added ability to plot custom range to GUI

svpv/gui.py

@@ -34,6 +34,8 @@ def __init__(self, par):
         self.set_sample_selector()
         self.genotype_selector = None
         self.set_genotype_selector()
+        self.plot_custom = None
+        self.set_plot_custom()
         self.filters = None
         self.set_filters()
         self.sv_chooser = None
@@ -57,7 +59,7 @@ def setup_static_features(self):
             self.list.destroy()
         self.list = tk.Button(self.buttons_1, text="Apply Filters", command=self.apply_filters)
         self.list.grid(row=0, column=1, padx=40, sticky=tk.E)
-        self.buttons_1.grid(row=3, column=0, columnspan=2, sticky=tk.EW, padx=10)
+        self.buttons_1.grid(row=4, column=0, columnspan=2, sticky=tk.EW, padx=10)
 
         if self.buttons_2:
             self.buttons_2.destroy()
@@ -68,7 +70,7 @@ def setup_static_features(self):
         self.viewGTs.grid(row=0, column=0, padx=25, sticky=tk.W)
         if self.viewSV:
             self.viewSV.destroy()
-        self.viewSV = tk.Button(self.buttons_2, text="Plot Selected SV", command=self.view_sv)
+        self.viewSV = tk.Button(self.buttons_2, text="Plot Selected SV", command=self.plot_sv)
         self.viewSV.grid(row=0, column=1, padx=25, sticky=tk.W)
         if self.plotAll:
             self.plotAll.destroy()
@@ -80,7 +82,7 @@ def setup_static_features(self):
         self.display_cb = tk.Checkbutton(self.buttons_2, text='display plot on creation', variable=self.display_var,
                                          onvalue=1, offvalue=0)
         self.display_cb.grid(row=1, column=1, padx=25, sticky=tk.E)
-        self.buttons_2.grid(row=5, column=0, columnspan=2, sticky=tk.EW, padx=10)
+        self.buttons_2.grid(row=6, column=0, columnspan=2, sticky=tk.EW, padx=10)
 
     def text_size(self, opt):
         if opt == 1:
@@ -112,23 +114,29 @@ def set_genotype_selector(self):
         self.genotype_selector = gw.SampleGenotypeSelector(self, self.current_samples)
         self.genotype_selector.grid(row=1, column=1, sticky=tk.NSEW, padx=10)
 
+    def set_plot_custom(self):
+        if self.plot_custom:
+            self.plot_custom.destroy()
+        self.plot_custom = gw.PlotCustom(self)
+        self.plot_custom.grid(row=2, column=0, columnspan=2, sticky=tk.NSEW, pady=2, padx=10)
+
     def set_filters(self):
         if self.filters:
             self.filters.destroy()
         self.filters = gw.Filters(self)
-        self.filters.grid(row=2, column=0, columnspan=2, sticky=tk.NSEW, pady=2, padx=10)
+        self.filters.grid(row=3, column=0, columnspan=2, sticky=tk.NSEW, pady=2, padx=10)
 
     def set_sv_chooser(self):
         if self.sv_chooser:
             self.sv_chooser.destroy()
         self.sv_chooser = gw.SvChooser(self, self.svs, self.par.run.vcf.count)
-        self.sv_chooser.grid(row=4, column=0, sticky=tk.NSEW, padx=10, columnspan=2)
+        self.sv_chooser.grid(row=5, column=0, sticky=tk.NSEW, padx=10, columnspan=2)
 
     def set_info_box(self, message=''):
         if self.info_box:
             self.info_box.destroy()
         self.info_box = gw.InfoBox(self, message)
-        self.info_box.grid(row=6, column=0, sticky=tk.NSEW, padx=10, columnspan=2)
+        self.info_box.grid(row=7, column=0, sticky=tk.NSEW, padx=10, columnspan=2)
 
     def reset_filters(self):
         self.set_info_box()
@@ -209,14 +217,16 @@ def apply_filters(self):
         self.svs = self.par.run.vcf.filter_svs(self.par.filter)
         self.set_sv_chooser()
 
-    def view_sv(self):
+    def plot_sv(self, sv=None):
         self.set_info_box()
         if not self.current_samples:
             self.info_box.message.config(text="Error: No Samples Selected")
-        elif self.sv_chooser.sv_fl.selected_idx is None:
+        elif self.sv_chooser.sv_fl.selected_idx is None and sv is None:
             self.info_box.message.config(text="Error: No SV Selected")
         else:
-            plot = Plot(self.svs[self.sv_chooser.sv_fl.selected_idx], self.current_samples, self.par)
+            if not sv:
+                sv = self.svs[self.sv_chooser.sv_fl.selected_idx]
+            plot = Plot(sv, self.current_samples, self.par)
             if self.display_var.get():
                 self.filename = plot.plot_figure(group=self.par.plot.grouping, display=self.par.run.display)
             else:

svpv/gui_widgets.py

@@ -3,6 +3,7 @@
 # author: Jacob Munro, Victor Chang Cardiac Research Institute
 # """
 from __future__ import print_function
+from .vcf import SV
 try:
     import Tkinter as tk
     import tkFileDialog
@@ -62,7 +63,6 @@ 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):
         tk.LabelFrame.__init__(self, parent, text="Sample Selection")
@@ -139,6 +139,26 @@ def get_selection(self):
                 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(custom)
 
 class Filters(tk.LabelFrame):
     def __init__(self, parent):

svpv/plot.py

@@ -27,7 +27,7 @@ def __init__(self, sv, samples, par):
         h_bkpt_wind = (par.run.bkpt_win * par.run.rd_len) // 2
 
         # show depth over whole region but zoom in on breakpoints if necessary
-        if sv.svtype in ('DEL', 'DUP', 'CNV', 'INV'):
+        if sv.svtype in ('DEL', 'DUP', 'CNV', 'INV', 'CUSTOM'):
             start = sv.pos - par.run.expansion * (sv.end - sv.pos + 1)
             end = sv.end + par.run.expansion * (sv.end - sv.pos + 1)
             self.region_bins = Bins(sv.chrom, start, end, ideal_num_bins=par.run.num_bins)
@@ -163,6 +163,8 @@ def print_data(self):
                     svs.append(sv)
         if svs:
             SV.print_SVs(svs, svs_file, self.par.run.vcf.name)
+        if self.sv.svtype == 'CUSTOM':
+            SV.print_SVs([self.sv], svs_file, 'CUSTOM')
         # ref vcf
         if self.par.run.ref_vcf:
             svs = []