/
base_gui_launch.py
executable file
·176 lines (151 loc) · 7.78 KB
/
base_gui_launch.py
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##!/usr/bin/env python
import Tkinter as tk
import tkSimpleDialog as tkd
import os
import subprocess
import ToolTip
curpath= os.path.realpath(__file__)
curpath = curpath.split('/')
curpath = '/'.join(curpath[:-1])
curpath += '/'
print curpath
python_path = '/software/so/el6.3/PythonPackages-2.7.6/bin/python'
annotate_script = os.path.abspath(curpath+'Annotate/annotate.py')
predict_script = os.path.abspath(curpath+'Predict/prediction_pipeline.py')
prioritize_script = os.path.abspath(curpath+'Prioritize/prioritization_pipeline.py')
relaunch_script = os.path.abspath(curpath+'pipeline_control/qsubclass.py')
pipe_element_script = os.path.abspath(curpath+'pipeline_control/pipeline_element.py')
kill_script = os.path.abspath(curpath+'pipeline_control/kill_jobs.py')
font_type ="Helvetica"
def predict_win():
'''
Opens the Prediction dialog box
'''
NewWin = tkd.Predict_window(root)
if NewWin.result != None:
commandline = """--infolder {0[infolder]} --outfolder {0[outfolder]} --qsubname {0[qsubname]} --config {0[config]} --max_coverage {0[max_cov]}""".format(NewWin.result)
commandline += """ --namestart {0[namestart]} --namelength {0[namelength]} --firstreadextension {0[read1]} --secondreadextension {0[read2]} --indelcaller {0[indel]}""".format(NewWin.result)
commandline += """ --cpu {0[cpu]} --mem {0[mem]} """.format(NewWin.result)
if NewWin.result['force']==1:
commandline += " --fusevariants "
commandline +=""" --qoptions " {0[qopts]}" """.format(NewWin.result) #The space before { is key for the command line to work
if NewWin.result.get('sample_list',False):
commandline += " --sample_list "+NewWin.result.get('sample_list',False)
commandline = python_path + ' ' + predict_script + ' ' + commandline + '&'
#print commandline
subprocess.Popen(commandline,shell=True)
def annotate_win():
'''
Opens the Annotation dialog box
'''
NewWin= tkd.Annotate_window(root)
if NewWin.result != None:
commandline = """-i {0[infile]} --variantType {0[vartype]} --sampleGenotypeMode {0[gtype]} --geneDef {0[gdef]}""".format(NewWin.result)
if NewWin.result['force']==1:
commandline += " -f "
if NewWin.result['only_gen']==1:
commandline += " -o"
commandline = python_path + ' ' + annotate_script + ' ' + commandline + '&'
#print commandline
subprocess.Popen(commandline,shell=True)
def prioritize_win():
'''
Opens the Prioritization dialog box
'''
NewWin = tkd.Prioritize_window(root)
if NewWin.result != None:
commandline = """--outfolder {0[outfolder]} --qsubname {0[qsubname]} --jobname {0[jobname]} --familytype {0[familytype]} --geneexclusion {0[gex_file]}""".format(NewWin.result)
if NewWin.result['force']==1:
commandline += " --force "
if NewWin.result['multisample']==1:
commandline += " --multisample"
for el in NewWin.result['inheritance']:
commandline += ' --inheritance %s'%el
if NewWin.result.get('config'):
commandline += " --config %s"%NewWin.result["config"]
if NewWin.result.get('family'):
commandline += " --family %s"%NewWin.result["family"]
if NewWin.result.get('white_list'):
commandline += " --white_list %s"%NewWin.result["white_list"]
commandline +=""" --qoptions " {0[qopts]}" """.format(NewWin.result)#The space before { is key for the command line to work
commandline = python_path + ' ' + prioritize_script + ' ' + commandline
print commandline
subprocess.Popen(commandline,shell=True)
def Resume_window():
'''
Re-launch a qsub or pipe job in case it crashed or to re-launch it
It supports a resume option fully operational for the prioritize phase
Less complete for the predict phase (just checks the step state without checking the needed outputs)
'''
NewWin = tkd.Resume_window(root)
if NewWin.result != None:
#print NewWin.result
commandline =""" {0[filename]} "{0[qopts]}" """.format(NewWin.result) #The space before { is key for the command line to work
commandline = python_path + ' ' + relaunch_script + ' ' + commandline + '&'
print commandline
subprocess.Popen(commandline,shell=True)
def Kill_window():
'''
Browse for a .qsub file which hosts running jobs and kill them all
'''
NewWin = tkd.Kill_window(root)
if NewWin.result != None:
#print NewWin.result
commandline =""" {0[filename]} """.format(NewWin.result) #The space before { is key for the command line to work
commandline = python_path + ' ' + kill_script + ' ' + commandline + '&'
#print commandline
subprocess.Popen(commandline,shell=True)
#print commandline
##############################
#### MAIN
##############################
#colors
back_color = "#7e3878"#aa00ff"
emerald ='#008a00'
mango ='#da532c'#e8980e'#'#fa6800'
cobalt ='#2d89ef'#'#0050ef'
steel ="#1d1d1d"#647687'
green ='#60a917'
orange = '#fa6800'#'#cd3700''#f09609'
azzurro = '#1ba1f2'
text_color='white'#'#ffffff'
root = tk.Tk()
w = root.winfo_screenwidth()
h = root.winfo_screenheight()
wh=700 #Window height
ww=500 #Window width
bw =15 #Button width
bh=4
txt_dim =20
root.title('')
root.geometry('%dx%d+%d+%d'%(ww,wh,w/2 - ww/2,h/2 -wh/2))
root.resizable(0,0)
root.configure(background=back_color)
##Buttons
w = tk.Label(root, text="\neDiVa\nWhat do you want to do?\n",background=back_color,fg=text_color,font=(font_type, txt_dim),
)
Predict = tk.Button(root,text='Predict', command=predict_win,width=bw,height=bh,fg=text_color,font=(font_type, txt_dim)
,highlightbackground= emerald,relief='flat',background= emerald,activebackground= green )
Annotate = tk.Button(root,text='Annotate', command=annotate_win,width=bw,height=bh,fg=text_color,font=(font_type, txt_dim)
,highlightbackground= mango,relief='flat',background=mango,activebackground= orange )
Prioritize = tk.Button(root,text='Prioritize', command=prioritize_win,width=bw,height=bh,fg=text_color,font=(font_type, txt_dim)
,highlightbackground=cobalt,relief='flat',background=cobalt,activebackground= azzurro )
Quit = tk.Button(root,text='Quit', command=root.destroy,width=bw,height=bh,fg=text_color,font=(font_type,txt_dim)
,highlightbackground= steel,relief='flat',background= steel,activebackground='#76608a' )
Rerun = tk.Button(root,text='Rerun', command=Resume_window,width=bw,height=bh,fg=text_color,font=(font_type,txt_dim)
,highlightbackground= '#2C4566',relief='flat',background= '#2C4566',activebackground='#76608a' )
Kill = tk.Button(root,text='Stop', command=Kill_window,width=bw,height=bh,fg=text_color,font=(font_type,txt_dim)
,highlightbackground= '#2c3e50',relief='flat',background= '#2c3e50',activebackground='#76608a' )
w.grid(row=0,rowspan=3,columnspan=3,sticky='W'+'E'+'S'+'N')
Annotate.grid(row=4,column=1,sticky='EW')
Predict.grid(row=3,column=1,sticky='EW')
Prioritize.grid(row=3,column=2,sticky='WE')
Quit.grid(row=4,column=2,sticky='WE')
Rerun.grid(row=5,column=1,sticky='EW')
Kill.grid(row=5,column=2,sticky='WE')
ToolTip.ToolTip(Predict, follow_mouse=1, text="eDiVa Varitant Prediction pipeline for sample-wise variant calling.")
ToolTip.ToolTip(Prioritize, follow_mouse=1, text="eDiVa Varitant filtering and ranking pipeline for trios-families.")
ToolTip.ToolTip(Annotate, follow_mouse=1, text="eDiVa Annotation for VCF files.")
ToolTip.ToolTip(Rerun, follow_mouse=1, text="Rerun a previously defined pipeline with new computing parameters.")
ToolTip.ToolTip(Kill, follow_mouse=1, text="Kill multiple jobs depending on a single pipeline.")
root.mainloop()