sampleLF.grid(row=8,
column=0,
columnspan=4,
sticky=W,
padx=20,
pady=10)
#####################
self.add_info(eframe)
self.option_controller()
def option_controller(self, *args, **kwargs):
PipelineFrame.option_controller(self)
if self.Pipeline.get() == 'initialqcrnaseq':
self.om4.grid_forget()
self.sampleLF.grid_forget()
else:
self.om4.grid(row=6, column=1, sticky=W, padx=10, pady=5)
self.sampleLF.grid(row=8,
column=0,
columnspan=4,
sticky=W,
padx=20,
pady=10)
def makejson_wrapper(self, *args, **kwargs):
self.makejson(*args, **kwargs)
def add_info(self, parent):
if not self.info:
self.info = LabelFrame(parent, text="Sample Information")
self.groups_button = Button(self.info,
text="Set Groups",
command=self.popup_groups)
self.contrasts_button = Button(self.info,
text="Set Contrasts",
command=self.popup_contrasts)
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
self.groups_button.grid(row=5, column=5, padx=10, pady=5)
self.contrasts_button.grid(row=5, column=6, padx=10, pady=5)
self.info.grid(row=10,
column=0,
columnspan=6,
sticky=W,
padx=20,
pady=10)
def popup_groups(self):
self.popup_window("Groups Information", "groups.tab")
def popup_contrasts(self):
self.popup_window("Contrasts Information", "contrasts.tab")
def popup_window(self, text, filename):
top = Toplevel()
info = LabelFrame(top, text=text) #"Group Information")
info_text = Text(
info,
width=50,
height=8,
#bg=projectBgColor,
#fg=projectFgColor,
font=("nimbus mono bold", "11"))
def savefunc():
self.writepaste(filename, info_text)
def loadfunc():
self.readpaste(filename, info_text)
info_save_button = Button(info, text="Save", command=savefunc)
info_load_button = Button(info, text="Load", command=loadfunc)
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
info_load_button.grid(row=5, column=5, padx=10, pady=5)
info_save_button.grid(row=5, column=6, padx=10, pady=5)
info_text.grid(row=1,
rowspan=3,
column=1,
columnspan=7,
padx=5,
pady=5)
info.grid(row=7, column=0, columnspan=6, sticky=W, padx=20, pady=10)
top.focus_force()
def makejson(self, *args):
#print(args[0])
caller = args[0]
#global PD
#global UnitsBak
#global RGbak
D = dict()
try:
F = open(self.workpath.get() + "/samples", "r")
f = F.read().split("\n")
F.close()
for line in f:
L = line.split()
a = L.pop(0)
D[a] = L
samples = D
except:
samples = {"na": "na"}
D = dict()
try:
F = open(self.workpath.get() + "/pairs", "r")
f = F.read().split()
F.close()
for i in range(0, len(f), 2):
# a=f[i].split(".")[0]
# b=f[i+1].split(".")[0]
a = f[i]
b = f[i + 1]
D[a + "+" + b] = [a, b]
pairs = D
except:
pairs = {"na": "na"}
D = dict()
try:
F = open(self.workpath.get() + "/contrasts.tab", "r")
# f=F.read().split('\n')
# F.close()
# D["rsamps"]=f[0].split()
# D["rgroups"]=f[1].split()
# D["rcontrasts"]=f[2].split()
# D["rlabels"]=f[3].split()
f = F.readlines()
F.close()
## sampl=[]
## grp=[]
cont = []
## lbl=[]
for x in f:
if len(x.split()) == 2:
cont.append(x.split()[0])
cont.append(x.split()[1])
D["rcontrasts"] = cont
# contrasts["rcontrasts"]=cont
contrasts = D
except:
contrasts = {"rcontrasts": "na"}
## contrasts={"rsamps":"na","rgroups":"na","rcontrasts":"na","rlabels":"na"}
##------
D = dict()
try:
F = open(self.workpath.get() + "/groups.tab", "r")
f = F.readlines()
F.close()
sampl = []
grp = []
# cont=[]
lbl = []
for x in f:
# if len(x.split()) == 4 or len(x.split()) == 3:
if len(x.split()) == 3:
sampl.append(x.split()[0])
grp.append(x.split()[1])
lbl.append(x.split()[2])
D["rsamps"] = sampl
D["rgroups"] = grp
D["rlabels"] = lbl
# D["rcontrasts"]="na"
# contrasts=D
groups = D
except:
# contrasts={"rsamps":"na","rgroups":"na","rcontrasts":"na","rlabels":"na"}
groups = {"rsamps": "na", "rgroups": "na", "rlabels": "na"}
##------
D = dict()
FT = filetype #.get()
# p = Popen("ls "+workpath.get()+"/*."+FT, shell=True, stdin=PIPE, stdout=PIPE, stderr=DEVNULL, close_fds=True)
p = Popen("find " + self.workpath.get() +
" -maxdepth 1 -type l -printf '%f\n' ",
shell=True,
stdin=PIPE,
stdout=PIPE,
stderr=DEVNULL,
close_fds=True)
a = p.stdout.read().decode(encoding='UTF-8').split("\n")
RG = dict()
b = a.pop()
# tkinter.messagebox.showerror("",a)
# if freezeunits.get()=="no":
for i in a:
key = re.sub(".realign", "", i.split("/")[-1])
key = re.sub(".bai", "", key)
key = re.sub(".bam", "", key)
key = re.sub(".sam", "", key)
key = re.sub(".recal", "", key)
key = re.sub(".dedup", "", key)
key = re.sub(".sorted", "", key)
key = re.sub(".fin", "", key)
key = re.sub(".R[12]", "", key)
key = re.sub("_R[12]", "", key)
key = re.sub(".fastq", "", key)
key = re.sub(".gz", "", key)
# key=re.sub("[\._](R[12]\.)*"+FT+"$","",i.split("/")[-1])
# key=re.sub(".R[12]."+FT+"$","",i.split("/")[-1])
# key=re.sub("([._]R[12][._])*([fin|sorted|dedup|recal|realign])*\.{0}$".format(FT),"",i.split("/")[-1])
D[key] = key
RG[key] = {
'rgsm': key,
'rglb': 'na',
'rgpu': 'na',
'rgpl': 'ILLUMINA',
'rgcn': 'na'
}
units = D
UnitsBak = D
try:
F = open(self.workpath.get() + "/rg.tab", "r")
f = F.read().splitlines()
F.close()
for theLine in f:
if not re.match("^ID", theLine):
(rgid, rgsm, rglb, rgpl, rgpu, rgcn) = theLine.split("\t")
RG[rgid] = {
'rgsm': rgsm,
'rglb': rglb,
'rgpu': rgpu,
'rgpl': rgpl,
'rgcn': rgcn
}
except:
pass
RGbak = RG
# else:
# units=UnitsBak
# RG=RGbak
#
PD = dict()
smparams = []
for i in range(len(self.parameters)):
if cp[i].var.get() == "1":
smparams.append(parameters[i])
AD = eval(
open(join(PIPELINER_HOME,
self.annotation.get() + ".json"), "r").read())
SD = AD['references']['rnaseq']['STARDIR']
# tkinter.messagebox.showinfo("initLock","SD={0}".format(SD))
gi = self.global_info
PD = {
'project': {
'pfamily':
gi.pfamily.get(),
'units':
units,
'samples':
samples,
'pairs':
pairs,
'id':
gi.eprojectid.get(),
'pi':
gi.epi.get(),
'organism':
gi.eorganism.get(),
'analyst':
gi.eanalyst.get(),
'poc':
gi.epoc.get(),
'pipeline':
self.Pipeline.get(),
'version':
"1.0",
'annotation':
gi.annotation.get(),
'datapath':
self.datapath.get(),
'targetspath':
self.targetspath.get(),
'filetype':
filetype,
'binset':
"standard-bin",
'username':
gi.euser.get(),
'flowcellid':
gi.eflowcell.get(),
'platform':
gi.eplatform.get(),
'custom':
customRules,
'efiletype':
efiletype,
'workpath':
self.workpath.get(),
'batchsize':
batchsize,
"smparams":
smparams,
"rgid":
RG,
"cluster":
"cluster_medium.json",
"description":
gi.description.get('1.0', END),
"technique":
gi.technique.get(),
"TRIM":
"yes",
"groups":
groups,
"contrasts":
contrasts,
"SJDBOVERHANG":
self.rReadlen.get().split(" ")[3],
"STRANDED":
self.rStrand.get().split(",")[0],
"DEG":
self.rDeg.get().split(",")[0].lower(),
"STARSTRANDCOL":
"{0}".format(int(self.rStrand.get().split(",")[0]) + 2),
"MINSAMPLES":
self.rMinsamples.get(),
"MINCOUNTGENES":
self.rMincount.get(),
"MINCOUNTJUNCTIONS":
self.rMincount.get(),
"MINCOUNTGENEJUNCTIONS":
self.rMincount.get(),
"STARDIR":
SD + self.rReadlen.get().split(" ")[3],
"PICARDSTRAND": [
"NONE", "FIRST_READ_TRANSCRIPTION_STRAND",
"SECOND_READ_TRANSCRIPTION_STRAND"
][int(self.rStrand.get().split(",")[0])]
}
}
J = json.dumps(PD, sort_keys=True, indent=4, ensure_ascii=True)
gi.jsonconf.delete("1.0", END)
gi.jsonconf.insert(INSERT, J)
self.saveproject(gi.jsonconf.get("1.0", END))
style = Style()
# both theme_create and theme_settings worked
style.theme_create(
"yummy",
parent="clam",
settings={
#style.theme_settings('default', {
# start of theme extract
'Labelframe.border': {
"element create": ('image', "frame", ('disabled', "frame-d"), {
'border': 5,
'sticky': "nsew"
})
} #'padding':5,
# end of theme extract - don't forget to add comma at end when inserting
})
style.theme_use('yummy') # 'default'
widg = LabelFrame(fr, text='Piratz!')
widg.grid(column=0, row=11, sticky='nsew', padx=5, pady=5, ipadx=5, ipady=5)
f0 = Label(widg, text='Something to say')
f0.grid()
widg1 = LabelFrame(fr, text='Piratz!\nextra line')
widg1.grid(column=0, row=12, sticky='nsew', padx=5, pady=5, ipadx=5,
ipady=5) # ipadx=5, ipady=5
f1 = Label(widg1, text='Something else to say\nwith an extra line')
f1.grid()
run_state(fr, widg, widg1)
root.mainloop()
def build(self):
"""Widget construction."""
lf1 = LabelFrame(self.fr0, text='rgb')
lf1.grid(column=0, row=0, sticky='new')
lf1.columnconfigure(1, weight=1)
rl0 = Label(lf1, text='red ')
rl0.grid(column=0, row=0, sticky='s')
self.rcan = Canvas(lf1,
width=self.canvas_w,
height=self.canvas_h,
bd=0,
highlightthickness=0)
self.rcan.grid(column=1,
row=0,
sticky='sew',
padx=self.sliderlength // 2)
self.rcan.bind("<Configure>", self.resize_rcan)
rsc = TtkScale(lf1,
self.scale_l,
from_=0,
to=255,
variable=self.rvar,
orient='horizontal',
command=self.rhandle,
tickinterval=20)
rsc.grid(column=1, row=1, sticky='new')
vcmdsb = root.register(sb_okay)
rsb = Spinbox(lf1,
from_=0,
to=255,
textvariable=self.rvar,
validate='key',
validatecommand=(vcmdsb, '%d', '%P', '%S', 255),
command=self.rhandle,
width=5)
rsb.grid(column=2, row=1, sticky='nw')
rsb.bind('<KeyRelease>', self.checksb)
rel = Label(lf1)
rel.grid(column=2, row=2)
gl0 = Label(lf1, text='green')
gl0.grid(column=0, row=3)
self.gcan = Canvas(lf1,
width=self.canvas_w,
height=self.canvas_h,
bd=0,
highlightthickness=0)
self.gcan.grid(column=1,
row=3,
sticky='sew',
padx=self.sliderlength // 2)
self.gcan.bind("<Configure>", self.resize_gcan)
gsc = TtkScale(lf1,
self.scale_l,
from_=0,
to=255,
variable=self.gvar,
orient='horizontal',
command=self.ghandle,
tickinterval=20)
gsc.grid(column=1, row=4, sticky='new')
gsb = Spinbox(lf1,
from_=0,
to=255,
textvariable=self.gvar,
validate='key',
validatecommand=(vcmdsb, '%d', '%P', '%S', 255),
command=self.ghandle,
width=5)
gsb.grid(column=2, row=4, sticky='nw')
gsb.bind('<KeyRelease>', self.checksb)
gel = Label(lf1)
gel.grid(column=2, row=5)
bl0 = Label(lf1, text='blue ')
bl0.grid(column=0, row=6, sticky='s')
self.bcan = Canvas(lf1,
width=self.canvas_w,
height=self.canvas_h,
bd=0,
highlightthickness=0)
self.bcan.grid(column=1,
row=6,
sticky='new',
padx=self.sliderlength // 2)
self.bcan.bind("<Configure>", self.resize_bcan)
bsc = TtkScale(lf1,
self.scale_l,
from_=0,
to=255,
variable=self.bvar,
orient='horizontal',
command=self.bhandle,
tickinterval=20)
bsc.grid(column=1, row=7, sticky='new')
bsb = Spinbox(lf1,
from_=0,
to=255,
textvariable=self.bvar,
validate='key',
validatecommand=(vcmdsb, '%d', '%P', '%S', 255),
command=self.bhandle,
width=5)
bsb.grid(column=2, row=7, sticky='nw')
bsb.bind('<KeyRelease>', self.checksb)
bel = Label(lf1)
bel.grid(column=2, row=8)
lf3 = LabelFrame(self.fr0, text='colour mix')
lf3.grid(column=1, row=0, sticky='nw')
self.cmcan = cmcan = Canvas(lf3,
width=30,
height=30,
bd=0,
highlightthickness=0)
cmcan.grid(column=0, row=0, sticky='n', columnspan=2)
cmcan.grid_propagate(0)
vdraw_gradient(self.cmcan, (255, 0, 0), alpha=255)
cml = Label(lf3, text='hash\nvalue')
cml.grid(column=0, row=1)
vcmd = root.register(is_okay)
self.ent0 = ent0 = Entry(lf3,
width=8,
validate='key',
validatecommand=(vcmd, '%i', '%P', '%S'),
textvariable=self.evar)
ent0.grid(column=1, row=1)
ent0.bind('<KeyRelease>', self.checkhash)
lf5 = LabelFrame(lf3, text='related colours', style='Wide.TLabelframe')
lf5.grid(column=0, row=2, sticky='nw', columnspan=2)
self.srcls = []
self.vrcls = []
self.srccans = []
self.vrccans = []
relateds = [25, 50, 75, 100]
stexts = ['25% sat', '50% sat', '75% sat', '100% sat']
vtexts = ['25% val', '50% val', '75% val', '100% val']
for ix, rel in enumerate(relateds):
Label(lf5, text=stexts[ix]).grid(row=1 + 2 * ix,
column=0,
sticky='n')
self.srcls.append(Label(lf5))
self.srcls[ix].grid(row=1 + 2 * ix, column=1, sticky='n')
self.srccans.append(
Canvas(lf5, width=30, height=30, bd=0, highlightthickness=0))
self.srccans[ix].grid(row=2 * ix,
column=0,
sticky='n',
columnspan=2)
Label(lf5, text=vtexts[ix]).grid(row=9 + 2 * ix,
column=0,
sticky='n')
self.vrcls.append(Label(lf5))
self.vrcls[ix].grid(row=9 + 2 * ix, column=1, sticky='n')
self.vrccans.append(
Canvas(lf5, width=30, height=30, bd=0, highlightthickness=0))
self.vrccans[ix].grid(row=8 + 2 * ix,
column=0,
sticky='n',
columnspan=2)
self.cccan = Canvas(lf5,
width=30,
height=30,
bd=0,
highlightthickness=0)
self.cccan.grid(column=0, row=17, sticky='n', columnspan=2)
self.ccla = Label(lf5, text="comp'y")
self.ccla.grid(column=0, row=18, sticky='n')
self.ccl = Label(lf5, text="")
self.ccl.grid(column=1, row=18, sticky='n')
al0 = Label(lf1, text='alpha')
al0.grid(column=0, row=10, sticky='s')
self.acan = Canvas(lf1,
width=self.canvas_w,
height=self.canvas_h,
bd=0,
highlightthickness=0)
self.acan.grid(column=1,
row=10,
sticky='new',
padx=self.sliderlength // 2)
self.acan.bind("<Configure>", self.resize_acan)
asc = TtkScale(lf1,
self.scale_l,
from_=0,
to=255,
variable=self.avar,
orient='horizontal',
command=self.ahandle,
tickinterval=20)
asc.grid(column=1, row=11, sticky='new')
asb = Spinbox(lf1,
from_=0,
to=255,
textvariable=self.avar,
validate='key',
validatecommand=(vcmdsb, '%d', '%P', '%S', 255),
command=self.ahandle,
width=5)
asb.grid(column=2, row=11, sticky='nw')
asb.bind('<KeyRelease>', self.checksba)
ael = Label(lf1, text=' ')
ael.grid(column=2, row=12, sticky='s')
draw_gradient(self.rcan, (0, 0, 0), (255, 0, 0), width=self.canvas_w)
draw_gradient(self.gcan, (255, 0, 0), (255, 0, 255),
width=self.canvas_w)
draw_gradient(self.bcan, (255, 0, 0), (255, 255, 0),
width=self.canvas_w)
draw_agradient(self.acan, (127, 127, 127), (255, 0, 0),
width=self.canvas_w)
lf4 = LabelFrame(self.fr0, text='hsv')
lf4.grid(column=2, row=0, sticky='news')
lf4.columnconfigure(1, weight=1)
hl0 = Label(lf4, text='hue ')
hl0.grid(column=0, row=0, sticky='s')
self.hcan = Canvas(lf4,
width=self.canvas_w,
height=self.canvas_h,
bd=0,
highlightthickness=0)
self.hcan.grid(column=1,
row=0,
sticky='sew',
padx=self.sliderlength // 2)
self.hcan.bind("<Configure>", self.resize_hcan)
hsc = TtkScale(lf4,
self.scale_l,
from_=0,
to=360,
variable=self.hvar,
orient='horizontal',
command=self.hhandle,
tickinterval=30)
hsc.grid(column=1, row=1, sticky='new')
vcmdsb = root.register(sb_okay)
hsb = Spinbox(lf4,
from_=0,
to=360,
textvariable=self.hvar,
validate='key',
validatecommand=(vcmdsb, '%P', '%S', 360),
command=self.hhandle,
width=5)
hsb.grid(column=2, row=1, sticky='nw')
hsb.bind('<KeyRelease>', self.checksbh)
hel = Label(lf4)
hel.grid(column=2, row=2)
sl0 = Label(lf4, text='sat ')
sl0.grid(column=0, row=3)
self.scan = Canvas(lf4,
width=self.canvas_w,
height=self.canvas_h,
bd=0,
highlightthickness=0)
self.scan.grid(column=1,
row=3,
sticky='sew',
padx=self.sliderlength // 2)
self.scan.bind("<Configure>", self.resize_scan)
ssc = TtkScale(lf4,
self.scale_l,
from_=0,
to=100,
variable=self.svar,
orient='horizontal',
command=self.shandle,
tickinterval=10)
ssc.grid(column=1, row=4, sticky='new')
ssb = Spinbox(lf4,
from_=0,
to=100,
textvariable=self.svar,
validate='key',
validatecommand=(vcmdsb, '%P', '%S', 100),
command=self.shandle,
width=5)
ssb.grid(column=2, row=4, sticky='nw')
ssb.bind('<KeyRelease>', self.checksb100)
sel = Label(lf4)
sel.grid(column=2, row=5)
vl0 = Label(lf4, text='value')
vl0.grid(column=0, row=6, sticky='s')
self.vcan = Canvas(lf4,
width=self.canvas_w,
height=self.canvas_h,
bd=0,
highlightthickness=0)
self.vcan.grid(column=1,
row=6,
sticky='new',
padx=self.sliderlength // 2)
self.vcan.bind("<Configure>", self.resize_vcan)
vsc = TtkScale(lf4,
self.scale_l,
from_=0,
to=100,
variable=self.vvar,
orient='horizontal',
command=self.vhandle,
tickinterval=10)
vsc.grid(column=1, row=7, sticky='new')
vsb = Spinbox(lf4,
from_=0,
to=100,
textvariable=self.vvar,
validate='key',
validatecommand=(vcmdsb, '%P', '%S', 100),
command=self.vhandle,
width=5)
vsb.grid(column=2, row=7, sticky='nw')
vsb.bind('<KeyRelease>', self.checksb100)
vel = Label(lf4)
vel.grid(column=2, row=8)
# assume initial setting 0,100,100 hsv
to_colour = hsv_to_rgb(*(0, 100, 100))
hue_gradient(self.hcan, width=self.canvas_w)
draw_gradient(self.scan, (255, 255, 255),
to_colour,
width=self.canvas_w)
draw_gradient(self.vcan, (0, 0, 0), to_colour, width=self.canvas_w)
self.can_hsv = can_hsv = Canvas(lf4,
width=self.wheel_w,
height=self.wheel_w,
bg='#d9d9d9')
can_hsv.grid(column=0, row=9, columnspan=3, pady=25, sticky='n')
self.hsv_gamut = PhotoImage(file='../figures/colour_wheel.png')
can_hsv.create_image(0, 0, anchor='nw', image=self.hsv_gamut)
self.ring = circle(can_hsv,
307,
158,
self.ring_radius,
width=self.ring_width,
outline='#555555',
activeoutline='black',
tags='ring')
can_hsv.bind('<Button-1>', self.click_ring)
can_hsv.tag_bind('ring', '<B1-Motion>', self.drag_ring)
self.related(0, 100, 100, 255, 0, 0)
def _gui():
try:
from tkinter import Tk, ttk, filedialog, messagebox, StringVar, IntVar
from tkinter.ttk import Button, Entry, Frame, Label, LabelFrame, Notebook, Radiobutton, Style
except:
sys.exit("Unable to load tkinter. Aborting.")
def _check_single(): #check the input and accordingly give the output... for the f_single tab
if txt_f_single_entry.get()=="":
lbl_f_single_result.config(text="", style="TLabel")
elif check_afm(txt_f_single_entry.get()):
lbl_f_single_result.config(text="Έγκυρο ΑΦΜ.", style="valid.TLabel")
else:
lbl_f_single_result.config(text="Άκυρο ΑΦΜ.", style="invalid.TLabel")
def _select_input_file():
strv_f_file_input.set(filedialog.askopenfilename(title="Άνοιγμα αρχείου"))
if strv_f_file_input.get() != "" and strv_f_file_output.get() != "":
btn_f_file_submit.config(state="normal")
else: btn_f_file_submit.config(state="disabled")
#TODO a much better mechanism to enable / disable btn_f_file_submit is needed.
def _select_output_file():
strv_f_file_output.set(filedialog.asksaveasfilename(title="Αποθήκευση ως..."))
if strv_f_file_input.get() != "" and strv_f_file_output.get() != "":
btn_f_file_submit.config(state="normal")
else: btn_f_file_submit.config(state="disabled")
def _check_file():#TODO this could / should be merged with the TUI version...
input_filepath = strv_f_file_input.get()
output_filepath = strv_f_file_output.get()
filter_output = intvar_filter_sel.get()
try:
input_file = open(input_filepath, "r")
output_file = open(output_filepath, "w")
except:
messagebox.showerror(title="Σφάλμα", message="Αδυναμία διαχείρησης των αρχείων που ορίσατε.\n\nΠαρακαλώ επιβεβαιώστε πως το αρχείο με τα δεδομένα υπάρχει, πως έχετε δικαιώματα ανάγνωσης, και πως έχετε δικαιώματα εγγραφής στον κατάλογο εξαγωγής των αποτελεσμάτων.")
return
counter = {True:0, False:0}
for entry in input_file:
validation = check_afm(entry.strip())
counter[validation]+=1
if filter_output == 3 and validation == False:
output_file.write(entry)
elif filter_output == 2 and validation == True:
output_file.write(entry)
elif filter_output == 1:
output_file.write(entry.strip() + "\t" + str(validation) + "\n\r")
lbl_f_file_result.config(text="Σύνολο: "+str(counter[True]+counter[False])+"\nΈγκυρα: "+str(counter[True])+"\nΆκυρα: "+str(counter[False]))
#create the window
main_window = Tk()
main_window.title("Έλεγχος εγκυρότητας Α.Φ.Μ. (v 2.0)")
main_window.geometry("600x180")
main_window.minsize(600,180)
#fool arround with styling
style = ttk.Style()
style.configure("valid.TLabel", background="green")
style.configure("empty.TLabel", background="white")
style.configure("invalid.TLabel", background="red")
style.configure("TNotebook", padding = 10)
#create the Notebook
tabs = Notebook(main_window)
f_single = Frame(tabs)
f_file = Frame(tabs)
tabs.add(f_single, text="Μεμονομένα Α.Φ.Μ.")
tabs.add(f_file, text="Λίστα από αρχείο")#add state="disabled" prior to git push until ready
tabs.pack(anchor="nw")
#add some widgets in f_single tab
lbl_f_single_instructions = Label(f_single, text="Εισάγετε έναν ΑΦΜ για έλεγχο")
lbl_f_single_instructions.grid(column=0, row=0)
lbl_f_single_result = Label(f_single, text="", width=10, justify="center")
lbl_f_single_result.grid(column=1, row=0, rowspan=2, sticky="ewns")
txt_f_single_entry = Entry(f_single, width=11)
txt_f_single_entry.focus()
txt_f_single_entry.bind("<KeyRelease>", lambda e: _check_single() )
txt_f_single_entry.grid(column=0,row=1)
#btn_f_single_submit = Button(f_single, text="Έλεγχος", command=_check_single)
#btn_f_single_submit.grid(column=0,row=2)
#add some widgets in f_file tab
lbl_f_file_finput = Label(f_file, text="Άνοιγμα...")
lbl_f_file_finput.grid(column=0, row=0)
strv_f_file_input = StringVar()
txt_f_file_finput = Entry(f_file, textvariable = strv_f_file_input)
txt_f_file_finput.grid(column=1, row=0)
btn_f_file_finput = Button(f_file, text="...", width=3, command=_select_input_file)
btn_f_file_finput.grid(column=2, row=0, sticky="W")
lbl_f_file_foutput = Label(f_file, text="Αποθήκευση ως...")
lbl_f_file_foutput.grid(column=0, row=1)
strv_f_file_output = StringVar()
txt_f_file_foutput = Entry(f_file, textvariable = strv_f_file_output)
txt_f_file_foutput.grid(column=1, row=1)
btn_f_file_foutput = Button(f_file, text="...", width=3, command=_select_output_file)
btn_f_file_foutput.grid(column=2, row=1, sticky="W")
lf_filter = LabelFrame(f_file, text="Επιστροφή")
lf_filter.grid(column=3, row=0, rowspan=2, sticky="ewns")
intvar_filter_sel = IntVar()
rb_filter_all = Radiobutton(lf_filter, text="Όλων", variable=intvar_filter_sel, value=1) #TODO maybe add command
rb_filter_all.pack(anchor="w")
rb_filter_all.invoke()
rb_filter_true = Radiobutton(lf_filter, text="Έγκυρων", variable=intvar_filter_sel, value=2)
rb_filter_true.pack(anchor="w")
rb_filter_false = Radiobutton(lf_filter, text="Άκυρων", variable=intvar_filter_sel, value=3)
rb_filter_false.pack(anchor="w")
lf_result = LabelFrame(f_file, text="Σύνοψη")
lf_result.grid(column=4, row=0, rowspan=2, sticky="ewns")
lbl_f_file_result = Label(lf_result, text="", width=12)#TODO bring results
lbl_f_file_result.pack()
btn_f_file_submit = Button(f_file, text="Επεξεργασία", state="disabled", command=_check_file)
btn_f_file_submit.grid(column=0, row=2, columnspan=3)
btn_main_exit = Button(main_window, text="Έξοδος", command=sys.exit)
btn_main_exit.pack(anchor="se")
main_window.mainloop()
def _create_text_tab(self, nb):
self.dir0 = 1
self.dir1 = 1
# populate the third frame with other widgets
fr = Frame(nb, name='fr')
lF = LabelFrame(fr, text="Slider")
fr1 = Frame(lF)
fr1.grid(row=0, column=0, sticky='nsew')
from_ = 100
to = 0
value = 0
step = 10
fontSize = 9
self.scvar = IntVar()
scRange = self.any_number_range(from_, to, step)
scLen = len(scRange[1]) * (fontSize + 10)
self.sc = Scale(fr1,
from_=from_,
to=to,
variable=self.scvar,
orient='vertical',
length=scLen,
command=self.v_scale)
self.sc.set(value)
l1 = Label(fr1, textvariable=self.scvar, width=5)
l1.grid(row=0, column=0, padx=5, pady=5)
self.sc.grid(row=0, column=1, padx=5, pady=5)
fr4 = Frame(fr1)
fr4.grid(row=0, column=2)
sc_split = '\n'.join(scRange[0].split())
lb = Label(fr1, text=sc_split, font=('Courier New', str(fontSize)))
lb.grid(row=0, column=2, padx=5, pady=5)
fr2 = Frame(lF, name='fr2')
fr2.grid(row=0, column=1, sticky='nsew')
self.schvar = IntVar()
a = 0
b = 100
schRange = self.any_number_range(a, b, s=10)
schLen = Font().measure(schRange[0])
self.sch = Scale(fr2,
from_=a,
to=b,
length=schLen,
variable=self.schvar,
orient='horizontal',
command=self.h_scale)
self.sch.set(0)
l2 = Label(fr2, textvariable=self.schvar)
l2.grid(row=1, column=1, pady=2)
self.sch.grid(row=2, column=1, padx=5, pady=5, sticky='nsew')
l3 = Label(fr2, text=schRange[0], font=('Courier New', str(fontSize)))
l3.grid(row=3, column=1, padx=5, pady=5)
lF.grid(row=0, column=0, sticky='nesw', pady=5, padx=5)
lF1 = LabelFrame(fr, text="Progress", name='lf')
pb1var = IntVar()
pb2var = IntVar()
self.pbar = Progressbar(lF1,
variable=pb1var,
length=150,
mode="indeterminate",
name='pb1',
orient='horizontal')
self.pb2 = Progressbar(lF1,
variable=pb2var,
length=150,
mode='indeterminate',
name='pb2',
orient='vertical')
self.pbar["value"] = 25
self.h_progress()
self.v_progress()
self.pbar.grid(row=1, column=0, padx=5, pady=5, sticky='nw')
self.pb2.grid(row=1, column=1, padx=5, pady=5, sticky='nw')
l3 = Label(lF1, textvariable=pb1var)
l3.grid(row=0, column=0, pady=2, sticky='nw')
l4 = Label(lF1, textvariable=pb2var)
l4.grid(row=0, column=1, pady=2, sticky='nw')
sg1 = Sizegrip(fr)
sg1.grid(row=2, column=2, sticky='e')
lF1.grid(row=1, column=0, sticky='nesw', pady=5, padx=5)
# add to notebook (underline = index for short-cut character)
nb.add(fr, text='Sliders & Others', underline=0)
class Page1(Frame):
def __init__(self, master):
Frame.__init__(self, master)
self.style = Style()
self.time_frame = LabelFrame(self, text='Time Setting')
self.hour_label = Label(self.time_frame, text='Hours')
self.hour_box = Spinbox(self.time_frame, from_=0, to=24)
self.minute_label = Label(self.time_frame, text='Minutes')
self.minute_box = Spinbox(self.time_frame, from_=0, to=60)
self.second_label = Label(self.time_frame, text='Seconds')
self.second_box = Spinbox(self.time_frame, from_=0, to=60)
self.break_label = Label(self.time_frame, text='Time During Sessions')
self.break_var = IntVar()
self.break_var.set(4)
self.break_radio_button_3 = Radiobutton(self.time_frame,
text='3 min',
variable=self.break_var,
value=3)
self.break_radio_button_4 = Radiobutton(self.time_frame,
text='4 min',
variable=self.break_var,
value=4)
self.break_radio_button_5 = Radiobutton(self.time_frame,
text='5 min',
variable=self.break_var,
value=5)
self.break_radio_button_6 = Radiobutton(self.time_frame,
text='6 min',
variable=self.break_var,
value=6)
self.break_radio_button_7 = Radiobutton(self.time_frame,
text='7 min',
variable=self.break_var,
value=7)
self.name_label = Label(self.time_frame, text='Task Name')
self.name_entry = Entry(self.time_frame)
self.reminder_label = Label(self.time_frame, text='Reminder')
self.reminder_entry = Entry(self.time_frame)
self.generate_button = Button(self,
text='Generate Task',
command=self.create_task)
self.save_button = Button(self,
text='Save Configuration',
command=self.save_config)
self.load_button = Button(self,
text='Load Configuration',
command=self.load_config)
self.clear_button = Button(self, text='Clear', command=self.clear)
# GRIDDING OPERATIONS
self.hour_label.grid(row=1, column=0)
self.hour_box.grid(row=1, column=1)
self.minute_label.grid(row=1, column=2)
self.minute_box.grid(row=1, column=3)
self.second_label.grid(row=1, column=4)
self.second_box.grid(row=1, column=5)
self.break_label.grid(row=2, column=0)
self.break_radio_button_3.grid(row=2, column=1)
self.break_radio_button_4.grid(row=2, column=2)
self.break_radio_button_5.grid(row=2, column=3)
self.break_radio_button_6.grid(row=2, column=4)
self.break_radio_button_7.grid(row=2, column=5)
self.name_label.grid(row=3, column=0)
self.name_entry.grid(row=3, column=1, columnspan=5, sticky='ew')
self.reminder_label.grid(row=4, column=0)
self.reminder_entry.grid(row=4, column=1, columnspan=5, sticky='ew')
self.generate_button.grid(row=1, column=0, sticky='snew')
self.save_button.grid(row=2, column=0, sticky='snew')
self.load_button.grid(row=3, column=0, sticky='snew')
self.clear_button.grid(row=4, column=0, sticky='snew')
self.time_frame.grid(row=0, column=0)
self.grid(row=0, column=0)
def create_task(self):
# Task signature: (task_name, task_duration, break_duration, task_reminder=None)
hours = self.hour_box.get()
minutes = self.minute_box.get()
seconds = self.second_box.get()
break_time = self.break_var.get()
if hours and seconds and minutes:
total_time = int(hours) * 3600 + int(minutes) * 60 + int(seconds)
return Task(self.name_entry.get(), total_time, break_time)
elif hours == 's':
return Task('sample task', 5, 3 / 60)
def save_config(self):
with open('config.pickle', 'wb+') as config:
pickle.dump(self.create_task(), config)
def load_config(self):
with open('config.pickle', 'rb') as config:
unpickled_task = pickle.load(config)
Task.tasks.append(unpickled_task)
def clear(self):
self.name_entry.delete(0, 'end')
self.reminder_entry.delete(0, 'end')
self.hour_box.set('')
self.minute_box.set('')
self.second_box.set('')
class ChIPSeqFrame( PipelineFrame ) :
def __init__(self, pipepanel, pipeline_name, *args, **kwargs) :
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.info = None
eframe = self.eframe = LabelFrame(self,text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid( row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5 )
label = Label(eframe,text="Pipeline")#,fg=textLightColor,bg=baseColor)
label.grid(row=3,column=0,sticky=W,padx=10,pady=5)
Pipelines=["ChIPSeq"]
Pipeline = self.Pipeline = StringVar()
Pipeline.set(Pipelines[0])
om = OptionMenu(eframe, Pipeline, *Pipelines, command=self.option_controller)
om.config()#bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config()#bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3,column=1,sticky=W,padx=10,pady=5)
label.grid(row=6, column=0, columnspan=5, sticky=W, padx=10, pady=5)
self.add_info(eframe)
'''
def set_data_directory( self ):
fname = askdirectory( initialdir = USER_HOME,
title="Select Data Directory")
self.datapath.set(fname)
#count number
self.data_count['text'] = str(
len([fn for fn in listdir(fname) if fn.endswith(filetype) or fn.endswith('.fastq')] )
)
print( "Found", self.data_count['text'], filetype, "files!" )
'''
def add_info( self, parent ) :
if not self.info :
self.info = LabelFrame(parent, text='Peak Call Info')
self.info_text = Text( self.info,
width=50,
height=8,
#bg=projectBgColor,
#fg=projectFgColor,
font=("nimbus mono bold","11")
)
self.info_save_button = Button(self.info,
text="Save",
command = self.writeinfo )
self.info_load_button = Button(self.info,
text="Load",
command = self.readinfo )
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
self.info_load_button.grid( row=5, column=5, padx=10, pady=5 )
self.info_save_button.grid( row=5, column=6, padx=10, pady=5 )
self.info_text.grid( row=1, rowspan=3,
column=1, columnspan=7,
padx=5, pady=5 )
self.info.grid(row=7,column=0, columnspan=6, sticky=W, padx=20, pady=10 )
def writeinfo( self ) :
self.writepaste( 'peakcallinfo.csv', self.info_text )
def readinfo( self ) :
self.readpaste( 'peakcallinfo.csv', self.info_text )
