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() expdata = wxobj.expSelected() if not transit_tools.validate_both_datasets(ctrldata, expdata): return None #Validate transposon types if not transit_tools.validate_transposons_used(ctrldata+expdata, transposons): return None #Read the parameters from the wxPython widgets ignoreCodon = True samples = int(wxobj.rankproductSampleText.GetValue()) normalization = wxobj.rankproductNormChoice.GetString(wxobj.rankproductNormChoice.GetCurrentSelection()) replicates="Sum" adaptive = False doHistogram = False NTerminus = float(wxobj.globalNTerminusText.GetValue()) CTerminus = float(wxobj.globalCTerminusText.GetValue()) LOESS = False #Get output path defaultFileName = "rankproduct_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, expdata, annotationPath, output_file, normalization, samples, adaptive, doHistogram, replicates, 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 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() expdata = wxobj.expSelected() if not transit_tools.validate_both_datasets(ctrldata, expdata): return None #Validate transposon types if not transit_tools.validate_transposons_used(ctrldata+expdata, transposons): return None #Read the parameters from the wxPython widgets ignoreCodon = True normalization = wxobj.utestNormChoice.GetString(wxobj.utestNormChoice.GetCurrentSelection()) replicates= None includeZeros = wxobj.utestZeroCheckBox.GetValue() NTerminus = float(wxobj.globalNTerminusText.GetValue()) CTerminus = float(wxobj.globalCTerminusText.GetValue()) LOESS = wxobj.utestLoessCheck.GetValue() #Get output path defaultFileName = "utest_%s_output" % (normalization) if includeZeros: defaultFileName+= "_iz" defaultFileName+=".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, expdata, annotationPath, output_file, normalization, includeZeros, replicates, 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() expdata = wxobj.expSelected() if not transit_tools.validate_both_datasets(ctrldata, expdata): return None #Validate transposon types if not transit_tools.validate_transposons_used(ctrldata + expdata, transposons): return None #Read the parameters from the wxPython widgets ignoreCodon = True samples = int(wxobj.resamplingSampleText.GetValue()) normalization = wxobj.resamplingNormChoice.GetString( wxobj.resamplingNormChoice.GetCurrentSelection()) replicates = "Sum" adaptive = wxobj.resamplingAdaptiveCheckBox.GetValue() doHistogram = wxobj.resamplingHistogramCheckBox.GetValue() includeZeros = wxobj.resamplingZeroCheckBox.GetValue() pseudocount = float(wxobj.resamplingPseudocountText.GetValue()) NTerminus = float(wxobj.globalNTerminusText.GetValue()) CTerminus = float(wxobj.globalCTerminusText.GetValue()) LOESS = wxobj.resamplingLoessCheck.GetValue() #Get output path defaultFileName = "resampling_output_s%d_pc%1.2f" % (samples, pseudocount) if adaptive: defaultFileName += "_adaptive" if includeZeros: defaultFileName += "_iz" defaultFileName += ".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, expdata, annotationPath, output_file, normalization, samples, adaptive, doHistogram, includeZeros, pseudocount, replicates, 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 output path defaultFileName = "{0}.prot_table".format(os.path.splitext(os.path.basename(annotationPath))[0]) defaultDir = os.getcwd() output_path = wxobj.SaveFile(defaultDir, defaultFileName) if not output_path: return None output_file = open(output_path, "w") return self(annotationPath, output_file, 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)
def fromGUI(self, wxobj): """ """ #Get Annotation file annotationPath = wxobj.annotation if not transit_tools.validate_annotation(annotationPath): return None #Get selected files ctrldataA = wxobj.ctrlSelected() expdataA = wxobj.expSelected() if not transit_tools.validate_both_datasets(ctrldataA, expdataA): return None #Validate transposon types if not transit_tools.validate_transposons_used(ctrldataA+expdataA, transposons): return None # Get other datasets: dlg = DatasetDialog(wxobj) result = dlg.ShowModal() if result == dlg.ID_DONE and wxobj: status = 1 ctrldataB = dlg.ctrlSelected() expdataB = dlg.expSelected() if not transit_tools.validate_both_datasets(ctrldataB, expdataB): #dlg.Close() #dlg.Destroy() return None if not transit_tools.validate_transposons_used(ctrldataB+expdataB, transposons): dlg.Close() dlg.Destroy() return None else: dlg.Close() dlg.Destroy() return None # Close dlg.Close() dlg.Destroy() #Read the parameters from the wxPython widgets ignoreCodon = True samples = int(wxobj.giSampleText.GetValue()) rope = float(wxobj.giROPEText.GetValue()) normalization = wxobj.giNormChoice.GetString(wxobj.giNormChoice.GetCurrentSelection()) replicates="Sum" includeZeros = wxobj.giZeroCheckBox.GetValue() NTerminus = float(wxobj.globalNTerminusText.GetValue()) CTerminus = float(wxobj.globalCTerminusText.GetValue()) LOESS = wxobj.giLoessCheck.GetValue() #Get output path defaultFileName = "genetic_interactions_output_s%d" % (samples) if includeZeros: defaultFileName+= "_iz" defaultFileName+=".dat" defaultDir = os.getcwd() output_path = wxobj.SaveFile(defaultDir, defaultFileName) if not output_path: return None output_file = open(output_path, "w") return self(ctrldataA, ctrldataB, expdataA, expdataB, annotationPath, output_file, normalization, samples, rope, includeZeros, replicates, LOESS, ignoreCodon, NTerminus, CTerminus, wxobj)
def fromGUI(self, wxobj): """ """ #Get Annotation file annot_paths = wxobj.annotation.split(",") annotationPath = annot_paths[0] diffStrains = False annotationPathExp = "" if len(annot_paths) == 2: annotationPathExp = annot_paths[1] diffStrains = True if not transit_tools.validate_annotation(annotationPath): return None if annotationPathExp and not transit_tools.validate_annotation(annotationPathExp): return None #Get selected files ctrldata = wxobj.ctrlSelected() expdata = wxobj.expSelected() if not transit_tools.validate_both_datasets(ctrldata, expdata): return None #Validate transposon types if not transit_tools.validate_transposons_used(ctrldata+expdata, transposons): return None #Read the parameters from the wxPython widgets ignoreCodon = True samples = int(wxobj.resamplingSampleText.GetValue()) normalization = wxobj.resamplingNormChoice.GetString(wxobj.resamplingNormChoice.GetCurrentSelection()) replicates="Sum" adaptive = wxobj.resamplingAdaptiveCheckBox.GetValue() doHistogram = wxobj.resamplingHistogramCheckBox.GetValue() includeZeros = wxobj.resamplingZeroCheckBox.GetValue() pseudocount = float(wxobj.resamplingPseudocountText.GetValue()) LOESS = wxobj.resamplingLoessCheck.GetValue() # Global Parameters NTerminus = float(wxobj.globalNTerminusText.GetValue()) CTerminus = float(wxobj.globalCTerminusText.GetValue()) ctrl_lib_str = wxobj.ctrlLibText.GetValue() exp_lib_str = wxobj.expLibText.GetValue() #Get output path defaultFileName = "resampling_output_s%d_pc%1.2f" % (samples, pseudocount) if adaptive: defaultFileName+= "_adaptive" if includeZeros: defaultFileName+= "_iz" defaultFileName+=".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, expdata, annotationPath, output_file, normalization, samples, adaptive, doHistogram, includeZeros, pseudocount, replicates, LOESS, ignoreCodon, NTerminus, CTerminus, ctrl_lib_str, exp_lib_str, wxobj, Z = False, diffStrains = diffStrains, annotation_path_exp = annotationPathExp)