#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Scoary - Microbial Pan-GWAS GUI
By Ola Brynildsrud
Norwegian Institute of Public Health
olbb@fhi.no
"""
import sys, os
import threading
try:
import Tkinter
except ImportError:
#Python 3 issues
try:
import tkinter as Tkinter
except:
sys.exit("Need to have Tkinter / tkinter installed")
try:
import tkFileDialog
except ImportError:
# Python 3 issues
try:
from tkinter import filedialog
tkFileDialog = filedialog
except:
sys.exit("Could not find tkFileDialog / filedialog")
try:
import ttk
except ImportError:
# Python 3 issues
try:
from tkinter import ttk as ttk
except:
sys.exit("Could not find ttk / tkinter.ttk")
try:
ttk
Tkinter
except NameError:
sys.exit("Need the following installed: Tkinter, tkFileDialog, ttk")
try:
import os
except ImportError:
sys.exit("Need to be able to import os")
try:
import argparse
except ImportError:
sys.exit("Need to be able to import argparse")
try:
import scoary.methods as sm
import scoary
except ImportError:
sys.exit("Could not find the main Scoary executable")
from pkg_resources import resource_string, resource_filename
class ScoaryGUI(Tkinter.Tk):
"""
Create the main GUI window
"""
def __init__(self,parent):
Tkinter.Tk.__init__(self,parent)
self.parent = parent
self.Scoary_parameters = {"GPA": None,"Trait":None,"Tree":None,
"Restrict":None, "Writetree": False,
"Delimiter":",", "Startcol": "15",
"Maxhits":None, "Notime":False,
"Outdir":None, "Permutations":0,
"No_pairwise":False, "Collapse":False,
"Cutoffs": {"I": [1,0.05],
"B": [0,1.0],
"BH": [0,1.0],
"PW": [0,1.0],
"EPW": [1,0.05],
"P":[0,1.0]},
}
self.initialize_menu()
self.toppart = Tkinter.Frame(self,height="350",width="800")
self.bottompart = Tkinter.Frame(self,height="50",width="800")
self.toppart.pack(side='top',expand=False)
self.bottompart.pack(side='bottom',expand=True,fill='both')
self.nwpart = Tkinter.Frame(self.toppart,
height="350",
width="250")
self.nepart = Tkinter.LabelFrame(self.toppart,
height="350",
width="550",
text="Control panel")
self.nwpart.pack(side='left',expand=False)
self.nepart.pack(side='right',expand=True)
# Add further frames to top or bottom
self.logocanvas = Tkinter.Canvas(self.nwpart,
height="250",
width="250",
relief="ridge",
bd=0,
highlightthickness=0)
self.logocanvas.pack(side='top',expand=False)
self.citationframe = Tkinter.Frame(self.nwpart,
height="100",
width="250")
self.citationframe.pack(side='bottom',expand=False,fill='none')
self.initialize_controlboard()
self.initialize_logo()
self.initialize_citation()
self.initialize_statusframe()
######## MENUS ########
def initialize_menu(self):
"""
Initialize the menu at the top
"""
self.menubar = Tkinter.Menu(self,relief="flat")
filemenu = Tkinter.Menu(self.menubar,tearoff=0)
filemenu.add_command(label="About",command=self.AboutScoary)
filemenu.add_separator()
filemenu.add_command(label="Quit",command=self.quit)
self.filemenu = filemenu
self.menubar.add_cascade(label="File",menu=self.filemenu)
optsmenu = Tkinter.Menu(self.menubar,tearoff=0)
optsmenu.add_command(label="Clear", command=self.ClearAll)
optsmenu.add_command(label="Test example",
command=self.TestExample)
self.optsmenu = optsmenu
self.menubar.add_cascade(label="Options",menu=self.optsmenu)
self.config(menu=self.menubar)
def initialize_citation(self):
"""
Initialize the citation frame - below the logo
"""
myfontstyle = ("Arial",8)
self.citation = Tkinter.Label(self.citationframe,
text=self.citationtext(),
anchor='center',
justify='center',
font=myfontstyle)
self.citation.pack(expand=True)
def initialize_statusframe(self):
"""
Initialize the frame and statusbar occupying the bottom
"""
frame = self.bottompart
frame.pb = ttk.Progressbar(frame,
orient='horizontal',
mode='determinate',
maximum=100)
frame.pb.pack(fill='both',expand=True,side='top')
frame.lab = Tkinter.Label(frame,text=u"Awaiting input options")
frame.lab.pack(in_=frame.pb,expand=True)
#sys.stdout = StdoutToLabel(frame.lab, progressbar=frame.pb)
sys.stdout = StdoutToLabel(frame.lab,
progressbar=frame.pb,
width=frame.cget('width'))
def initialize_controlboard(self):
"""
Initialize the controlboard - where all the settings are set.
"""
board = self.nepart
self.GPAentryVariable = Tkinter.StringVar()
board.GPAentry = \
Tkinter.Entry(board,
textvariable = self.GPAentryVariable,
width=60)
board.GPAentry.grid(column=0,row=0,sticky='W',columnspan=2)
self.GPAentryVariable.set("Path to gene presence absence file")
self.TraitsentryVariable = Tkinter.StringVar()
board.Traitsentry = \
Tkinter.Entry(board,
textvariable=self.TraitsentryVariable,
width=60)
board.Traitsentry.grid(column=0,row=1,sticky='W',columnspan=2)
self.TraitsentryVariable.set("Path to traits/phenotype file")
self.TreeentryVariable = Tkinter.StringVar()
board.Treeentry = \
Tkinter.Entry(board,
textvariable=self.TreeentryVariable,
width=60)
board.Treeentry.grid(column=0,row=2,sticky='W',columnspan=2)
self.TreeentryVariable.set(
"(Optional) Path to custom tree file")
self.RestrictVariable = Tkinter.StringVar()
board.Restrictentry = \
Tkinter.Entry(board,
textvariable=self.RestrictVariable,
width=60)
board.Restrictentry.grid(column=0,row=3,sticky='W',columnspan=2)
self.RestrictVariable.set(
"(Optional) Path to file naming isolates to include")
self.Outputdir = Tkinter.StringVar()
board.Outputentry = \
Tkinter.Entry(board,
textvariable=self.Outputdir,
width=60)
board.Outputentry.grid(column=0,row=4,sticky='W',columnspan=2)
self.Outputdir.set("(Optional) Output directory")
browsebuttonGPA = \
Tkinter.Button(board,
text=u"Browse...",
command=self.BrowseButtonClickGPA)
browsebuttonGPA.grid(column=2,row=0,sticky='e')
browsebuttonTraits = \
Tkinter.Button(board,
text=u"Browse...",
command=self.BrowseButtonClickTraits)
browsebuttonTraits.grid(column=2,row=1,sticky='e')
browsebuttonTreeFile = \
Tkinter.Button(board,
text=u"Browse...",
command=self.BrowseButtonClickTreeFile)
browsebuttonTreeFile.grid(column=2,row=2,sticky='e')
browsebuttonRestrict = \
Tkinter.Button(board,
text=u"Browse...",
command=self.BrowseButtonClickRestrict)
browsebuttonRestrict.grid(column=2,row=3,sticky='e')
browsebuttonOutput = \
Tkinter.Button(board,
text=u"Browse...",
command=self.BrowseButtonClickOutput)
browsebuttonOutput.grid(column=2,row=4,sticky='e')
# Initialize frame for cutoffs
board.pframe = Tkinter.LabelFrame(board,
text="Cut-offs",
relief='ridge')
board.pframe.grid(column=0,row=5,sticky='w')
self.initialize_pvalueframe()
# Initialize frame for misc options
board.miscframe = Tkinter.LabelFrame(board,
text="Misc options",
relief='ridge')
board.miscframe.grid(column=1,row=5,sticky='e',columnspan=2)
self.initialize_miscopts()
## Create extra space
board.emptyspace = Tkinter.Frame(board)
board.emptyspace.grid(column=0,row=6,columnspan=3,pady=(20,20))
masterbuttonfont = ("Courier", 16)
RunButton = Tkinter.Button(board.emptyspace,
text=u"Run analysis",
font=masterbuttonfont,
command=self.RunAnalysis,
padx=15,pady=10)
RunButton.grid(column=2,row=0)
QuitButton = Tkinter.Button(board.emptyspace,
text=u"Quit",
font=masterbuttonfont,
command=self.quit,padx=15,pady=10)
QuitButton.grid(column=1,row=0)
HelpButton = Tkinter.Button(board.emptyspace,
text=u"Help",
font=masterbuttonfont,
command=self.HelpButton,
padx=15,pady=10)
HelpButton.grid(column=0,row=0)
def initialize_miscopts(self):
"""
Initialize the miscellaneous options
"""
board = self.nepart
miscframe = board.miscframe
# Max hits
self.mhtext = Tkinter.StringVar()
miscframe.mhlab = Tkinter.Label(miscframe,
textvariable=self.mhtext)
miscframe.mhlab.grid(column=0,row=0,sticky='w')
self.mhtext.set("Max hits")
self.maxhitsvar = Tkinter.StringVar()
miscframe.maxhitsentry = \
Tkinter.Entry(miscframe,
textvariable=self.maxhitsvar,
width=8)
miscframe.maxhitsentry.grid(column=1,row=0)
self.maxhitsvar.set("")
# Delimiter
self.delimtext = Tkinter.StringVar()
miscframe.delim = \
Tkinter.Label(miscframe,
textvariable=self.delimtext)
miscframe.delim.grid(column=0,row=1,sticky='w')
self.delimtext.set("Delimiter")
self.delimvar = Tkinter.StringVar()
miscframe.delimentry = \
Tkinter.Entry(miscframe,
textvariable=self.delimvar,
width=8)
miscframe.delimentry.grid(column=1,row=1)
self.delimvar.set(",")
# Starting column
self.sctext = Tkinter.StringVar()
miscframe.sclab = \
Tkinter.Label(miscframe,
textvariable=self.sctext)
miscframe.sclab.grid(row=2,column=0,sticky='w')
self.sctext.set("Startcol GPA file")
self.scvar = Tkinter.StringVar()
miscframe.sc = Tkinter.Entry(miscframe,textvariable=self.scvar,width=8)
miscframe.sc.grid(row=2,column=1)
self.scvar.set("15")
# Permutations
self.permtext = Tkinter.StringVar()
miscframe.permlab = \
Tkinter.Label(miscframe,
textvariable=self.permtext)
miscframe.permlab.grid(row=3,column=0,sticky='w')
self.permtext.set("Permutations")
self.permvar = Tkinter.StringVar()
miscframe.perm = \
Tkinter.Entry(miscframe,
textvariable=self.permvar,
width=8)
miscframe.perm.grid(row=3,column=1)
self.permvar.set("0")
# No timestamp
self.notimevar = Tkinter.IntVar()
miscframe.notime = \
Tkinter.Checkbutton(miscframe,
text=u"No timestamp",
onvalue=1,
offvalue=0,
variable=self.notimevar)
miscframe.notime.grid(row=5,column=0,sticky='w')
# Write tree
self.writetreevar = Tkinter.IntVar()
miscframe.writetree = \
Tkinter.Checkbutton(miscframe,
text=u"Write tree",
onvalue=1,
offvalue=0,
variable=self.writetreevar)
miscframe.writetree.grid(row=6,column=0,sticky='w')
# No_pairwise
self.nopairwisevar = Tkinter.IntVar()
miscframe.nopairwise = \
Tkinter.Checkbutton(miscframe,
text=u"No pairwise",
onvalue=1,
offvalue=0,
variable=self.nopairwisevar)
miscframe.nopairwise.grid(row=7,column=0,sticky='w')
# Collapse
self.collapsevar = Tkinter.IntVar()
miscframe.collapse = \
Tkinter.Checkbutton(miscframe,
text=u"Collapse corr",
onvalue=1,
offvalue=0,
variable=self.collapsevar)
miscframe.collapse.grid(row=8,column=0,sticky='w')
def initialize_pvalueframe(self):
"""
Initialize the filtration controlboard
"""
board = self.nepart
pframe = board.pframe
# Add p-value checkboxes
self.naivetext = Tkinter.StringVar()
self.pVar = Tkinter.IntVar()
self.pVar.set(1)
self.pBVar = Tkinter.IntVar()
self.pBHVar = Tkinter.IntVar()
self.pstext = Tkinter.StringVar()
self.pPWVar = Tkinter.IntVar()
self.pEPWVar = Tkinter.IntVar()
self.pEPWVar.set(1)
self.pPermVar = Tkinter.IntVar()
pframe.naivelab = \
Tkinter.Label(pframe,
textvariable=self.naivetext)
self.naivetext.set(u"Pop structure-naive filters")
pframe.pNcheck = \
Tkinter.Checkbutton(pframe,
text=u"Naive (Fisher's)",
onvalue=1,
offvalue=0,
variable=self.pVar)
pframe.pBcheck = \
Tkinter.Checkbutton(pframe,
text=u"Bonferroni",
onvalue=1,
offvalue=0,
variable=self.pBVar)
pframe.pBHcheck = \
Tkinter.Checkbutton(
pframe,
text=u"Benjamini-Hochberg",
onvalue=1,
offvalue=0,
variable=self.pBHVar)
pframe.pslab = \
Tkinter.Label(pframe,
textvariable=self.pstext)
self.pstext.set(u"Pop structure-aware filters")
pframe.pPWcheck = \
Tkinter.Checkbutton(pframe,
text=u"Pairwise comparison (Best)",
onvalue=1,
offvalue=0,
variable=self.pPWVar)
pframe.pEPWcheck = \
Tkinter.Checkbutton(pframe,
text=u"Pairwise comparison (Entire)",
onvalue=1,
offvalue=0,
variable=self.pEPWVar)
pframe.pPermcheck = \
Tkinter.Checkbutton(pframe,
text=u"Empirical p-value (Permutation)",
onvalue=1,
offvalue=0,
variable=self.pPermVar)
pframe.naivelab.grid(column=0,row=0,sticky='w')
pframe.pNcheck.grid(column=0,row=1,sticky='w')
pframe.pBcheck.grid(column=0,row=2,sticky='w')
pframe.pBHcheck.grid(column=0,row=3,sticky='w')
pframe.pslab.grid(column=0,row=4,sticky='w')
pframe.pPWcheck.grid(column=0,row=5,sticky='w')
pframe.pEPWcheck.grid(column=0,row=6,sticky='w')
pframe.pPermcheck.grid(column=0,row=7,sticky='w')
# Add p-value entry cells
self.pNaive = Tkinter.StringVar()
self.pBonf = Tkinter.StringVar()
self.pBH = Tkinter.StringVar()
self.pPW = Tkinter.StringVar()
self.pEPW = Tkinter.StringVar()
self.pPerm = Tkinter.StringVar()
pframe.pNaiveEntry = Tkinter.Entry(pframe,
textvariable=self.pNaive,
width=8)
pframe.pBonfEntry = Tkinter.Entry(pframe,
textvariable=self.pBonf,
width=8)
pframe.pBHEntry = Tkinter.Entry(pframe,
textvariable=self.pBH,
width=8)
pframe.pPWEntry = Tkinter.Entry(pframe,
textvariable=self.pPW,
width=8)
pframe.pEPWEntry = Tkinter.Entry(pframe,
textvariable=self.pEPW,
width=8)
pframe.pPermEntry = Tkinter.Entry(pframe,
textvariable=self.pPerm,
width=8)
pframe.pNaiveEntry.grid(column=1,row=1,sticky='w')
pframe.pBonfEntry.grid(column=1,row=2,sticky='w')
pframe.pBHEntry.grid(column=1,row=3,sticky='w')
pframe.pPWEntry.grid(column=1,row=5,sticky='w')
pframe.pEPWEntry.grid(column=1,row=6,sticky='w')
pframe.pPermEntry.grid(column=1,row=7,sticky='w')
self.pNaive.set("0.05")
self.pBonf.set("1.0")
self.pBH.set("1.0")
self.pPW.set("1.0")
self.pEPW.set("0.05")
self.pPerm.set("1.0")
######## EVENTS ########
def AboutScoary(self):
"""
Placeholder button. Planned short information about the method
"""
topwin = Tkinter.Toplevel(self)
button = \
Tkinter.Button(topwin,
text=str("https://github.com/AdmiralenOla/Scoary"))
button.pack()
def BrowseButtonClickGPA(self):
"""
Browse button for gene presence absence field
"""
myfile = \
tkFileDialog.askopenfilename(
filetypes=[('comma-separated values', '.csv'),
('all files','.*')])
self.GPAentryVariable.set(myfile)
def BrowseButtonClickTraits(self):
"""
Browse button for traits field
"""
myfile = \
tkFileDialog.askopenfilename(
filetypes=[('comma-separated values', '.csv'),
('all files','.*')])
self.TraitsentryVariable.set(myfile)
def BrowseButtonClickTreeFile(self):
"""
Browse button for tree field
"""
myfile = \
tkFileDialog.askopenfilename(
filetypes=[('newick tree files', '.nwk'),
('all files','.*')])
self.TreeentryVariable.set(myfile)
def BrowseButtonClickRestrict(self):
"""
Browse button for isolate restriction field
"""
myfile = \
tkFileDialog.askopenfilename(
filetypes=[('comma-separated values','.csv'),
('all files','.*')])
self.RestrictVariable.set(myfile)
def BrowseButtonClickOutput(self):
"""
Browse button for choosing output dir
"""
mydir = tkFileDialog.askdirectory(mustexist=True)
self.Outputdir.set(mydir)
def HelpButton(self):
"""
Placeholder button. Redirects to website
"""
print("Visit https://github.com/AdmiralenOla/Scoary for help")
def ClearAll(self):
"""
Sets all variables to defaults
"""
self.GPAentryVariable.set("Path to gene presence absence file")
self.TraitsentryVariable.set("Path to traits/phenotype file")
self.TreeentryVariable.set("(Optional) Path to custom tree "
"file")
self.RestrictVariable.set("(Optional) Path to file naming "
"isolates to include")
self.Outputdir.set("")
self.maxhitsvar.set("")
self.delimvar.set(",")
self.scvar.set("15")
self.notimevar.set(0)
self.writetreevar.set(0)
self.permvar.set("0")
self.pVar.set(1)
self.pBVar.set(0)
self.pBHVar.set(0)
self.pPWVar.set(0)
self.pEPWVar.set(1)
self.pNaive.set("0.05")
self.pBonf.set("1.0")
self.pBH.set("1.0")
self.pPW.set("1.0")
self.pEPW.set("0.05")
self.pPerm.set("1.0")
self.nopairwisevar.set(0)
def TestExample(self):
"""
Sets all variables corresponding to --test in the methods script
"""
self.GPAentryVariable.set(
str(os.path.join(resource_filename(__name__, 'exampledata'),
'Gene_presence_absence.csv')))
self.TraitsentryVariable.set(
str(os.path.join(resource_filename(__name__, 'exampledata'),
'Tetracycline_resistance.csv')))
self.TreeentryVariable.set("")
self.RestrictVariable.set("")
self.Outputdir.set("./")
self.maxhitsvar.set("")
self.delimvar.set(",")
self.scvar.set("15")
self.notimevar.set(0)
self.writetreevar.set(0)
self.permvar.set("0")
self.pVar.set(1)
self.pBVar.set(0)
self.pBHVar.set(0)
self.pPWVar.set(0)
self.pEPWVar.set(1)
self.pNaive.set("0.05")
self.pBonf.set("1.0")
self.pBH.set("1.0")
self.pPW.set("1.0")
self.pEPW.set("0.05")
self.pPerm.set("1.0")
self.nopairwisevar.set(0)
######## RUNNING THE ANALYSIS ########
def RunAnalysis(self):
"""
Upon click "Run analysis" - Reads all the set parameters and
calls run method
"""
self.Scoary_parameters["GPA"] = self.GPAentryVariable.get()
self.Scoary_parameters["Traits"] = \
self.TraitsentryVariable.get()
self.Scoary_parameters["Tree"] = self.TreeentryVariable.get()
self.Scoary_parameters["Outdir"] = self.Outputdir.get()
self.Scoary_parameters["Restrict"] = self.RestrictVariable.get()
self.Scoary_parameters["Writetree"] = self.writetreevar.get()
self.Scoary_parameters["Delimiter"] = self.delimvar.get()
self.Scoary_parameters["Startcol"] = self.scvar.get()
self.Scoary_parameters["Maxhits"] = self.maxhitsvar.get()
self.Scoary_parameters["Notime"] = self.notimevar.get()
self.Scoary_parameters["Permutations"] = self.permvar.get()
self.Scoary_parameters["No_pairwise"] = self.nopairwisevar.get()
self.Scoary_parameters["Collapse"] = self.collapsevar.get()
self.Scoary_parameters["Cutoffs"]["I"][0] = self.pVar.get()
self.Scoary_parameters["Cutoffs"]["I"][1] = self.pNaive.get()
self.Scoary_parameters["Cutoffs"]["B"][0] = self.pBVar.get()
self.Scoary_parameters["Cutoffs"]["B"][1] = self.pBonf.get()
self.Scoary_parameters["Cutoffs"]["BH"][0] = self.pBHVar.get()
self.Scoary_parameters["Cutoffs"]["BH"][1] = self.pBH.get()
self.Scoary_parameters["Cutoffs"]["PW"][0] = self.pPWVar.get()
self.Scoary_parameters["Cutoffs"]["PW"][1] = self.pPW.get()
self.Scoary_parameters["Cutoffs"]["EPW"][0] = self.pEPWVar.get()
self.Scoary_parameters["Cutoffs"]["EPW"][1] = self.pEPW.get()
self.Scoary_parameters["Cutoffs"]["P"][0] = self.pPermVar.get()
self.Scoary_parameters["Cutoffs"]["P"][1] = self.pPerm.get()
self.PrepareScoaryCMDline()
def PrepareScoaryCMDline(self):
"""
Prepares arguments to correspond with argparse namespace and
runs. Listens to sys.stdout and updates statusbar.
"""
citation=False
RunScoary = True
correction = []
p_value_cutoff = []
for m in self.Scoary_parameters["Cutoffs"]:
if self.Scoary_parameters["Cutoffs"][m][0] == 1:
correction.append(m)
try:
p_value_cutoff.append(
float(self.Scoary_parameters["Cutoffs"][m][1]))
except ValueError:
print("Please enter real numbers in the p value "
"fields")
RunScoary = False
break
delimiter = self.Scoary_parameters["Delimiter"]
genes = (self.Scoary_parameters["GPA"] if
self.Scoary_parameters["GPA"] not in
["","Path to gene presence absence file"] else None)
try:
max_hits = (int(self.Scoary_parameters["Maxhits"]) if
self.Scoary_parameters["Maxhits"] not in [""]
else None)
except ValueError:
print("Please enter a real number (or nothing) in the max "
"hits field")
max_hits = None
RunScoary = False
try:
permutations = (abs(int(
self.Scoary_parameters["Permutations"])) if
self.Scoary_parameters["Permutations"]
not in [""]
else 0)
except ValueError:
print("Please enter a real number (or nothing) in the max "
"hits field")
permutations = 0
RunScoary = False
newicktree = (self.Scoary_parameters["Tree"] if
self.Scoary_parameters["Tree"] not in
["", "(Optional) Path to custom tree file"]
else None)
no_time = (True if self.Scoary_parameters["Notime"] == 1
else False)
outdir = (self.Scoary_parameters["Outdir"] if
self.Scoary_parameters["Outdir"] not in
["","(Optional) Output directory"]
else "./")
restrict_to = (self.Scoary_parameters["Restrict"] if
self.Scoary_parameters["Restrict"] not in
["","(Optional) Path to file naming isolates to "
"include"]
else None)
start_col = self.Scoary_parameters["Startcol"]
test = False
threads = 1
traits = (self.Scoary_parameters["Traits"] if
self.Scoary_parameters["Traits"] not in
["","Path to traits/phenotype file"]
else None)
upgma_tree = (True if self.Scoary_parameters["Writetree"] == 1
else False)
write_reduced=False
collapse= (True if self.Scoary_parameters["Collapse"] == 1
else False)
no_pairwise = (True if self.Scoary_parameters["No_pairwise"] == 1
else False)
myargs = argparse.Namespace(citation=citation,
correction=correction,
p_value_cutoff=p_value_cutoff,
delimiter=delimiter,
genes=genes,
grabcols=[],
max_hits=max_hits,
newicktree=newicktree,
no_time=no_time,
restrict_to=restrict_to,
outdir=outdir,
permute=permutations,
start_col=start_col,
test=test,
threads=threads,
traits=traits,
upgma_tree=upgma_tree,
write_reduced=write_reduced,
collapse=collapse,
no_pairwise=no_pairwise)
if RunScoary:
try:
sm.main(args=myargs,
cutoffs=dict(
list(zip(correction, p_value_cutoff))),
statusbar=sys.stdout)
except SystemExit as SE:
# Set status bar color to red?
if str(SE) == "0":
print("Analysis complete!")
else:
print("Fatal error: %s" % str(SE))
# Listen to stdout and update statusbar
######## MISC METHODS ########
def initialize_logo(self):
"""
Initialize logo
"""
photo=Tkinter.PhotoImage(data=self.Photobase64())
self.logocanvas.img = photo
self.logocanvas.create_image(0,0,anchor='nw',image=photo)
def citationtext(self):
"""
Returns citation info
"""
text = "SCOARY version %s \n\n" \
"Please cite as: \n" \
"Brynildsrud O, Bohlin J, Scheffer L, \n" \
"Eldholm V. Rapid scoring of genes in \n" \
"microbial pan-genome-wide association \n" \
"studies with Scoary. Genome Biol. \n" \
"2016;17:238" % scoary.__version__
return text
def Photobase64(self):
"""
base64 encoding of the logo
"""
photo= """
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"""
return photo
class StdoutToLabel(Tkinter.Label):
"""
The special widget that listens to sys.stdout and updates its
label accordingly. This widget also owns the progressbar it is
placed on and updates it every time sys.stdout is called.
Use stop() to stop retrieving from sys.stdout.
Credit: http://stackoverflow.com/questions/2914603/
"""
def __init__(self, widget, progressbar=None, width='default'):
Tkinter.Label.__init__(self)
self.defstdout = sys.stdout
self.widget = widget
self.progressbar = progressbar
if width == 'default':
try:
self.width = widget.cget('width')
except:
self.width = None
else:
self.width = width
def flush(self):
"""
Frame sys.stdout's flush method.
"""
self.defstdout.flush()
def write(self, string, end=None):
"""
Frame sys.stdout's write method. Puts input
strings in the widget.
"""
self.defstdout.write(string)
if string == "\n":
pass
elif (len(string) > 100 and
self.width is not None and
self.width > 0):
if ("Fatal error" in string):
self.widget.config(text=
"Fatal error: See log file for details")
else:
self.widget.config(text="See log file for details")
elif string is not None:
last_char = string[-1]
if last_char != '\n' and string.startswith('\r'):
number = string.lstrip("\r").rstrip("%")
number = number.split(".")[0]
number = int(number)
self.progressbar["value"] = number
elif last_char != '\n':
self.widget.config(text=string)
elif last_char == '\n' and string.startswith('\r'):
number = string.lstrip("\r").rstrip("%")
number = number.split(".")[0]
number = int(number)
self.progressbar["value"] = number
else:
self.widget.config(text=string[:-1])
self.update()
self.progressbar.update()
def start(self):
"""
Starts retrieving.
"""
sys.stdout = self
def stop(self):
"""
Stops retrieving.
"""
sys.stdout = self.defstdout
@property
def errors(self):
return self.defstdout.errors
@property
def encoding(self):
return self.defstdout.encoding
def main():
root = ScoaryGUI(None)
root.title("Scoary")
root.geometry("800x400")
root.resizable(0,0)
root.mainloop()
if __name__ == "__main__":
pass
