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
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()
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()
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()
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 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
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)
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
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)
