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)
