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
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 test_file_types(self):
types = tnseq_tools.get_file_types(all_data_list)
types = set(types)
self.assertEqual(len(types), 1)
self.assertTrue("himar1" in types)
def test_file_types(self):
types = tnseq_tools.get_file_types(all_data_list)
types = set(types)
self.assertEqual(len(types), 1)
self.assertTrue("himar1" in types)
