def RunEnd(self):
"""Restart GUI and needed variables. This is a minimal implementation.
Override as needed
"""
#region ---------------------------------------------------------> Msg
if self.runEnd:
dtsWindow.MessageDialog(
'success',
f"{config.msg['Success']}\n\nRunning time: {self.deltaT}",
parent=self.parent,
)
else:
pass
#endregion ------------------------------------------------------> Msg
#region -------------------------------------------------> Restart GUI
self.btnGroup.btnRun.Enable()
self.btnGroup.btnRun.SetLabel(config.label['ButtonGroup']['Run'])
self.statusbar.SetStatusText("")
if self.runEnd:
#--> Remove value of Output File to avoid overwriting it
self.outFile.tc.SetValue("")
else:
pass
#endregion ----------------------------------------------> Restart GUI
#region -------------------------------------------> Restart variables
self.runEnd = False
#endregion ----------------------------------------> Restart variables
return True
def WriteOutput(self):
""" Write the output """
#region ---------------------------------------------------------> Msg
msg = config.msg['Step']['Output']
wx.CallAfter(dtsWidget.StatusBarUpdate, self.statusbar, msg)
#endregion ------------------------------------------------------> Msg
#region ---------------------------> Check there is something to write
if self.ptotal == 0:
msg = config.msg['Error'][self.name]['NoPeptide']
dtsWindow.MessageDialog('errorF', msg, self)
return False
else:
pass
#endregion ------------------------> Check there is something to write
#region -------------------------------------------------------> Write
#--> Write input data
oFile = open(self.oFile, 'w')
oFile.write('Input data:\n')
dtsFF.WriteDict2File(oFile, self.d)
oFile.write('\n')
#---
#--> Write output
oFile.write('Output data:\n')
oFile.write(str(self.header) + '\n')
dtsFF.WriteList2File(oFile, self.dataO)
oFile.write('\n')
#---
#--> File last line
dtsFF.WriteLastLine2File(oFile, config.title['MainW'])
#---
#--> Close file and final summary in statusbar
oFile.close()
msg = (f"Final count --> Total Lines: {self.ltotal}, "
f"Empty Lines: {self.lempty}, "
f"Peptides: {self.ptotal}")
wx.CallAfter(dtsWidget.StatusBarUpdate, self.statusbar, msg)
#---
#endregion ----------------------------------------------------> Write
return True
#---
#endregion ------------------------------------------------> Class methods
#---
#endregion ----------------------------------------------------------> Classes
def WriteOutput(self):
""" Write the output """
#region ---------------------------------------------------------> Msg
msg = config.msg['Step']['Output']
wx.CallAfter(dtsWidget.StatusBarUpdate, self.statusbar, msg)
#endregion ------------------------------------------------------> Msg
#region ---------------------------> Check there is something to write
if self.protsselT == 0:
msg = config.msg['Error'][self.name]['NoProtFound']
dtsWindow.MessageDialog('errorF', msg, self)
return False
else:
pass
#endregion ------------------------> Check there is something to write
#region -------------------------------------------------------> Write
#--> Write input data
oFile = open(self.oFile, 'w')
oFile.write('Input data:\n')
dtsFF.WriteDict2File(oFile, self.d)
oFile.write('\n')
#---
#--> Write output
oFile.write('Output data:\n')
header = 'Gene\tProtein\t' + "\t".join(
['1-' + str(x) for x in self.resExt])
oFile.write(header + '\n')
self.dataO.sort(key=itemgetter(0, 1))
dtsFF.WriteList2File(oFile, self.dataO)
oFile.write('\n')
#---
#--> File last line
dtsFF.WriteLastLine2File(oFile, config.title['MainW'])
#---
#--> Close file and final summary in statusbar
oFile.close()
msg = (f"Final count --> Total lines: {self.ltotal}, "
f"Empty lines: {self.lempty}, "
f"Total Proteins: {self.prottotal}, "
f"Matched Proteins: {self.protsselT}")
wx.CallAfter(dtsWidget.StatusBarUpdate, self.statusbar, msg)
#---
#endregion ----------------------------------------------------> Write
return True
def OnOkCheck(self, event):
"""Check widgets created after window initialization and perform checks
involving several widgets
Parameters
----------
event : wx.Event
Information about the event
"""
#region ----------------------------------------------> Skip if Cancel
if event.GetEventObject().GetId() == wx.ID_OK:
pass
else:
event.Skip()
return True
#endregion -------------------------------------------> Skip if Cancel
#region ---------------------------------------------------> Variables
#--> For unique values
values = []
#--> For numbers increase. Starts in 0 because validator check n > 0
a = 0
#--> To track all NA
valuesNA = 0
#endregion ------------------------------------------------> Variables
#region -------------------------------------------------------> Check
#--> Make sure there are widgets to check
if self.tcPosList is None:
event.Skip()
return False
else:
pass
#--> Check values
for k, v in enumerate(self.tcPosList):
#--> Skip first elements, it is the header
if k == 0:
continue
else:
pass
#--> Get value and fill valuesNA
if (val := v.GetValue()) == 'NA':
valuesNA += 1
else:
pass
#--> If all NA continue
if valuesNA == k:
continue
elif valuesNA > 0:
msg = config.msg['Error'][self.name]['Position']
dtsWindow.MessageDialog('errorF', msg, parent=self)
return False
else:
pass
#--> Check value
if v.GetValidator().Validate(self):
pass
else:
return False
#--> Check unique values & increasing
if (p := int(val)) not in values:
if p > a:
values.append(p)
a = p
else:
msg = config.msg['Error'][self.name]['PosIncrease']
dtsWindow.MessageDialog('errorF', msg, parent=self)
return False
pass
else:
return False
#--> Check unique values & increasing
if (p := int(val)) not in values:
if p > a:
values.append(p)
a = p
else:
msg = config.msg['Error'][self.name]['PosIncrease']
dtsWindow.MessageDialog('errorF', msg, parent=self)
return False
else:
msg = config.msg['Error'][self.name]['PosUnique']
msg = msg + f"\n\nIncorrect value: {p}\n"
dtsWindow.MessageDialog('errorF', msg, parent=self)
return False
#--> Set Pos
if valuesNA == k:
self.Pos = False
else:
self.Pos = True
#endregion ----------------------------------------------------> Check
event.Skip()
#---
def OnExport(self, tc):
"""Export the postions & AA to the given wx.TextCtrl
def CheckInput(self):
"""Chek user input. Overrides BaseTab.CheckInput"""
#region ---------------------------------------------------------> Msg
msgM = config.msg['Step']['Check']
#endregion ------------------------------------------------------> Msg
#region -------------------------------------------> Individual Fields
msg = f"{msgM}: {config.label[self.name]['FastaFile']}"
wx.CallAfter(dtsWidget.StatusBarUpdate, self.statusbar, msg)
if self.fastaFile.tc.GetValidator().Validate(self):
pass
else:
return False
msg = f"{msgM}: {config.label[self.name]['GeneFile']}"
wx.CallAfter(dtsWidget.StatusBarUpdate, self.statusbar, msg)
if self.geneFile.tc.GetValidator().Validate(self):
pass
else:
return False
msg = f"{msgM}: {config.label[self.name]['OutFile']}"
wx.CallAfter(dtsWidget.StatusBarUpdate, self.statusbar, msg)
if self.outFile.tc.GetValidator().Validate(self):
pass
else:
return False
msg = f"{msgM}: {config.label[self.name]['ResidueExtract']}"
wx.CallAfter(dtsWidget.StatusBarUpdate, self.statusbar, msg)
if self.residueExtract.tc.GetValidator().Validate(self):
pass
else:
return False
#endregion ----------------------------------------> Individual Fields
#region ------------------------------------------------> File content
#--> Gene names
self.gFile = self.geneFile.tc.GetValue()
self.geneList = []
with open(self.gFile, 'r') as gFile:
for line in gFile:
g = "".join(line.split())
g = g.replace('"', "")
if g == '':
continue
else:
pass
self.geneList.append(g)
if ";" in g:
[self.geneList.append(x) for x in g.split(";")]
else:
pass
if not self.geneList:
msg = config.error[self.name]['NoGene']
dtsWindow.MessageDialog('errorF', msg, parent=self.parent)
return False
else:
pass
#---
#endregion ---------------------------------------------> File content
return True
def WriteOutput(self):
""""""
#region ---------------------------------------------------------> Msg
msg = config.msg['Step']['Output']
wx.CallAfter(dtsWidget.StatusBarUpdate, self.statusbar, msg)
#endregion ------------------------------------------------------> Msg
#region ---------------------------> Check there is something to write
if self.countTotal == 0:
msg = config.msg['Error'][self.name]['NoConsensusFound']
dtsWindow.MessageDialog('errorF', msg, self)
return False
else:
pass
#endregion ------------------------> Check there is something to write
#region -------------------------------------------------------> Write
#--> Write input data
oFile = open(self.oFile, 'w')
oFile.write('Input data:\n')
dtsFF.WriteDict2File(oFile, self.d)
oFile.write('\n')
#---
#--> Write output
oFile.write('Output data:\n')
oFile.write(f"Total proteins\t{self.prottotal}\n")
oFile.write(f"Complete proteins\t{self.prottotal-self.protfrag}\n")
oFile.write(f"Fragment proteins\t{self.protfrag}\n")
oFile.write(f"Consensus sequence in proteins\t{len(self.protSeq)}\n")
header = f'\nCount\tSequence\tPercent\tProtein IDs'
oFile.write(header + '\n')
for k, v in self.seqProt.items():
oFile.write(
f"{v['Count']}\t{k}\t{v['PerCent']}\t{v['pID'][0:-2]}\n")
if not self.Pos:
oFile.write(f"\nProtein IDs\tSequences\n")
for k, v in self.protSeq.items():
oFile.write(f"{k}\t{v[0:-2]}\n")
oFile.write("\n")
else:
pass
#---
#--> File last line
if self.Pos:
oFile.write("\n")
else:
pass
dtsFF.WriteLastLine2File(oFile, config.title['MainW'])
#---
#--> Close file and final summary in statusbar
oFile.close()
msg = (f"Analysing --> Total lines: {self.ltotal}, "
f"Empty lines: {self.lempty}, "
f"Total proteins: {self.prottotal}, "
f"Matched proteins: {len(self.protSeq)}")
wx.CallAfter(dtsWidget.StatusBarUpdate, self.statusbar, msg)
#---
#endregion ----------------------------------------------------> Write
return True