def fromGUI(self, wxobj): """ """ #Get Annotation file annotationPath = wxobj.annotation if not transit_tools.validate_annotation(annotationPath): return None #Get selected files ctrldata = wxobj.ctrlSelected() if not transit_tools.validate_control_datasets(ctrldata): return None #Validate transposon types if not transit_tools.validate_transposons_used(ctrldata, transposons): return None #Read the parameters from the wxPython widgets ignoreCodon = True NTerminus = float(wxobj.globalNTerminusText.GetValue()) CTerminus = float(wxobj.globalCTerminusText.GetValue()) replicates = "Sum" normalization = None LOESS = False #Get output path defaultFileName = "example_output.dat" defaultDir = os.getcwd() output_path = wxobj.SaveFile(defaultDir, defaultFileName) if not output_path: return None output_file = open(output_path, "w") return self(ctrldata, annotationPath, output_file, replicates, normalization, LOESS, ignoreCodon, NTerminus, CTerminus, wxobj)
def fromGUI(self, wxobj): """ """ #Get Annotation file annotationPath = wxobj.annotation if not transit_tools.validate_annotation(annotationPath): return None #Get selected files ctrldata = wxobj.ctrlSelected() if not transit_tools.validate_control_datasets(ctrldata): return None #Validate transposon types if not transit_tools.validate_transposons_used(ctrldata, transposons): return None # Choose normalization method normalization = wxobj.chooseNormalization() LOESS = False ignoreCodon = True NTerminus = 0.0 CTerminus = 0.0 #Get output path defaultFileName = "combined_wig_output.dat" defaultDir = os.getcwd() output_path = wxobj.SaveFile(defaultDir, defaultFileName) if not output_path: return None output_file = open(output_path, "w") return self(ctrldata, annotationPath, output_file, normalization, LOESS, ignoreCodon, NTerminus, CTerminus, wxobj)
def fromGUI(self, wxobj): """ """ # Get Annotation file annotationPath = wxobj.annotation if not transit_tools.validate_annotation(annotationPath): return None # Get selected files ctrldata = wxobj.ctrlSelected() if not transit_tools.validate_control_datasets(ctrldata): return None # Validate transposon types types = tnseq_tools.get_file_types(ctrldata) if "himar1" in types: answer = transit_tools.ShowAskWarning( "Warning: One of the selected wig files looks like a Himar1 dataset. This method is designed to work on Tn5 wig files. Proceeding will fill in missing data with zeroes. Click OK to continue." ) if answer == wx.ID_CANCEL: return None # Read the parameters from the wxPython widgets ignoreCodon = True minread = int( wxobj.tn5GapsReadChoice.GetString( wxobj.tn5GapsReadChoice.GetCurrentSelection())) NTerminus = float(wxobj.globalNTerminusText.GetValue()) CTerminus = float(wxobj.globalCTerminusText.GetValue()) replicates = wxobj.tn5GapsRepChoice.GetString( wxobj.tn5GapsRepChoice.GetCurrentSelection()) normalization = None LOESS = False # Get output path name = transit_tools.basename(ctrldata[0]) defaultFileName = "tn5_gaps_output_m%d_r%s.dat" % (minread, replicates) defaultDir = os.getcwd() output_path = wxobj.SaveFile(defaultDir, defaultFileName) if not output_path: return None output_file = open(output_path, "w") return self( ctrldata, annotationPath, output_file, replicates, normalization, LOESS, ignoreCodon, minread, NTerminus, CTerminus, wxobj, )
def fromGUI(self, wxobj): """ """ #Get Annotation file annotationPath = wxobj.annotation if not transit_tools.validate_annotation(annotationPath): return None #Get selected files ctrldata = wxobj.ctrlSelected() if not transit_tools.validate_control_datasets(ctrldata): return None #Validate transposon types if not transit_tools.validate_transposons_used(ctrldata, transposons): return None #Read the parameters from the wxPython widgets samples = int(wxobj.binomialSampleText.GetValue()) burnin = int(wxobj.binomialBurnText.GetValue()) ignoreCodon = True NTerminus = float(wxobj.globalNTerminusText.GetValue()) CTerminus = float(wxobj.globalCTerminusText.GetValue()) replicates = "Sum" normalization = None LOESS = False #Get output path name = transit_tools.basename(ctrldata[0]) defaultFileName = "binomial_output.dat" defaultDir = os.getcwd() output_path = wxobj.SaveFile(defaultDir, defaultFileName) if not output_path: return None output_file = open(output_path, "w") return self(ctrldata, annotationPath, output_file, samples=samples, burnin=burnin, replicates=replicates, normalization=normalization, LOESS=LOESS, ignoreCodon=ignoreCodon, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
def fromGUI(self, wxobj): """ """ #Get Annotation file annotationPath = wxobj.annotation if not transit_tools.validate_annotation(annotationPath): return None #Get selected files ctrldata = wxobj.ctrlSelected() if not transit_tools.validate_control_datasets(ctrldata): return None #Validate transposon types types = tnseq_tools.get_file_types(ctrldata) if 'himar1' in types: answer = transit_tools.ShowAskWarning("Warning: One of the selected wig files looks like a Himar1 dataset. This method is designed to work on Tn5 wig files. Proceeding will fill in missing data with zeroes. Click OK to continue.") if answer == wx.ID_CANCEL: return None #Read the parameters from the wxPython widgets ignoreCodon = True minread = int(wxobj.tn5GapsReadChoice.GetString(wxobj.tn5GapsReadChoice.GetCurrentSelection())) NTerminus = float(wxobj.globalNTerminusText.GetValue()) CTerminus = float(wxobj.globalCTerminusText.GetValue()) replicates= wxobj.tn5GapsRepChoice.GetString(wxobj.tn5GapsRepChoice.GetCurrentSelection()) normalization = None LOESS = False #Get output path name = transit_tools.basename(ctrldata[0]) defaultFileName = "tn5_gaps_output_m%d_r%s.dat" % (minread, replicates) defaultDir = os.getcwd() output_path = wxobj.SaveFile(defaultDir, defaultFileName) if not output_path: return None output_file = open(output_path, "w") return self(ctrldata, annotationPath, output_file, replicates, normalization, LOESS, ignoreCodon, minread, NTerminus, CTerminus, wxobj)
def fromGUI(self, wxobj): """ """ #Get Annotation file annotationPath = wxobj.annotation if not transit_tools.validate_annotation(annotationPath): return None #Get selected files ctrldata = wxobj.ctrlSelected() if not transit_tools.validate_control_datasets(ctrldata): return None #Validate transposon types if not transit_tools.validate_transposons_used(ctrldata, transposons): return None #Read the parameters from the wxPython widgets replicates = wxobj.hmmRepChoice.GetString(wxobj.hmmRepChoice.GetCurrentSelection()) ignoreCodon = True NTerminus = float(wxobj.globalNTerminusText.GetValue()) CTerminus = float(wxobj.globalCTerminusText.GetValue()) normalization = wxobj.hmmNormChoice.GetString(wxobj.hmmNormChoice.GetCurrentSelection()) LOESS = False LOESS = wxobj.hmmLoessCheck.GetValue() #Get output path name = transit_tools.basename(ctrldata[0]) defaultFileName = "hmm_output.dat" defaultDir = os.getcwd() output_path = wxobj.SaveFile(defaultDir, defaultFileName) if not output_path: return None output_file = open(output_path, "w") return self(ctrldata, annotationPath, output_file, replicates, normalization, LOESS, ignoreCodon, NTerminus, CTerminus, wxobj)
def fromGUI(self, wxobj): """ """ #Get Annotation file annotationPath = wxobj.annotation if not transit_tools.validate_annotation(annotationPath): return None #Get selected files ctrldata = wxobj.ctrlSelected() if not transit_tools.validate_control_datasets(ctrldata): return None #Validate transposon types if not transit_tools.validate_transposons_used(ctrldata, transposons): return None # Choose normalization method normalization = wxobj.chooseNormalization() LOESS = False ignoreCodon = True NTerminus = 0.0 CTerminus = 0.0 #Get output path defaultFileName = "igv_output.txt" defaultDir = os.getcwd() output_path = wxobj.SaveFile(defaultDir, defaultFileName) if not output_path: return None output_file = open(output_path, "w") return self(ctrldata, annotationPath, output_file, normalization, LOESS, ignoreCodon, NTerminus, CTerminus, wxobj)
def fromGUI(self, wxobj): """ """ #Get Annotation file annotationPath = wxobj.annotation if not transit_tools.validate_annotation(annotationPath): return None #Get selected files ctrldata = wxobj.ctrlSelected() if not transit_tools.validate_control_datasets(ctrldata): return None #Validate transposon types if not transit_tools.validate_transposons_used(ctrldata, transposons): return None #Read the parameters from the wxPython widgets try: minread = int( wxobj.gumbelReadChoice.GetString( wxobj.gumbelReadChoice.GetCurrentSelection())) except: warnings.warn( "Warning: problem reading minimum read parameter. Assuming a value of '1'" ) minread = 1 try: samples = int(wxobj.gumbelSampleText.GetValue()) except: warnings.warn( "Warning: problem reading samples parameter. Assuming a value of '10000'" ) samples = 10000 try: burnin = int(wxobj.gumbelBurninText.GetValue()) except: warnings.warn( "Warning: problem reading burnin parameter. Assuming a value of '500'" ) burnin = 500 try: trim = int(wxobj.gumbelTrimText.GetValue()) except: warnings.warn( "Warning: problem reading trim parameter. Assuming a value of '1'" ) trim = 1 try: replicates = wxobj.gumbelRepChoice.GetString( wxobj.gumbelRepChoice.GetCurrentSelection()) except: warnings.warn( "Warning: problem reading replicates parameter. Assuming a value of 'Mean'" ) replicates = "Mean" ignoreCodon = True try: NTerminus = float(wxobj.globalNTerminusText.GetValue()) except: warnings.warn( "Warning: problem reading NTerminus parameter. Assuming a value of '0.00'" ) NTerminus = 0.0 try: CTerminus = float(wxobj.globalCTerminusText.GetValue()) except: warnings.warn( "Warning: problem reading CTerminus parameter. Assuming a value of '0.00'" ) CTerminus = 0.0 normalization = None LOESS = False #Get output path name = transit_tools.basename(ctrldata[0]) defaultFileName = "gumbel_%s_s%d_b%d_t%d.dat" % (".".join( name.split(".")[:-1]), samples, burnin, trim) defaultDir = os.getcwd() output_path = wxobj.SaveFile(defaultDir, defaultFileName) if not output_path: return None output_file = open(output_path, "w") return self(ctrldata, annotationPath, output_file, samples, burnin, trim, minread, replicates, normalization, LOESS, ignoreCodon, NTerminus, CTerminus, wxobj)
def fromGUI(self, wxobj): """ """ #Get Annotation file annotationPath = wxobj.annotation if not transit_tools.validate_annotation(annotationPath): return None #Get selected files ctrldata = wxobj.ctrlSelected() if not transit_tools.validate_control_datasets(ctrldata): return None #Validate transposon types if not transit_tools.validate_transposons_used(ctrldata, transposons): return None #Read the parameters from the wxPython widgets try: minread = int(wxobj.gumbelReadChoice.GetString(wxobj.gumbelReadChoice.GetCurrentSelection())) except: warnings.warn("Warning: problem reading minimum read parameter. Assuming a value of '1'") minread = 1 try: samples = int(wxobj.gumbelSampleText.GetValue()) except: warnings.warn("Warning: problem reading samples parameter. Assuming a value of '10000'") samples = 10000 try: burnin = int(wxobj.gumbelBurninText.GetValue()) except: warnings.warn("Warning: problem reading burnin parameter. Assuming a value of '500'") burnin = 500 try: trim = int(wxobj.gumbelTrimText.GetValue()) except: warnings.warn("Warning: problem reading trim parameter. Assuming a value of '1'") trim = 1 try: replicates = wxobj.gumbelRepChoice.GetString(wxobj.gumbelRepChoice.GetCurrentSelection()) except: warnings.warn("Warning: problem reading replicates parameter. Assuming a value of 'Mean'") replicates = "Mean" ignoreCodon = True try: NTerminus = float(wxobj.globalNTerminusText.GetValue()) except: warnings.warn("Warning: problem reading NTerminus parameter. Assuming a value of '0.00'") NTerminus = 0.0 try: CTerminus = float(wxobj.globalCTerminusText.GetValue()) except: warnings.warn("Warning: problem reading CTerminus parameter. Assuming a value of '0.00'") CTerminus = 0.0 normalization = None LOESS = False #Get output path name = transit_tools.basename(ctrldata[0]) defaultFileName = "gumbel_%s_s%d_b%d_t%d.dat" % (".".join(name.split(".")[:-1]), samples, burnin, trim) defaultDir = os.getcwd() output_path = wxobj.SaveFile(defaultDir, defaultFileName) if not output_path: return None output_file = open(output_path, "w") return self(ctrldata, annotationPath, output_file, samples, burnin, trim, minread, replicates, normalization, LOESS, ignoreCodon, NTerminus, CTerminus, wxobj)