def __init__(self, parent, id):
wx.Frame.__init__(self,
parent,
id,
'GENe BLAST Automation and Gene Cataloger',
size=(800, 335),
style=wx.MINIMIZE_BOX | wx.SYSTEM_MENU | wx.CAPTION
| wx.CLOSE_BOX | wx.CLIP_CHILDREN)
self.Center()
self.panel = wx.Panel(self)
#Check to see if there are other instances of this same program. If so, close out.
self.name = "GENeGUI"
self.instance = wx.SingleInstanceChecker(self.name)
if self.instance.IsAnotherRunning():
wx.MessageBox("Another instance is running already.",
"Only one GENe instance at a time.")
time.sleep(5)
sys.exit()
#IO Info
self.openFileName = ''
self.saveFileName = ''
#Static Texts
self.openFileText = wx.StaticText(self.panel, label='', pos=(147, 18))
self.saveFileText = wx.StaticText(self.panel, label='', pos=(192, 49))
self.colScroll = wx.StaticText(self.panel,
label='Column Containing Sequences',
pos=(600, 5))
self.progressText = wx.StaticText(self.panel,
label="Waiting to run.",
pos=(10, 260))
self.localDBText = wx.StaticText(self.panel,
label="Local Database:",
pos=(85, 190))
self.serverDBText = wx.StaticText(self.panel,
label="Server Database:",
pos=(410, 190))
self.searchText = wx.StaticText(self.panel,
label="BLAST Search Type:",
pos=(410, 153))
self.evalText = wx.StaticText(self.panel,
label="e-value maximum:",
pos=(85, 153))
#Load Bar
self.progressBar = wx.Gauge(self.panel,
-1,
1,
pos=(10, 280),
size=(590, 20))
#Buttons
catalogButton = wx.Button(self.panel,
label="Run GENe",
pos=(600, 260),
size=(186, 50))
openFileButton = wx.Button(self.panel,
label="Open Excel File",
pos=(10, 10),
size=(125, 30))
saveFileButton = wx.Button(self.panel,
label="Choose Save Destination",
pos=(10, 40),
size=(175, 30))
helpButton = wx.Button(self.panel,
label="Help",
pos=(735, 245),
size=(50, 25))
errorLogButton = wx.Button(self.panel,
label="Open Error Log",
pos=(600, 245),
size=(133, 25))
self.Bind(wx.EVT_BUTTON, self.saveExcelFile, saveFileButton)
self.Bind(wx.EVT_BUTTON, self.openExcelFile, openFileButton)
self.Bind(wx.EVT_BUTTON, self.runCataloger, catalogButton)
self.Bind(wx.EVT_BUTTON, self.openREADME, helpButton)
self.Bind(wx.EVT_BUTTON, self.openErrorLog, errorLogButton)
self.Bind(wx.EVT_CLOSE, self.closewindow)
#Check Boxes
self.localCheck = wx.CheckBox(self.panel,
-1,
"Local Blast Search (Requires BLAST+)",
pos=(85, 90))
self.serverCheck = wx.CheckBox(
self.panel,
-1,
"NCBI Server Blast Search (No installation required)",
pos=(400, 90))
self.serverCheck.SetValue(True)
self.queryType = 'queryServer'
self.xenoCheck = wx.CheckBox(
self.panel,
-1,
"Use Xenopus Laevis algorithm - When disabled, GENe simply records top three BLAST hits.",
pos=(85, 115))
self.xenoCheck.SetValue(True)
self.xenopusAlgo = True
self.Bind(wx.EVT_CHECKBOX, self.selectXeno, self.xenoCheck)
self.Bind(wx.EVT_CHECKBOX, self.selectLocal, self.localCheck)
self.Bind(wx.EVT_CHECKBOX, self.selectServer, self.serverCheck)
#Choices
self.dbChoice = wx.Choice(self.panel, -1, pos = (540, 188), choices = ['nr', 'refseq', 'swissprot', 'pat', 'month', 'pdb', 'refseq_mrna', 'refseq_genomic', 'est', 'est_human', \
'est_mouse', 'est_others', 'gss', 'htgs', 'pat', 'dbsts', 'chromosome', 'genome', 'HTGS', 'RefSeq RNA', 'RefSeq Protein', 'Build RNA', 'Build Protein', 'ESTs'])
self.dbChoice.SetStringSelection('nr')
self.serverDatabase = 'nr'
self.searchChoice = wx.Choice(
self.panel,
-1,
pos=(540, 150),
choices=['blastn', 'blastp', 'blastx', 'tblastn', 'tblastx'])
self.searchChoice.SetStringSelection('blastn')
self.searchType = 'blastn'
#Text Entry
self.dbTextBox = wx.TextCtrl(self.panel,
-1,
'nt',
size=(120, -1),
pos=(220, 188))
self.localDatabase = 'nt'
self.evalTextBox = wx.TextCtrl(self.panel,
-1,
'3',
size=(120, -1),
pos=(220, 150))
self.eValCap = None
#Scroll Counter Boxes
self.seqColumn = wx.SpinCtrl(self.panel,
value='0',
pos=(680, 24),
size=(60, -1))
self.seqColumn.SetRange(0, 1000)
self.seqCol = 0
#Initialize GENe instance
self.newCatalog = GENe(self)
def __init__(self,parent,id):
wx.Frame.__init__(self,parent,id,'GENe BLAST Automation and Gene Cataloger', size=(800,335), style=wx.MINIMIZE_BOX|wx.SYSTEM_MENU|wx.CAPTION|wx.CLOSE_BOX|wx.CLIP_CHILDREN)
self.Center()
self.panel = wx.Panel(self)
#Check to see if there are other instances of this same program. If so, close out.
self.name = "GENeGUI"
self.instance = wx.SingleInstanceChecker(self.name)
if self.instance.IsAnotherRunning():
wx.MessageBox("Another instance is running already.", "Only one GENe instance at a time.")
time.sleep(5)
sys.exit()
#IO Info
self.openFileName = ''
self.saveFileName = ''
#Static Texts
self.openFileText = wx.StaticText(self.panel, label = '', pos = (147, 18))
self.saveFileText = wx.StaticText(self.panel, label = '', pos = (192, 49))
self.colScroll = wx.StaticText(self.panel, label = 'Column Containing Sequences', pos = (600, 5))
self.progressText = wx.StaticText(self.panel, label = "Waiting to run." , pos = (10, 260))
self.localDBText = wx.StaticText(self.panel, label = "Local Database:" , pos = (85, 190))
self.serverDBText = wx.StaticText(self.panel, label = "Server Database:" , pos = (410, 190))
self.searchText = wx.StaticText(self.panel, label = "BLAST Search Type:" , pos = (410, 153))
self.evalText = wx.StaticText(self.panel, label = "e-value maximum:" , pos = (85, 153))
#Load Bar
self.progressBar = wx.Gauge(self.panel, -1, 1, pos= (10,280), size= (590,20))
#Buttons
catalogButton = wx.Button(self.panel, label = "Run GENe", pos = (600,260), size = (186, 50))
openFileButton = wx.Button(self.panel, label = "Open Excel File", pos = (10,10), size = (125, 30))
saveFileButton = wx.Button(self.panel, label = "Choose Save Destination", pos = (10,40), size = (175,30))
helpButton = wx.Button(self.panel, label = "Help", pos = (735,245), size = (50, 25))
errorLogButton = wx.Button(self.panel, label = "Open Error Log", pos = (600, 245), size = (133, 25))
self.Bind(wx.EVT_BUTTON, self.saveExcelFile, saveFileButton)
self.Bind(wx.EVT_BUTTON, self.openExcelFile, openFileButton)
self.Bind(wx.EVT_BUTTON, self.runCataloger, catalogButton)
self.Bind(wx.EVT_BUTTON, self.openREADME, helpButton)
self.Bind(wx.EVT_BUTTON, self.openErrorLog, errorLogButton)
self.Bind(wx.EVT_CLOSE, self.closewindow)
#Check Boxes
self.localCheck = wx.CheckBox(self.panel, -1, "Local Blast Search (Requires BLAST+)", pos = (85,90))
self.serverCheck = wx.CheckBox(self.panel, -1, "NCBI Server Blast Search (No installation required)", pos = (400,90))
self.serverCheck.SetValue(True)
self.queryType = 'queryServer'
self.xenoCheck = wx.CheckBox(self.panel, -1, "Use Xenopus Laevis algorithm - When disabled, GENe simply records top three BLAST hits.", pos = (85, 115))
self.xenoCheck.SetValue(True)
self.xenopusAlgo = True
self.Bind(wx.EVT_CHECKBOX, self.selectXeno, self.xenoCheck)
self.Bind(wx.EVT_CHECKBOX, self.selectLocal, self.localCheck)
self.Bind(wx.EVT_CHECKBOX, self.selectServer, self.serverCheck)
#Choices
self.dbChoice = wx.Choice(self.panel, -1, pos = (540, 188), choices = ['nr', 'refseq', 'swissprot', 'pat', 'month', 'pdb', 'refseq_mrna', 'refseq_genomic', 'est', 'est_human', \
'est_mouse', 'est_others', 'gss', 'htgs', 'pat', 'dbsts', 'chromosome', 'genome', 'HTGS', 'RefSeq RNA', 'RefSeq Protein', 'Build RNA', 'Build Protein', 'ESTs'])
self.dbChoice.SetStringSelection('nr')
self.serverDatabase = 'nr'
self.searchChoice = wx.Choice(self.panel, -1, pos = (540, 150), choices = ['blastn', 'blastp', 'blastx', 'tblastn', 'tblastx'])
self.searchChoice.SetStringSelection('blastn')
self.searchType = 'blastn'
#Text Entry
self.dbTextBox = wx.TextCtrl (self.panel, -1, 'nt', size = (120, -1), pos = (220, 188))
self.localDatabase = 'nt'
self.evalTextBox = wx.TextCtrl(self.panel, -1, '3', size = (120,-1), pos = (220, 150))
self.eValCap = None
#Scroll Counter Boxes
self.seqColumn = wx.SpinCtrl(self.panel, value='0', pos = (680,24), size = (60, -1))
self.seqColumn.SetRange(0,1000)
self.seqCol = 0
#Initialize GENe instance
self.newCatalog = GENe(self)
class GENeGUI(wx.Frame):
def __init__(self, parent, id):
wx.Frame.__init__(self,
parent,
id,
'GENe BLAST Automation and Gene Cataloger',
size=(800, 335),
style=wx.MINIMIZE_BOX | wx.SYSTEM_MENU | wx.CAPTION
| wx.CLOSE_BOX | wx.CLIP_CHILDREN)
self.Center()
self.panel = wx.Panel(self)
#Check to see if there are other instances of this same program. If so, close out.
self.name = "GENeGUI"
self.instance = wx.SingleInstanceChecker(self.name)
if self.instance.IsAnotherRunning():
wx.MessageBox("Another instance is running already.",
"Only one GENe instance at a time.")
time.sleep(5)
sys.exit()
#IO Info
self.openFileName = ''
self.saveFileName = ''
#Static Texts
self.openFileText = wx.StaticText(self.panel, label='', pos=(147, 18))
self.saveFileText = wx.StaticText(self.panel, label='', pos=(192, 49))
self.colScroll = wx.StaticText(self.panel,
label='Column Containing Sequences',
pos=(600, 5))
self.progressText = wx.StaticText(self.panel,
label="Waiting to run.",
pos=(10, 260))
self.localDBText = wx.StaticText(self.panel,
label="Local Database:",
pos=(85, 190))
self.serverDBText = wx.StaticText(self.panel,
label="Server Database:",
pos=(410, 190))
self.searchText = wx.StaticText(self.panel,
label="BLAST Search Type:",
pos=(410, 153))
self.evalText = wx.StaticText(self.panel,
label="e-value maximum:",
pos=(85, 153))
#Load Bar
self.progressBar = wx.Gauge(self.panel,
-1,
1,
pos=(10, 280),
size=(590, 20))
#Buttons
catalogButton = wx.Button(self.panel,
label="Run GENe",
pos=(600, 260),
size=(186, 50))
openFileButton = wx.Button(self.panel,
label="Open Excel File",
pos=(10, 10),
size=(125, 30))
saveFileButton = wx.Button(self.panel,
label="Choose Save Destination",
pos=(10, 40),
size=(175, 30))
helpButton = wx.Button(self.panel,
label="Help",
pos=(735, 245),
size=(50, 25))
errorLogButton = wx.Button(self.panel,
label="Open Error Log",
pos=(600, 245),
size=(133, 25))
self.Bind(wx.EVT_BUTTON, self.saveExcelFile, saveFileButton)
self.Bind(wx.EVT_BUTTON, self.openExcelFile, openFileButton)
self.Bind(wx.EVT_BUTTON, self.runCataloger, catalogButton)
self.Bind(wx.EVT_BUTTON, self.openREADME, helpButton)
self.Bind(wx.EVT_BUTTON, self.openErrorLog, errorLogButton)
self.Bind(wx.EVT_CLOSE, self.closewindow)
#Check Boxes
self.localCheck = wx.CheckBox(self.panel,
-1,
"Local Blast Search (Requires BLAST+)",
pos=(85, 90))
self.serverCheck = wx.CheckBox(
self.panel,
-1,
"NCBI Server Blast Search (No installation required)",
pos=(400, 90))
self.serverCheck.SetValue(True)
self.queryType = 'queryServer'
self.xenoCheck = wx.CheckBox(
self.panel,
-1,
"Use Xenopus Laevis algorithm - When disabled, GENe simply records top three BLAST hits.",
pos=(85, 115))
self.xenoCheck.SetValue(True)
self.xenopusAlgo = True
self.Bind(wx.EVT_CHECKBOX, self.selectXeno, self.xenoCheck)
self.Bind(wx.EVT_CHECKBOX, self.selectLocal, self.localCheck)
self.Bind(wx.EVT_CHECKBOX, self.selectServer, self.serverCheck)
#Choices
self.dbChoice = wx.Choice(self.panel, -1, pos = (540, 188), choices = ['nr', 'refseq', 'swissprot', 'pat', 'month', 'pdb', 'refseq_mrna', 'refseq_genomic', 'est', 'est_human', \
'est_mouse', 'est_others', 'gss', 'htgs', 'pat', 'dbsts', 'chromosome', 'genome', 'HTGS', 'RefSeq RNA', 'RefSeq Protein', 'Build RNA', 'Build Protein', 'ESTs'])
self.dbChoice.SetStringSelection('nr')
self.serverDatabase = 'nr'
self.searchChoice = wx.Choice(
self.panel,
-1,
pos=(540, 150),
choices=['blastn', 'blastp', 'blastx', 'tblastn', 'tblastx'])
self.searchChoice.SetStringSelection('blastn')
self.searchType = 'blastn'
#Text Entry
self.dbTextBox = wx.TextCtrl(self.panel,
-1,
'nt',
size=(120, -1),
pos=(220, 188))
self.localDatabase = 'nt'
self.evalTextBox = wx.TextCtrl(self.panel,
-1,
'3',
size=(120, -1),
pos=(220, 150))
self.eValCap = None
#Scroll Counter Boxes
self.seqColumn = wx.SpinCtrl(self.panel,
value='0',
pos=(680, 24),
size=(60, -1))
self.seqColumn.SetRange(0, 1000)
self.seqCol = 0
#Initialize GENe instance
self.newCatalog = GENe(self)
def errorPop(self, string, end=False):
'''Given a string that presumably contains an error message, this method will create a popup displaying that message'''
wx.MessageBox(string, "GENe Error or Update")
if end == True:
self.closewindow(None)
def runCataloger(self, event):
"Main method. Passess in most of the GUI's instnace variables to GENe and runs GENe in a thread."
#Make sure there is only one instance of GENe running as a result of this program.
if self.newCatalog.running == False:
#Collect contents from text boxes and GUI choices.
self.eValCap = float(self.evalTextBox.GetValue())
self.serverDatabase = self.dbChoice.GetStringSelection()
self.searchType = self.searchChoice.GetStringSelection()
self.seqCol = int(self.seqColumn.GetValue())
#Format the 'local database' variable for proper use in GENe (differs per operating system)
self.localDatabase = self.dbTextBox.GetValue()
### Double quotes for windows
if 'win32' in sys.platform:
self.localDatabase = '"' + self.localDatabase + '"'
### Single quotes for UNIX (MacOS and Linux)
else:
self.localDatabase = "'" + self.localDatabase + "'"
print "Databases you chose: ", self.localDatabase
#Set instance variables in GENe
self.newCatalog.seqCol = self.seqCol
self.newCatalog.eValCap = self.eValCap
self.newCatalog.queryType = self.queryType
self.newCatalog.searchType = self.searchType
self.newCatalog.xenopusAlgo = self.xenopusAlgo
self.newCatalog.localDatabase = self.localDatabase
self.newCatalog.serverDatabase = self.serverDatabase
#Force user to pick a file if they haven't already.
if self.openFileName == '':
self.openExcelFile(None)
return
if self.saveFileName == '':
self.saveExcelFile(None)
return
#Run the GENe program
self.newCatalog.readBook()
self.progressBar.SetRange(self.newCatalog.numberOfQueries)
if self.queryType == 'queryServer':
self.progressText.SetLabel(
"Initializing Server BLAST Query...")
if self.queryType == 'queryLocal':
self.progressText.SetLabel(
"Running Local BLAST Query. This may take a very long time."
)
self.newCatalog.start()
def progressUpdate(self, progress):
'''Updates progress bar'''
if progress == -1:
self.progressBar.Pulse()
elif progress == -2:
self.progressText.SetLabel("Complete!")
elif progress == -3:
self.progressText.SetLabel("Terminated Early.")
self.progressBar.SetValue(0)
else:
self.progressBar.SetValue(progress)
progressString = str(progress) + ' of ' + str(
self.newCatalog.numberOfQueries) + " catalogged."
self.progressText.SetLabel(progressString)
def openExcelFile(self, event):
dialog = wx.FileDialog(self,
message="Open an Excel File",
style=wx.OPEN)
if dialog.ShowModal() == wx.ID_OK:
self.openFileName = dialog.GetPath()
if len(self.openFileName) > 55:
shortName = self.openFileName[0:55] + '...'
else:
shortName = self.openFileName
self.openFileText.SetLabel(shortName)
self.newCatalog.fileToOpen = self.openFileName
dialog.Destroy()
def saveExcelFile(self, event):
dialog = wx.FileDialog(self,
message="Choose save Destination",
style=wx.SAVE)
dialog.SetFilename('GENe Results.xls')
if dialog.ShowModal() == wx.ID_OK:
self.saveFileName = dialog.GetPath()
#Make sure that the file being saved is in excel format.
if '.xls' not in self.saveFileName:
self.saveFileName = self.saveFileName + '.xls'
#Shorten up the name to display on the Window
if len(self.saveFileName) > 60:
shortName = self.saveFileName[0:60] + '...'
else:
shortName = self.saveFileName
self.saveFileText.SetLabel(shortName)
self.newCatalog.saveAs = self.saveFileName
dialog.Destroy()
def selectLocal(self, event):
'''Checkbox method for local selection'''
if not self.localCheck.IsChecked():
self.localCheck.SetValue(True)
else:
self.serverCheck.SetValue(False)
self.queryType = 'queryLocal'
def selectServer(self, event):
'''Checkbox method for server selection'''
if not self.serverCheck.IsChecked():
self.serverCheck.SetValue(True)
else:
self.localCheck.SetValue(False)
self.queryType = 'queryServer'
def selectXeno(self, event):
'''Checkbox method for Xenopus Laevis algorithm vs. Top three hits selection'''
if self.xenoCheck.IsChecked():
self.xenopusAlgo = True
else:
self.xenopusAlgo = False
def openREADME(self, event):
subprocess.call(['open', '-a', 'TextEdit', 'README.txt'])
#webbrowser.open('README.txt')
def openErrorLog(self, event):
subprocess.call(['open', '-a', 'TextEdit', 'Errorlog.txt'])
def closewindow(self, event):
del self.instance
sys.exit()
self.Destroy()
class GENeGUI(wx.Frame):
def __init__(self,parent,id):
wx.Frame.__init__(self,parent,id,'GENe BLAST Automation and Gene Cataloger', size=(800,335), style=wx.MINIMIZE_BOX|wx.SYSTEM_MENU|wx.CAPTION|wx.CLOSE_BOX|wx.CLIP_CHILDREN)
self.Center()
self.panel = wx.Panel(self)
#Check to see if there are other instances of this same program. If so, close out.
self.name = "GENeGUI"
self.instance = wx.SingleInstanceChecker(self.name)
if self.instance.IsAnotherRunning():
wx.MessageBox("Another instance is running already.", "Only one GENe instance at a time.")
time.sleep(5)
sys.exit()
#IO Info
self.openFileName = ''
self.saveFileName = ''
#Static Texts
self.openFileText = wx.StaticText(self.panel, label = '', pos = (147, 18))
self.saveFileText = wx.StaticText(self.panel, label = '', pos = (192, 49))
self.colScroll = wx.StaticText(self.panel, label = 'Column Containing Sequences', pos = (600, 5))
self.progressText = wx.StaticText(self.panel, label = "Waiting to run." , pos = (10, 260))
self.localDBText = wx.StaticText(self.panel, label = "Local Database:" , pos = (85, 190))
self.serverDBText = wx.StaticText(self.panel, label = "Server Database:" , pos = (410, 190))
self.searchText = wx.StaticText(self.panel, label = "BLAST Search Type:" , pos = (410, 153))
self.evalText = wx.StaticText(self.panel, label = "e-value maximum:" , pos = (85, 153))
#Load Bar
self.progressBar = wx.Gauge(self.panel, -1, 1, pos= (10,280), size= (590,20))
#Buttons
catalogButton = wx.Button(self.panel, label = "Run GENe", pos = (600,260), size = (186, 50))
openFileButton = wx.Button(self.panel, label = "Open Excel File", pos = (10,10), size = (125, 30))
saveFileButton = wx.Button(self.panel, label = "Choose Save Destination", pos = (10,40), size = (175,30))
helpButton = wx.Button(self.panel, label = "Help", pos = (735,245), size = (50, 25))
errorLogButton = wx.Button(self.panel, label = "Open Error Log", pos = (600, 245), size = (133, 25))
self.Bind(wx.EVT_BUTTON, self.saveExcelFile, saveFileButton)
self.Bind(wx.EVT_BUTTON, self.openExcelFile, openFileButton)
self.Bind(wx.EVT_BUTTON, self.runCataloger, catalogButton)
self.Bind(wx.EVT_BUTTON, self.openREADME, helpButton)
self.Bind(wx.EVT_BUTTON, self.openErrorLog, errorLogButton)
self.Bind(wx.EVT_CLOSE, self.closewindow)
#Check Boxes
self.localCheck = wx.CheckBox(self.panel, -1, "Local Blast Search (Requires BLAST+)", pos = (85,90))
self.serverCheck = wx.CheckBox(self.panel, -1, "NCBI Server Blast Search (No installation required)", pos = (400,90))
self.serverCheck.SetValue(True)
self.queryType = 'queryServer'
self.xenoCheck = wx.CheckBox(self.panel, -1, "Use Xenopus Laevis algorithm - When disabled, GENe simply records top three BLAST hits.", pos = (85, 115))
self.xenoCheck.SetValue(True)
self.xenopusAlgo = True
self.Bind(wx.EVT_CHECKBOX, self.selectXeno, self.xenoCheck)
self.Bind(wx.EVT_CHECKBOX, self.selectLocal, self.localCheck)
self.Bind(wx.EVT_CHECKBOX, self.selectServer, self.serverCheck)
#Choices
self.dbChoice = wx.Choice(self.panel, -1, pos = (540, 188), choices = ['nr', 'refseq', 'swissprot', 'pat', 'month', 'pdb', 'refseq_mrna', 'refseq_genomic', 'est', 'est_human', \
'est_mouse', 'est_others', 'gss', 'htgs', 'pat', 'dbsts', 'chromosome', 'genome', 'HTGS', 'RefSeq RNA', 'RefSeq Protein', 'Build RNA', 'Build Protein', 'ESTs'])
self.dbChoice.SetStringSelection('nr')
self.serverDatabase = 'nr'
self.searchChoice = wx.Choice(self.panel, -1, pos = (540, 150), choices = ['blastn', 'blastp', 'blastx', 'tblastn', 'tblastx'])
self.searchChoice.SetStringSelection('blastn')
self.searchType = 'blastn'
#Text Entry
self.dbTextBox = wx.TextCtrl (self.panel, -1, 'nt', size = (120, -1), pos = (220, 188))
self.localDatabase = 'nt'
self.evalTextBox = wx.TextCtrl(self.panel, -1, '3', size = (120,-1), pos = (220, 150))
self.eValCap = None
#Scroll Counter Boxes
self.seqColumn = wx.SpinCtrl(self.panel, value='0', pos = (680,24), size = (60, -1))
self.seqColumn.SetRange(0,1000)
self.seqCol = 0
#Initialize GENe instance
self.newCatalog = GENe(self)
def errorPop(self, string, end = False):
'''Given a string that presumably contains an error message, this method will create a popup displaying that message'''
wx.MessageBox(string, "GENe Error or Update")
if end == True:
self.closewindow(None)
def runCataloger(self,event):
"Main method. Passess in most of the GUI's instnace variables to GENe and runs GENe in a thread."
#Make sure there is only one instance of GENe running as a result of this program.
if self.newCatalog.running == False:
#Collect contents from text boxes and GUI choices.
self.eValCap = float(self.evalTextBox.GetValue())
self.serverDatabase = self.dbChoice.GetStringSelection()
self.searchType = self.searchChoice.GetStringSelection()
self.seqCol = int(self.seqColumn.GetValue())
#Format the 'local database' variable for proper use in GENe (differs per operating system)
self.localDatabase = self.dbTextBox.GetValue()
### Double quotes for windows
if 'win32' in sys.platform:
self.localDatabase = '"' + self.localDatabase + '"'
### Single quotes for UNIX (MacOS and Linux)
else:
self.localDatabase = "'" + self.localDatabase + "'"
print "Databases you chose: ", self.localDatabase
#Set instance variables in GENe
self.newCatalog.seqCol = self.seqCol
self.newCatalog.eValCap = self.eValCap
self.newCatalog.queryType = self.queryType
self.newCatalog.searchType = self.searchType
self.newCatalog.xenopusAlgo = self.xenopusAlgo
self.newCatalog.localDatabase = self.localDatabase
self.newCatalog.serverDatabase = self.serverDatabase
#Force user to pick a file if they haven't already.
if self.openFileName == '':
self.openExcelFile(None)
return
if self.saveFileName == '':
self.saveExcelFile(None)
return
#Run the GENe program
self.newCatalog.readBook()
self.progressBar.SetRange(self.newCatalog.numberOfQueries)
if self.queryType == 'queryServer':
self.progressText.SetLabel("Initializing Server BLAST Query...")
if self.queryType == 'queryLocal':
self.progressText.SetLabel("Running Local BLAST Query. This may take a very long time.")
self.newCatalog.start()
def progressUpdate(self, progress):
'''Updates progress bar'''
if progress == -1:
self.progressBar.Pulse()
elif progress == -2:
self.progressText.SetLabel("Complete!")
elif progress == -3:
self.progressText.SetLabel("Terminated Early.")
self.progressBar.SetValue(0)
else:
self.progressBar.SetValue(progress)
progressString = str(progress) + ' of ' + str(self.newCatalog.numberOfQueries) + " catalogged."
self.progressText.SetLabel(progressString)
def openExcelFile(self, event):
dialog = wx.FileDialog(self, message= "Open an Excel File", style = wx.OPEN)
if dialog.ShowModal() == wx.ID_OK:
self.openFileName = dialog.GetPath()
if len(self.openFileName) > 55:
shortName = self.openFileName[0:55] + '...'
else:
shortName = self.openFileName
self.openFileText.SetLabel(shortName)
self.newCatalog.fileToOpen = self.openFileName
dialog.Destroy()
def saveExcelFile(self,event):
dialog = wx.FileDialog(self, message= "Choose save Destination", style = wx.SAVE)
dialog.SetFilename('GENe Results.xls')
if dialog.ShowModal() == wx.ID_OK:
self.saveFileName = dialog.GetPath()
#Make sure that the file being saved is in excel format.
if '.xls' not in self.saveFileName:
self.saveFileName = self.saveFileName + '.xls'
#Shorten up the name to display on the Window
if len(self.saveFileName) > 60:
shortName = self.saveFileName[0:60] + '...'
else:
shortName = self.saveFileName
self.saveFileText.SetLabel(shortName)
self.newCatalog.saveAs = self.saveFileName
dialog.Destroy()
def selectLocal(self, event):
'''Checkbox method for local selection'''
if not self.localCheck.IsChecked():
self.localCheck.SetValue(True)
else:
self.serverCheck.SetValue(False)
self.queryType = 'queryLocal'
def selectServer(self, event):
'''Checkbox method for server selection'''
if not self.serverCheck.IsChecked():
self.serverCheck.SetValue(True)
else:
self.localCheck.SetValue(False)
self.queryType = 'queryServer'
def selectXeno(self, event):
'''Checkbox method for Xenopus Laevis algorithm vs. Top three hits selection'''
if self.xenoCheck.IsChecked():
self.xenopusAlgo = True
else:
self.xenopusAlgo = False
def openREADME(self, event):
subprocess.call(['open', '-a', 'TextEdit', 'README.txt'])
#webbrowser.open('README.txt')
def openErrorLog(self, event):
subprocess.call(['open', '-a', 'TextEdit', 'Errorlog.txt'])
def closewindow(self, event):
del self.instance
sys.exit()
self.Destroy()