# # -*- coding: utf-8 -*-
# """
# author: Jacob Munro, Victor Chang Cardiac Research Institute
# """
from __future__ import print_function
from .vcf import SV
try:
import Tkinter as tk
import tkFileDialog
except ImportError:
import tkinter as tk
from tkinter import filedialog as tkFileDialog
import re
from shutil import copyfile
class MenuBar(tk.Menu):
def __init__(self, parent):
tk.Menu.__init__(self, parent)
self.parent = parent
self.file = tk.Menu(self, tearoff=0)
self.file.add_command(label='save figure as', command=self.asksaveasfilename)
self.file.add_command(label='exit', command=self.parent.quit)
self.add_cascade(label='File', menu=self.file)
self.size_var = tk.IntVar(value=2)
self.resize = tk.Menu(self, tearoff=0)
self.resize.add_radiobutton(label='x-small', var=self.size_var, value=1, command=self.update_size)
self.resize.add_radiobutton(label='small', var=self.size_var, value=2, command=self.update_size)
self.resize.add_radiobutton(label='medium', var=self.size_var, value=3, command=self.update_size)
self.resize.add_radiobutton(label='large', var=self.size_var, value=4, command=self.update_size)
self.resize.add_radiobutton(label='x-large', var=self.size_var, value=5, command=self.update_size)
self.add_cascade(label='View', menu=self.resize)
self.vcf_var = tk.IntVar(value=0)
self.vcf = tk.Menu(self, tearoff=0)
self.vcf.add_radiobutton(label=parent.par.run.vcf.name, var=self.vcf_var, value=0,
command=self.switch_vcf)
for i in range(len(parent.par.run.alt_vcfs)):
self.vcf.add_radiobutton(label=parent.par.run.alt_vcfs[i].name, var=self.vcf_var, value=i+1,
command=self.switch_vcf)
self.add_cascade(label='VCF', menu=self.vcf)
def asksaveasfilename(self):
if not self.parent.filename:
self.parent.set_info_box(message='Error: No figure has been created yet.')
else:
file_options = {}
file_options['initialdir'] = self.parent.par.run.out_dir
file_options['initialfile'] = re.sub('/.+/', '', self.parent.filename)
file_options['filetypes'] = [('pdf files', '.pdf')]
file_options['parent'] = self.parent
file_options['title'] = 'save figure as'
filename = tkFileDialog.askdirectory(**file_options)
if filename:
copyfile(self.parent.filename, filename)
def update_size(self):
self.parent.text_size(self.size_var.get())
def switch_vcf(self):
if self.vcf_var.get() != 0:
self.parent.switch_vcf(self.vcf_var.get()-1)
class SampleSelector(tk.LabelFrame):
def __init__(self, parent, samples, ped=None):
tk.LabelFrame.__init__(self, parent, text="Sample Selection")
self.parent = parent
self.samples = samples
self.ped = ped
self.families = []
if self.ped is None:
self.flb = FieldedListbox(self, ('Sample',), width=20, selectmode=tk.EXTENDED)
for s in self.samples:
self.flb.push_entry((s,))
self.flb.grid(row=0, column=0, padx=10, columnspan=2)
else:
self.flb = FieldedListbox(self, ('Sample', 'Family'), width=15, selectmode=tk.EXTENDED)
for s in self.samples:
if s in ped.families_by_sample:
self.families.append(ped.families_by_sample[s])
else:
self.families.append('NA')
self.flb.push_entry((s, self.families[-1]))
self.flb.grid(row=0, column=0, padx=10, columnspan=3)
self.select_b = tk.Button(self, text="Select", command=self.select)
self.select_b.grid(row=1, column=0, padx=10)
c = 1
if ped is not None:
self.select_fam_b = tk.Button(self, text="Select Family", command=self.select_fam)
self.select_fam_b.grid(row=1, column=c, padx=10)
c += 1
self.clear = tk.Button(self, text="Clear", command=self.clear)
self.clear.grid(row=1, column=c, padx=10)
def select(self):
if self.flb.sel_idxs:
self.parent.samples_update(self.flb.sel_idxs)
def select_fam(self):
idxs = []
fam = self.families[self.flb.sel_idxs[0]]
for i in range(len(self.families)):
if self.families[i] == fam:
idxs.append(i)
self.flb.select_idxs(idxs)
self.select()
def clear(self):
self.parent.current_samples = []
self.parent.set_genotype_selector()
class SampleGenotypeSelector(tk.LabelFrame):
def __init__(self, parent, samples):
tk.LabelFrame.__init__(self, parent, text="Sample Genotype Selection")
self.parent = parent
self.samples = samples
self.max_row = 5
if self.samples:
self.GT_CBs = []
self.c = 0
self.r = 0
self.set_samples()
else:
self.GT_CBs = None
self.lab = tk.Label(self,text="-- No samples Selected --")
self.lab.grid(row=0, sticky = tk.EW)
def set_samples(self):
for s in self.samples:
self.GT_CBs.append(GenotypeSelector(self, s))
self.GT_CBs[-1].grid(column=self.c, row=self.r, sticky = tk.EW)
self.r += 1
if self.r == self.max_row:
self.r = 0
self.c +=1
class GenotypeSelector(tk.LabelFrame):
def __init__(self, parent, name):
tk.LabelFrame.__init__(self, parent, text=name)
self.gts = ["0/0", "0/1", "1/1"]
self.checkVars = []
self.CBs = []
self.r = 0
self.c = 0
self.set_check_boxes()
def set_check_boxes(self):
for gt in self.gts:
self.checkVars.append(tk.IntVar(value=0))
self.CBs.append(tk.Checkbutton(self, text=gt, variable=self.checkVars[-1], onvalue=1, offvalue=0))
self.CBs[-1].grid(row = self.r, column=self.c, sticky=tk.EW)
self.c += 1
def get_selection(self):
gts = []
for i in range(0, len(self.gts)):
if self.checkVars[i].get():
gts.append(self.gts[i])
return gts
class PlotCustom(tk.LabelFrame):
def __init__(self, parent):
tk.LabelFrame.__init__(self, parent, text="Plot Custom Range")
self.parent = parent
self.lab = tk.Label(self, text='Custom range:')
self.rangeVar = tk.StringVar(value='chrX:YYYYYY-ZZZZZZ')
self.entry = tk.Entry(self, textvariable=self.rangeVar, width=25)
self.setter = tk.Button(self, text="Plot Custom", command=self.do_plot)
self.lab.grid(row=0, column=0, sticky=tk.NSEW)
self.entry.grid(row=0, column=1, sticky=tk.NSEW)
self.setter.grid(row=0, column=2, sticky=tk.NSEW)
def do_plot(self):
try:
chrom, pos, end = re.split('[:-]', self.rangeVar.get())[0:3]
custom = SV(chrom, pos, end, 'CUSTOM', '.', '.', '.')
except ValueError:
print("invalid region")
return None
self.parent.plot_sv(sv=custom)
class Filters(tk.LabelFrame):
def __init__(self, parent):
tk.LabelFrame.__init__(self, parent, text="Filters")
self.af_filter = AfFilter(self)
self.gene_filter = GeneFilter(self)
self.len_filter = LengthFilter(self)
self.type_filter = SvTypeFilter(self)
self.af_filter.grid(row=0, sticky=tk.NSEW, columnspan=2)
self.gene_filter.grid(row=0, column=2, sticky=tk.NSEW)
self.len_filter.grid(row=0, column=3, sticky=tk.NSEW)
self.type_filter.grid(row=0, column=4, sticky=tk.NSEW)
def reset(self):
self.af_filter.reset()
self.gene_filter.reset()
self.len_filter.reset()
self.type_filter.reset()
class SvTypeFilter(tk.LabelFrame):
types = (None, 'DEL', 'DUP', 'CNV', 'INV', 'INS', 'BND', 'TRA')
def __init__(self, parent):
tk.LabelFrame.__init__(self, parent)
self.type_var = tk.IntVar(value=0)
self.radio_buttons = [tk.Radiobutton(self, text='All', justify=tk.LEFT, variable=self.type_var, value=0)]
self.radio_buttons[-1].grid(row=0, column=0, sticky=tk.W)
r=1
c=0
for i in range(1, len(SvTypeFilter.types)):
self.radio_buttons.append(tk.Radiobutton(self, text=SvTypeFilter.types[i], justify=tk.LEFT,
variable=self.type_var, value=i))
self.radio_buttons[-1].grid(row=r, column=c, sticky=tk.W)
r += 1
if r > 3:
r = 0
c += 1
def reset(self):
self.type_var.set(0)
class GeneFilter(tk.LabelFrame):
def __init__(self, parent):
tk.LabelFrame.__init__(self, parent)
self.ref_gene_on = tk.IntVar(value=0)
self.ref_gene_on_cb = tk.Checkbutton(self, text="ref gene\nintersection", justify=tk.LEFT, variable=self.ref_gene_on)
self.ref_gene_on_cb.grid(row=0, column=0, sticky=tk.W)
self.gene_list_on = tk.IntVar(value=0)
self.gene_list_on_cb = tk.Checkbutton(self, text="gene list\nintersection", justify=tk.LEFT, variable=self.gene_list_on)
self.gene_list_on_cb.grid(row=1, column=0, sticky=tk.W)
self.exonic_on = tk.IntVar(value=0)
self.exonic_on_cb = tk.Checkbutton(self, text="exonic", justify=tk.LEFT, variable=self.exonic_on)
self.exonic_on_cb.grid(row=2, column=0, sticky=tk.W)
def reset(self):
self.ref_gene_on.set(0)
self.gene_list_on.set(0)
self.exonic_on.set(0)
class LengthFilter(tk.LabelFrame):
def __init__(self, parent):
tk.LabelFrame.__init__(self, parent)
self.title = tk.Label(self, text='SV Length')
self.len_GT_On = tk.IntVar(value=0)
self.len_GT_On_CB = tk.Checkbutton(self, text=">", justify=tk.LEFT, variable=self.len_GT_On)
self.len_GT_val = tk.Spinbox(self, values=(1,5,10,50,100,500), width=3)
self.len_GT_Units = tk.Spinbox(self, values=("bp", "kbp", "Mbp"), width=3)
self.len_LT_On = tk.IntVar(value=0)
self.len_LT_On_CB = tk.Checkbutton(self, text="<", justify=tk.LEFT, variable=self.len_LT_On)
self.len_LT_val = tk.Spinbox(self, values=(1,5,10,50,100,500), width=3)
self.len_LT_Units = tk.Spinbox(self, values=("bp", "kbp", "Mbp"), width=3)
self.title.grid(row=0, column=0, sticky=tk.EW, columnspan=4)
self.len_GT_On_CB.grid(row=1, column=0, sticky=tk.EW)
self.len_GT_val.grid(row=2, column=0, sticky=tk.EW)
self.len_GT_Units.grid(row=2, column=1, sticky=tk.EW)
self.len_LT_On_CB.grid(row=1, column=2, sticky=tk.EW)
self.len_LT_val.grid(row=2, column=2, sticky=tk.EW)
self.len_LT_Units.grid(row=2, column=3, sticky=tk.EW)
def reset(self):
self.len_GT_On.set(0)
self.len_LT_On.set(0)
self.len_GT_val.destroy()
self.len_GT_Units.destroy()
self.len_LT_val.destroy()
self.len_LT_Units.destroy()
self.len_GT_val = tk.Spinbox(self, values=(1, 5, 10, 50, 100, 500), width=3)
self.len_GT_Units = tk.Spinbox(self, values=("bp", "kbp", "Mbp"), width=3)
self.len_LT_val = tk.Spinbox(self, values=(1, 5, 10, 50, 100, 500), width=3)
self.len_LT_Units = tk.Spinbox(self, values=("bp", "kbp", "Mbp"), width=3)
self.len_GT_val.grid(row=2, column=0, sticky=tk.EW)
self.len_GT_Units.grid(row=2, column=1, sticky=tk.EW)
self.len_LT_val.grid(row=2, column=2, sticky=tk.EW)
self.len_LT_Units.grid(row=2, column=3, sticky=tk.EW)
class AfFilter(tk.LabelFrame):
def __init__(self, parent):
tk.LabelFrame.__init__(self, parent)
self.af_on = tk.IntVar(value=0)
self.af_on_cb = tk.Checkbutton(self, text="AF Threshold", variable=self.af_on)
self.af_on_cb.grid(row=0, column=0, padx=3, columnspan=2, sticky=tk.EW)
self.af_var = tk.DoubleVar()
self.af_gt_lt = tk.IntVar(value=1)
self.af_lt_radio_button = tk.Radiobutton(self, text="<", variable=self.af_gt_lt, value=1)
self.af_lt_radio_button.grid(row=1, column=0, sticky=tk.EW)
self.af_gt_radio_button = tk.Radiobutton(self, text=">", variable=self.af_gt_lt, value=2)
self.af_gt_radio_button.grid(row=1, column=1, sticky=tk.EW)
self.af_scale = tk.Scale(self, variable=self.af_var, from_=float(0), to=float(1), resolution=float(0.01),
orient=tk.HORIZONTAL)
self.af_scale.grid(row=2, column=0, padx=3, sticky=tk.EW, columnspan=2)
def reset(self):
self.af_on.set(0)
self.af_var.set(0)
self.af_gt_lt.set(1)
class SvChooser(tk.LabelFrame):
def __init__(self, parent, svs, sv_count):
tk.LabelFrame.__init__(self, parent, text="Structural Variant Call Selection")
self.sv_fl = None
if not svs:
self.lab = tk.Label(self,text="-- No matches --")
self.lab.grid(row=0, column=0, sticky = tk.EW)
self.num_svs_lab = tk.Label(self, text='-- of %d SVs' % sv_count)
else:
self.sv_fl = FieldedListbox(self, ("SV Type", "Chr A", "Pos A", "Chr B", "Pos B", "Length (bp)", "AF"))
for sv in svs:
self.sv_fl.push_entry(sv.string_tuple())
self.num_svs_lab = tk.Label(self, text='%d of %d SVs' % (len(svs), sv_count))
self.sv_fl.grid(row=0, sticky = tk.NSEW)
self.num_svs_lab.grid(row=1, column=0, sticky=tk.EW)
class InfoBox(tk.LabelFrame):
def __init__(self, parent, message):
tk.LabelFrame.__init__(self, parent, text="Info")
self.message = tk.Label(self, text=message, bg='white', width=55, justify=tk.LEFT)
self.message.pack()
def genotypes(self, sv, vcf_samples, run_samples):
message = ''
line = ''
for i, gt in enumerate(sv.GTs):
if '1' in gt:
if vcf_samples[i] in run_samples:
this = '%s:%s' % (vcf_samples[i], gt)
if len(line) == 0:
line = this
elif len(this) + len(line) >= 50:
message += line + ',\n'
line = this
else:
line += ', %s' % this
message += line
self.message.config(text=message, bg='white', width=55, justify=tk.LEFT)
# class for multiple listboxes linked by single scroll bar
class FieldedListbox(tk.Frame):
def __init__(self, parent, header, width=10, selectmode=tk.BROWSE):
tk.Frame.__init__(self, parent)
self.parent = parent
self.num_f = len(header)
self.headers = []
self.lbs = []
self.c = 0
self.sel_idxs = []
self.scroll = tk.Scrollbar(self, orient=tk.VERTICAL)
for i in range(0, self.num_f):
self.headers.append(tk.Label(self, text=header[i]))
self.headers[-1].grid(row=0, column=self.c, sticky=tk.EW)
self.lbs.append(tk.Listbox(self, width=width, selectmode=selectmode, yscrollcommand=self.yscroll, bg='white'))
self.lbs[-1].grid(row=1, column=self.c, sticky=tk.EW)
self.lbs[-1].bind("<<ListboxSelect>>", self.select)
self.c += 1
self.scroll.config(command=self.lbs[0].yview)
self.scroll.grid(row=1, column=self.c, sticky=tk.NS)
def select(self, val):
idxs = map(int, val.widget.curselection())
self.select_idxs(idxs)
def select_idxs(self, idxs):
for lb in self.lbs:
for i in self.sel_idxs:
lb.itemconfig(i, background='white')
lb.activate(i)
for i in idxs:
lb.activate(i)
lb.itemconfig(i, background='gray70', selectbackground='gray70')
self.sel_idxs = idxs
def yscroll(self, *args):
self.scroll.set(*args)
for i in range(0, self.num_f):
self.lbs[i].yview_moveto(args[0])
def push_entry(self, entry):
if not len(entry) == self.num_f:
return False
for i, f in enumerate(entry):
self.lbs[i].insert(tk.END, f)
return True
# return the index of selection
def get_selection(self):
print(self.lbs[0].curselection())
return map(int, self.lbs[0].curselection())
