README.md

 
 
 
-# TRANSIT 2.1.2
+# TRANSIT 2.2.1
 
 
 [![Build Status](https://travis-ci.org/mad-lab/transit.svg?branch=master)](https://travis-ci.org/mad-lab/transit)   [![Documentation Status](https://readthedocs.org/projects/transit/badge/?version=latest)](http://transit.readthedocs.io/en/latest/?badge=latest) 
 
 
 
+**Version 2.2.0 changes (June, 2018)**
+- Added analysis method for Genetic Interactions.
+- Added Mann-Whitney U-test for comparative analysis.
+- Made TRANSIT compatible with wxPython 4.0 (Phoenix).
+- Datasets now automatically selected when they are added to TRANSIT.
+- TRANSIT window now starts maximized.
+- Updated documentation.
+- Fixed bug with plots of finished results files.
+- Fixed bug in packaging of TPP, causing problem with console mode in new setuptools.
+- Other misc. bugs fixes
+
 
 **Version 2.1.2 changes (May, 2018)**
 - Improved resampling on comparisons with unbalanced number of replicates.
@@ -56,6 +67,26 @@ Welcome! This is the distribution for the TRANSIT and TPP tools developed by the
 TRANSIT is a tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.
 
 
+## Features
+TRANSIT offers a variety of features including:
+    
+-   More than **8 analysis methods**, including methods for determining **conditional essentiality** as well as **genetic interactions**.
+
+-   Ability to analyze datasets from libraries constructed using  **himar1 or tn5 transposons**.
+
+-   **TrackView** to help visualize read-counts accross the genome.
+
+-   Can **export datasets** into a variety of formats, including **IGV**.
+
+-   Includes a **variety of normalization methods**.
+
+-   **Quality Control** diagnostics, to idenfity poor quality datasets.
+
+-   Ability to install as a **python package**, to import and use in your own personal scripts.
+
+
+
+
 
 ## Mailing List
 

VERSION

-version: 2.1.2-1-gccf8-mod
+version: 2.2.0-6-g2c24-mod

debian/changelog

+tnseq-transit (2.2.1-1) unstable; urgency=medium
+
+  * New upstream version
+  * Standards-Version: 4.2.1
+
+ -- Andreas Tille <tille@debian.org>  Wed, 26 Sep 2018 21:02:59 +0200
+
 tnseq-transit (2.1.2-1) unstable; urgency=medium
 
   * New upstream version

debian/control

@@ -6,7 +6,7 @@ Priority: optional
 Build-Depends: debhelper (>= 11~),
                python-all-dev,
                python-setuptools
-Standards-Version: 4.1.4
+Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/tnseq-transit
 Vcs-Git: https://salsa.debian.org/med-team/tnseq-transit.git
 Homepage: http://pythonhosted.org/tnseq-transit/transit_overview.html

setup.py

@@ -78,7 +78,7 @@ setup(
     # your project is installed. For an analysis of "install_requires" vs pip's
     # requirements files see:
     # https://packaging.python.org/en/latest/requirements.html
-    install_requires=['setuptools', 'numpy', 'scipy', 'pillow', 'matplotlib'],
+    install_requires=['setuptools', 'numpy', 'scipy', 'pillow', 'matplotlib', 'wxpython'],
     
     #dependency_links = [
     #	"git+https://github.com/wxWidgets/wxPython.git#egg=wxPython"
@@ -113,8 +113,8 @@ setup(
     # pip to create the appropriate form of executable for the target platform.
     entry_points={
         'console_scripts': [
-            'transit=pytransit.__main__:main',
-            'tpp=pytpp.__main__:main',
+            'transit=pytransit.__main__:run_main',
+            'tpp=pytpp.__main__:run_main',
         ],
     },
 )

src/pytpp/__main__.py

@@ -34,11 +34,15 @@ from tpp_tools import *
 from tpp_gui import *
 
 
-def main(arguments=[]):
+def run_main():
+    (args, kwargs) = cleanargs(sys.argv[1:])
+    main(*args, **kwargs)
 
-    vars = Globals()
+def main(*args, **kwargs):
 
-    if len(arguments)==0 and hasWx:        
+    vars = Globals()
+    # Check for arguements
+    if not args and not kwargs and hasWx:        
         app = wx.App(False)
         form = MyForm(vars)
         form.update_dataset_list()
@@ -62,14 +66,13 @@ def main(arguments=[]):
         else:
             pass
 
-    elif len(arguments) <= 1 and not hasWx:
+    elif not args and not kwargs and not hasWx:
         print "Please install wxPython to run in GUI Mode."
         print "To run in Console Mode please follow these instructions:"
         print ""
         show_help()
 
     else:
-        (args, kwargs) = cleanargs(arguments)
 
         # Show help if needed
         if "help" in kwargs or "-help" in kwargs:
@@ -110,5 +113,5 @@ def main(arguments=[]):
 
 
 if __name__ == "__main__":
-    main(sys.argv[1:])
+    run_main()
 

src/pytransit/__init__.py

@@ -2,6 +2,6 @@
 __all__ = ["transit_tools", "tnseq_tools", "norm_tools", "stat_tools"]
 
 
-__version__ = "v2.1.2"
+__version__ = "v2.2.1"
 prefix = "[TRANSIT]"
 

src/pytransit/__main__.py

 
 import sys
+
 try:
     import wx
+    WX_VERSION = int(wx.version()[0])
     hasWx = True
-    #Check if wx is the newest 3.0+ version:
-    try:
-        from wx.lib.pubsub import pub
-        pub.subscribe
-        newWx = True
-    except AttributeError as e:
-        from wx.lib.pubsub import Publisher as pub
-        newWx = False
+
 except Exception as e:
     hasWx = False
+    WX_VERSION = 0
+    print "EXCEPTION:", str(e)
+
+if hasWx:
+    import wx.xrc
+    from wx.lib.buttons import GenBitmapTextButton
+
+    #Imports depending on version:
+    if WX_VERSION == 2:
+        from wx.lib.pubsub import Publisher as pub
+
+    if WX_VERSION == 3:
+        from wx.lib.pubsub import pub
+        pub.subscribe
+
+    if WX_VERSION == 4:
+        from wx.lib.pubsub import pub
+        pub.subscribe
+        import wx.adv
+
 
 import pytransit
 import pytransit.transit_tools as transit_tools
 import pytransit.analysis
+import pytransit.export
+
 
 method_wrap_width = 250
 methods = pytransit.analysis.methods
-export_methods = pytransit.analysis.export_methods
+export_methods = pytransit.export.methods
 all_methods = {}
 all_methods.update(methods)
-all_methods.update(export_methods)
+
+#all_methods.update(export_methods)
 
 wildcard = "Python source (*.py)|*.py|" \
             "All files (*.*)|*.*"
 transit_prefix = "[TRANSIT]"
 
 
-def main(args=None):
+
+def run_main():
+    (args, kwargs) = transit_tools.cleanargs(sys.argv[1:])
+    main(*args, **kwargs)
+
+def main(*args, **kwargs):
     #If no arguments, show GUI:
     DEBUG = "--debug" in sys.argv
     if DEBUG:
         sys.argv.remove("--debug")
+        kwargs.pop("-debug")
 
     # Check if running in GUI Mode
-    if len(sys.argv) == 1 and hasWx:
+    if not (args or kwargs) and hasWx:
 
+        import matplotlib
+        matplotlib.use("WXAgg")
         import matplotlib.pyplot
         import pytransit.transit_gui as transit_gui
         transit_tools.transit_message("Running in GUI Mode")
@@ -48,11 +74,13 @@ def main(args=None):
         frame = transit_gui.TnSeekFrame(None, DEBUG)
         #show the frame
         frame.Show(True)
+        frame.Maximize(True)
+
         #start the applications
         app.MainLoop()
     
     # Tried GUI mode but has no wxPython
-    elif len(sys.argv) == 1 and not hasWx:
+    elif not (args or kwargs) and not hasWx:
         print "Please install wxPython to run in GUI Mode."
         print "To run in Console Mode please follow these instructions:"
         print ""
@@ -64,8 +92,24 @@ def main(args=None):
     else:
         import matplotlib
         matplotlib.use("Agg")
-        method_name = sys.argv[1]
+        method_name = args[0]
         if method_name not in all_methods:
+            if method_name.lower() == "export":
+                export_method_name = ""
+                if len(args) > 1:
+                    export_method_name = args[1]
+                
+                if export_method_name not in export_methods:
+                    print "Error: Need to specify the export method."
+                    print "Please use one of the known methods (or see documentation to add a new one):"
+                    for m in export_methods:
+                        print "\t - %s" % m
+                    print "Usage: python %s export <method>" % sys.argv[0]
+                else:
+                    methodobj = export_methods[export_method_name].method.fromconsole()
+                    methodobj.Run()
+
+            else:
                 print "Error: The '%s' method is unknown." % method_name
                 print "Please use one of the known methods (or see documentation to add a new one):"
                 for m in all_methods:
@@ -80,5 +124,5 @@ def main(args=None):
 
 if __name__ == "__main__":
     main()
-
+    sys.exit(1)
 

src/pytransit/analysis/__init__.py

@@ -15,7 +15,8 @@ import griffin
 import resampling
 import hmm
 import rankproduct
-
+import gi
+import utest
 
 methods = {}
 methods["example"] = example.ExampleAnalysis()
@@ -26,6 +27,8 @@ methods["hmm"] = hmm.HMMAnalysis()
 methods["resampling"] = resampling.ResamplingAnalysis()
 methods["tn5gaps"] = tn5gaps.Tn5GapsAnalysis()
 methods["rankproduct"] = rankproduct.RankProductAnalysis()
+methods["utest"] = utest.UTestAnalysis()
+methods["gi"] = gi.GIAnalysis()
 #methods["mcce"] = mcce.MCCEAnalysis()
 #methods["mcce2"] = mcce2.MCCE2Analysis()
 #methods["motifhmm"] = motifhmm.MotifHMMAnalysis()

src/pytransit/analysis/base.py

@@ -3,18 +3,31 @@ import sys
 
 try:
     import wx
+    WX_VERSION = int(wx.version()[0])
     hasWx = True
-    #Check if wx is the newest 3.0+ version:
-    try:
-        from wx.lib.pubsub import pub
-        pub.subscribe
-        newWx = True
-    except AttributeError as e:
-        from wx.lib.pubsub import Publisher as pub
-        newWx = False
+
 except Exception as e:
     hasWx = False
-    newWx = False
+    WX_VERSION = 0
+    print "EXCEPTION:", str(e)
+
+if hasWx:
+    import wx.xrc
+    from wx.lib.buttons import GenBitmapTextButton
+
+    #Imports depending on version:
+    if WX_VERSION == 2:
+        from wx.lib.pubsub import Publisher as pub
+
+    if WX_VERSION == 3:
+        from wx.lib.pubsub import pub
+        pub.subscribe
+
+    if WX_VERSION == 4:
+        from wx.lib.pubsub import pub
+        pub.subscribe
+        import wx.adv
+
    
 import traceback
 import datetime
@@ -22,12 +35,15 @@ import pytransit.transit_tools as transit_tools
 
 file_prefix = "[FileDisplay]"
 
+
 class InvalidArgumentException(Exception):
     def __init__(self, message):
 
         # Call the base class constructor with the parameters it needs
         super(InvalidArgumentException, self).__init__(message)
 
+#
+
 if hasWx:
     class InfoIcon(wx.StaticBitmap):
         def __init__(self, panel, flag, bmp=None, tooltip=""):
@@ -44,56 +60,76 @@ class TransitGUIBase:
         self.wxobj = None
         self.short_name = "TRANSIT"
         self.long_name = "TRANSIT"
+        self.short_desc = "TRANSIT - Short Description"
+        self.long_desc =  "TRANSIT - Long Description"
+
+#
 
     def status_message(self, text, time=-1):
         #TODO: write docstring
         if self.wxobj:
-            if newWx:
+            if WX_VERSION > 2:
                 wx.CallAfter(pub.sendMessage, "status", msg=(self.short_name, text, time))
             else:
                 wx.CallAfter(pub.sendMessage, "status", (self.short_name, text, time))
             wx.Yield()
 
+#
+
     def console_message(self, text):
         #TODO: write docstring
         sys.stdout.write("[%s] %s\n" % (self.short_name, text))
 
+#
+
     def console_message_inplace(self, text):
         #TODO: write docstring
         sys.stdout.write("[%s] %s   \r" % (self.short_name, text) )
         sys.stdout.flush()
 
+#
+
     def transit_message(self, text):
         #TODO: write docstring
         self.console_message(text)
         self.status_message(text)
 
+#
+
     def transit_message_inplace(self, text):
         #TODO: write docstring
         self.console_message_inplace(text)
         self.status_message(text)
 
+#
 
     def transit_error(self,text):
         self.transit_message(text)
         if self.wxobj:
             transit_tools.ShowError(text)
 
+#
+
     def transit_warning(self,text):
         self.transit_message(text)
         if self.wxobj:
             transit_tools.ShowWarning(text)
 
+#
 
 class TransitFile (TransitGUIBase):
     #TODO write docstring
 
+#
+
     def __init__(self, identifier="#Unknown", colnames=[]):
         #TODO write docstring
         TransitGUIBase.__init__(self)
         self.identifier = identifier
         self.colnames = colnames
 
+#
+
     def getData(self, path, colnames):
         #TODO write docstring
         row = 0
@@ -116,15 +152,20 @@ class TransitFile (TransitGUIBase):
             row+=1
         return data
 
+#
+
     def getHeader(self, path):
         #TODO write docstring
         return "Generic Transit File Type."
 
+#
 
     def getMenus(self):
         menus = [("Display in Track View", self.displayInTrackView)]
         return menus
 
+#
+
     def displayInTrackView(self, displayFrame, event):
 
         #print "Self:", self
@@ -137,6 +178,8 @@ class TransitFile (TransitGUIBase):
         except Exception as e:
             print file_prefix, "Error occurred: %s" % e 
 
+#
+
 class AnalysisGUI:
     
     def __init__(self):
@@ -145,16 +188,22 @@ class AnalysisGUI:
         self.LABELSIZE = (100,-1)
         self.WIDGETSIZE = (100,-1)
 
+#
+
     def Hide(self):
         self.panel.Hide()
 
+#
+
     def Show(self):
         self.panel.Show()
 
+#
+
     def Enable(self):
         self.panel.Enable()
 
-
+#
 
     def definePanel(self, wxobj):
         #TODO: write docstring
@@ -164,8 +213,8 @@ class AnalysisGUI:
 
         Section = wx.BoxSizer( wx.VERTICAL )
 
-        Label = wx.StaticText(wPanel, id=wx.ID_ANY, label=str("Options"), pos=wx.DefaultPosition, size=wx.DefaultSize, style=0 )
-        Label.Wrap( -1 )
+        Label = wx.StaticText(wPanel, id=wx.ID_ANY, label=str("Method Options"), pos=wx.DefaultPosition, size=(130, -1), style=0 )
+        Label.SetFont( wx.Font( 10, wx.DEFAULT, wx.NORMAL, wx.BOLD) )
         Section.Add( Label, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
         
         Sizer1 = wx.BoxSizer( wx.HORIZONTAL )
@@ -182,6 +231,8 @@ class AnalysisGUI:
         Button.Bind( wx.EVT_BUTTON, self.wxobj.RunMethod )
         self.panel = wPanel
 
+#
+
     def defineTextBox(self, panel, labelText="", widgetText="", tooltipText="", labSize=None, widgetSize=None):
         if not labSize: labSize = self.LABELSIZE
         if not widgetSize: widgetSize = self.WIDGETSIZE
@@ -195,6 +246,8 @@ class AnalysisGUI:
         sizer.Add(InfoIcon(panel, wx.ID_ANY, tooltip=tooltipText), 0, wx.ALIGN_CENTER_VERTICAL, 5 )
         return (label, textBox, sizer)
 
+#
+
     def defineChoiceBox(self, panel, labelText="", widgetChoice=[""], tooltipText="", labSize=None, widgetSize=None):
         if not labSize: labSize = self.LABELSIZE
         if not widgetSize: widgetSize = self.WIDGETSIZE
@@ -209,6 +262,8 @@ class AnalysisGUI:
         sizer.Add(InfoIcon(panel, wx.ID_ANY, tooltip=tooltipText), 0, wx.ALIGN_CENTER_VERTICAL, 5 )
         return (label, choiceBox, sizer)
 
+#
+
     def defineCheckBox(self, panel, labelText="", widgetCheck=False, tooltipText="", widgetSize=None):
         if not widgetSize: widgetSize = self.WIDGETSIZE
         sizer = wx.BoxSizer( wx.HORIZONTAL )
@@ -218,33 +273,40 @@ class AnalysisGUI:
         sizer.Add(InfoIcon(panel, wx.ID_ANY, tooltip=tooltipText), 0, wx.ALIGN_CENTER_VERTICAL, 5 )
         return (checkBox, sizer)
 
+#
 
 class AnalysisMethod:
     '''
     Basic class for analysis methods. Inherited by SingleMethod and ComparisonMethod.
     '''
     
-    def __init__(self, short_name, long_name, description, output, annotation_path, wxobj=None):
+    def __init__(self, short_name, long_name, short_desc, long_desc, output, annotation_path, wxobj=None):
         self.short_name = short_name
         self.long_name = long_name
-        self.description = description
+        self.short_desc = short_desc
+        self.long_desc = long_desc
         self.output = output
         self.annotation_path = annotation_path
 
-        self.newWx = newWx
+        self.WX_VERSION = WX_VERSION 
         self.wxobj = wxobj
 
+#
 
     @classmethod 
     def fromGUI(self, wxobj):
         #TODO: write docstring
         raise NotImplementedError
 
+#
+
     @classmethod
     def fromargs(self, rawargs):
         #TODO: write docstring
         raise NotImplementedError
 
+#
+
     @classmethod
     def fromconsole(self):
         #TODO: write docstring
@@ -270,15 +332,20 @@ class AnalysisMethod:
             print self.usage_string()
         sys.exit() 
 
+#
+
     @classmethod
     def usage_string(self):
         #TODO: write docstring
         raise NotImplementedError
 
+#
+
     def Run(self):
         #TODO write docstring
         raise NotImplementedError
 
+#
 
     def print_members(self):
         #TODO: write docstring
@@ -286,6 +353,7 @@ class AnalysisMethod:
         for m in members:
             print "%s = %s" % (m, getattr(self, m))
 
+#
 
     def add_file(self, path=None, filetype=None):
 
@@ -298,73 +366,91 @@ class AnalysisMethod:
         data = {"path":path, "type":filetype, "date": datetime.datetime.today().strftime("%B %d, %Y %I:%M%p")}
 
         if self.wxobj:
-            if newWx:
+            if WX_VERSION > 2:
                 wx.CallAfter(pub.sendMessage, "file", data=data)
             else:
                 wx.CallAfter(pub.sendMessage, "file", data)
 
+#
+
     def finish(self):
         #TODO: write docstring
         if self.wxobj:
-            if newWx:
+            if WX_VERSION > 2:
                 wx.CallAfter(pub.sendMessage,"finish", msg=self.short_name.lower())
             else:
                 wx.CallAfter(pub.sendMessage,"finish", self.short_name.lower())
 
+#
+
     def progress_update(self, text, count):
         #TODO: write docstring
         if self.wxobj:
-            if newWx:
+            if WX_VERSION > 2:
                 wx.CallAfter(pub.sendMessage, "progress", msg=(self.short_name, count))
             else:
                 wx.CallAfter(pub.sendMessage, "progress", (self.short_name, count))
             wx.Yield()
 
+        self.transit_message_inplace(text)
+#
+
     def progress_range(self, count):
         #TODO: write docstring
         if self.wxobj:
-            if newWx:
+            if WX_VERSION > 2:
                 wx.CallAfter(pub.sendMessage, "progressrange", msg=count)
             else:
                 wx.CallAfter(pub.sendMessage, "progressrange", count)
             wx.Yield()
 
-        
+#       
 
     def status_message(self, text, time=-1):
         #TODO: write docstring
         if self.wxobj:
-            if newWx:
+            if WX_VERSION > 2:
                 wx.CallAfter(pub.sendMessage, "status", msg=(self.short_name, text, time))
             else:
                 wx.CallAfter(pub.sendMessage, "status", (self.short_name, text, time))
             wx.Yield()
 
+#
+
     def console_message(self, text):
         #TODO: write docstring
         sys.stdout.write("[%s] %s\n" % (self.short_name, text))
 
+#
+
     def console_message_inplace(self, text):
         #TODO: write docstring
         sys.stdout.write("[%s] %s   \r" % (self.short_name, text) )
         sys.stdout.flush()
 
+#
+
     def transit_message(self, text):
         #TODO: write docstring
         self.console_message(text)
         self.status_message(text)
 
+#
+
     def transit_message_inplace(self, text):
         #TODO: write docstring
         self.console_message_inplace(text)
         self.status_message(text)
 
+#
 
     def transit_error(self,text):
         self.transit_message(text)
         if self.wxobj:
             transit_tools.ShowError(text)
 
+#
+
     def transit_warning(self,text):
         self.transit_message(text)
         if self.wxobj:
@@ -376,8 +462,9 @@ class SingleConditionMethod(AnalysisMethod):
     Class to be inherited by analysis methods that determine essentiality in a single condition (e.g. Gumbel, Binomial, HMM).
     '''
 
-    def __init__(self, short_name, long_name, description, ctrldata, annotation_path, output, replicates="Sum", normalization=None, LOESS=False, ignoreCodon=True, NTerminus=0.0, CTerminus=0.0, wxobj=None):
-        AnalysisMethod.__init__(self, short_name, long_name, description, output, annotation_path, wxobj)
+    def __init__(self, short_name, long_name, short_desc, long_desc, ctrldata, annotation_path, output, replicates="Sum", normalization=None, LOESS=False, ignoreCodon=True, NTerminus=0.0, CTerminus=0.0, wxobj=None):
+        AnalysisMethod.__init__(self, short_name, long_name, short_desc, long_desc, output, 
+            annotation_path, wxobj)
         self.ctrldata = ctrldata
         self.replicates = replicates
         self.normalization = normalization
@@ -386,15 +473,16 @@ class SingleConditionMethod(AnalysisMethod):
         self.NTerminus = NTerminus
         self.CTerminus = CTerminus
 
-
+#
 
 class DualConditionMethod(AnalysisMethod):
     '''
     Class to be inherited by analysis methods that determine changes in essentiality between two conditions (e.g. Resampling, DEHMM).
     '''
 
-    def __init__(self, short_name, long_name, description, ctrldata, expdata, annotation_path, output, normalization, replicates="Sum", LOESS=False, ignoreCodon=True, NTerminus=0.0, CTerminus=0.0, wxobj=None):
-        AnalysisMethod.__init__(self, short_name, long_name, description, output, annotation_path, wxobj)
+    def __init__(self, short_name, long_name, short_desc, long_desc, ctrldata, expdata, annotation_path, output, normalization, replicates="Sum", LOESS=False, ignoreCodon=True, NTerminus=0.0, CTerminus=0.0, wxobj=None):
+        AnalysisMethod.__init__(self, short_name, long_name, short_desc, long_desc, 
+            output, annotation_path, wxobj)
         self.ctrldata = ctrldata
         self.expdata = expdata
         self.normalization = normalization
@@ -404,36 +492,67 @@ class DualConditionMethod(AnalysisMethod):
         self.NTerminus = NTerminus
         self.CTerminus = CTerminus
 
+#
 
+class QuadConditionMethod(AnalysisMethod):
+    '''
+    Class to be inherited by analysis methods that determine changes in essentiality between four conditions (e.g. GI).
+    '''
+
+    def __init__(self, short_name, long_name, short_desc, long_desc, ctrldataA, ctrldataB, expdataA, expdataB, annotation_path, output, normalization, replicates="Sum", LOESS=False, ignoreCodon=True, NTerminus=0.0, CTerminus=0.0, wxobj=None):
+        AnalysisMethod.__init__(self, short_name, long_name, short_desc, long_desc, 
+            output, annotation_path, wxobj)
+        self.ctrldataA = ctrldataA
+        self.ctrldataB = ctrldataB
+        self.expdataA = expdataA
+        self.expdataB = expdataB
+        self.normalization = normalization
+        self.replicates = replicates
+        self.LOESS = LOESS
+        self.ignoreCodon = ignoreCodon
+        self.NTerminus = NTerminus
+        self.CTerminus = CTerminus
+
+#
 
 class TransitAnalysis:
-    def __init__(self, sn, ln, desc, tn, method_class=AnalysisMethod, gui_class=AnalysisGUI, filetypes=[TransitFile]):
+    def __init__(self, sn, ln, short_desc, long_desc, tn, method_class=AnalysisMethod, gui_class=AnalysisGUI, filetypes=[TransitFile]):
         self.short_name = sn
         self.long_name = ln
-        self.description = desc
+        self.short_desc = short_desc
+        self.long_desc = long_desc
         self.transposons = tn
         self.method = method_class
         self.gui = gui_class()
         self.filetypes = filetypes
 
+#
 
     def __str__(self):
         return """Analysis Method:
     Short Name:  %s
     Long Name:   %s
-    Description: %s
+    Short Desc:  %s
+    Long Desc:   %s
     Method:      %s
-    GUI:         %s""" % (self.short_name, self.long_name, self.description, self.method, self.gui)
+    GUI:         %s""" % (self.short_name, self.long_name, self.short_desc, self.long_desc, self.method, self.gui)
 
+#
 
     def fullname(self):
-        return "[%s]  -  %s" % (self.short_name, self.long_name)
+        return "[%s]  -  %s" % (self.short_name, self.short_desc)
+
+#
 
     def getInstructionsText(self):
         return ""
 
+#
+
     def getDescriptionText(self):
-        return self.description 
+        return self.long_desc
+
+#
 
     def getTransposonsText(self):
         if len(self.transposons) == 0:
@@ -446,6 +565,7 @@ class TransitAnalysis:
             return "Intended for " + ", ".join(self.transposons[:-1]) + ", and " + self.transposons[-1]
     
 
+#
 
 if __name__ == "__main__":
     pass

src/pytransit/analysis/binomial.py

@@ -2,18 +2,31 @@ import sys
 
 try:
     import wx
+    WX_VERSION = int(wx.version()[0])
     hasWx = True
-    #Check if wx is the newest 3.0+ version:
-    try:
-        from wx.lib.pubsub import pub
-        pub.subscribe
-        newWx = True
-    except AttributeError as e:
-        from wx.lib.pubsub import Publisher as pub
-        newWx = False
+
 except Exception as e:
     hasWx = False
-    newWx = False
+    WX_VERSION = 0
+    print "EXCEPTION:", str(e)
+
+if hasWx:
+    import wx.xrc
+    from wx.lib.buttons import GenBitmapTextButton
+
+    #Imports depending on version:
+    if WX_VERSION == 2:
+        from wx.lib.pubsub import Publisher as pub
+
+    if WX_VERSION == 3:
+        from wx.lib.pubsub import pub
+        pub.subscribe
+
+    if WX_VERSION == 4:
+        from wx.lib.pubsub import pub
+        pub.subscribe
+        import wx.adv
+
 
 import os
 import time
@@ -34,8 +47,9 @@ import pytransit.stat_tools as stat_tools
 ############# GUI ELEMENTS ##################
 
 short_name = "binomial"
-long_name = "Hierarchical binomial model of essentiality with individual frequencies."
-description = """Hierarchical bayesian model of essentiality based on the binomial distribution. Estimates individual probabilities for insertion, leading to more conservative predictions.
+long_name = "Binomial"
+short_desc = "Hierarchical binomial model of essentiality with individual frequencies."
+long_desc = """Hierarchical bayesian model of essentiality based on the binomial distribution. Estimates individual probabilities for insertion, leading to more conservative predictions.
 
 Reference: DeJesus and Ioerger (2014; IEEE TCBB)
 """
@@ -46,7 +60,7 @@ columns = ["Orf","Name","Description","Mean Insertion","Sites per Replicate","To
 
 class BinomialAnalysis(base.TransitAnalysis):
     def __init__(self):
-        base.TransitAnalysis.__init__(self, short_name, long_name, description, transposons, BinomialMethod, BinomialGUI, [BinomialFile])
+        base.TransitAnalysis.__init__(self, short_name, long_name, short_desc, long_desc, transposons, BinomialMethod, BinomialGUI, [BinomialFile])
 
 
 ################## FILE ###################
@@ -83,8 +97,8 @@ class BinomialGUI(base.AnalysisGUI):
 
         binomialSection = wx.BoxSizer( wx.VERTICAL )
 
-        binomialLabel = wx.StaticText( binomialPanel, wx.ID_ANY, u"Binomial Options", wx.DefaultPosition, wx.DefaultSize, 0 )
-        binomialLabel.Wrap( -1 )
+        binomialLabel = wx.StaticText( binomialPanel, wx.ID_ANY, u"Binomial Options", wx.DefaultPosition, (130, -1), 0 )
+        binomialLabel.SetFont( wx.Font( 10, wx.DEFAULT, wx.NORMAL, wx.BOLD) )
         binomialSection.Add( binomialLabel, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
 
         binomialSizer1 = wx.BoxSizer( wx.HORIZONTAL )
@@ -161,7 +175,7 @@ class BinomialMethod(base.SingleConditionMethod):
                 beta_w=0.5,
                 wxobj=None):
 
-        base.SingleConditionMethod.__init__(self, short_name, long_name, description, ctrldata, annotation_path, output_file, replicates=replicates, normalization=normalization, LOESS=LOESS, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
+        base.SingleConditionMethod.__init__(self, short_name, long_name, short_desc, long_desc, ctrldata, annotation_path, output_file, replicates=replicates, normalization=normalization, LOESS=LOESS, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
 
         self.samples = samples
         self.burnin = burnin
@@ -453,9 +467,8 @@ class BinomialMethod(base.SingleConditionMethod):
 
 
             #Update progress
-            text = "Running Binomial Method... %2.0f%%" % (100.0*(i+1)/(sample_size))
+            text = "Running Binomial Method... %5.1f%%" % (100.0*(i+1)/(sample_size))
             self.progress_update(text, i)
-            self.transit_message_inplace(text)
 
         numpy.seterr(divide='warn')
 

src/pytransit/analysis/example.py

 import sys
+
 try:
     import wx
+    WX_VERSION = int(wx.version()[0])
     hasWx = True
-    #Check if wx is the newest 3.0+ version:
-    try:
-        from wx.lib.pubsub import pub
-        pub.subscribe
-        newWx = True
-    except AttributeError as e:
-        from wx.lib.pubsub import Publisher as pub
-        newWx = False
+
 except Exception as e:
     hasWx = False
-    newWx = False
+    WX_VERSION = 0
+    print "EXCEPTION:", str(e)
+
+if hasWx:
+    import wx.xrc
+    from wx.lib.buttons import GenBitmapTextButton
+
+    #Imports depending on version:
+    if WX_VERSION == 2:
+        from wx.lib.pubsub import Publisher as pub
+
+    if WX_VERSION == 3:
+        from wx.lib.pubsub import pub
+        pub.subscribe
+
+    if WX_VERSION == 4:
+        from wx.lib.pubsub import pub
+        pub.subscribe
+        import wx.adv
+
 
 import os
 import time
@@ -32,8 +46,9 @@ import pytransit.stat_tools as stat_tools
 ############# Description ##################
 
 short_name = "example"
-long_name = "Example method that calculates mean read-counts per gene."
-description = "A method made to serve as an example to implementing other methods."
+long_name = "Example"
+short_desc = "Example method that calculates mean read-counts per gene."
+long_desc = "A method made to serve as an example to implementing other methods."
 transposons = ["himar1", "tn5"]
 columns = ["Orf","Name","Desc","k","n","mean","nzmean"]
 
@@ -41,7 +56,7 @@ columns = ["Orf","Name","Desc","k","n","mean","nzmean"]
 
 class ExampleAnalysis(base.TransitAnalysis):
     def __init__(self):
-        base.TransitAnalysis.__init__(self, short_name, long_name, description, transposons, ExampleMethod, ExampleGUI, [ExampleFile])
+        base.TransitAnalysis.__init__(self, short_name, long_name, short_desc, long_desc, transposons, ExampleMethod, ExampleGUI, [ExampleFile])
 
 
 ################## FILE ###################
@@ -81,7 +96,7 @@ class ExampleMethod(base.SingleConditionMethod):
                 NTerminus=0.0,
                 CTerminus=0.0, wxobj=None):
 
-        base.SingleConditionMethod.__init__(self, short_name, long_name, description, ctrldata, annotation_path, output_file, replicates=replicates, normalization=normalization, LOESS=LOESS, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
+        base.SingleConditionMethod.__init__(self, short_name, long_name, short_desc, long_desc, ctrldata, annotation_path, output_file, replicates=replicates, normalization=normalization, LOESS=LOESS, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
 
 
 
@@ -194,8 +209,9 @@ class ExampleMethod(base.SingleConditionMethod):
             data.append("%s\t%s\t%s\t%s\t%s\t%1.2f\t%1.2f\n" % (gene.orf, gene.name, gene.desc, gene.k, gene.n, mean, nzmean))
 
            
-            self.progress_update("gumbel", count)
-            self.transit_message_inplace("Running Example Method... %1.1f%%" % (100.0*count/N))
+            # Update Progress 
+            text = "Running Example Method... %5.1f%%" % (100.0*count/N)
+            self.progress_update(text, count)
             
         
         self.output.write("#Example\n")

src/pytransit/analysis/griffin.py

@@ -2,18 +2,31 @@ import sys
 
 try:
     import wx
+    WX_VERSION = int(wx.version()[0])
     hasWx = True
-    #Check if wx is the newest 3.0+ version:
-    try:
-        from wx.lib.pubsub import pub
-        pub.subscribe
-        newWx = True
-    except AttributeError as e:
-        from wx.lib.pubsub import Publisher as pub
-        newWx = False
+
 except Exception as e:
     hasWx = False
-    newWx = False
+    WX_VERSION = 0
+    print "EXCEPTION:", str(e)
+
+if hasWx:
+    import wx.xrc
+    from wx.lib.buttons import GenBitmapTextButton
+
+    #Imports depending on version:
+    if WX_VERSION == 2:
+        from wx.lib.pubsub import Publisher as pub
+
+    if WX_VERSION == 3:
+        from wx.lib.pubsub import pub
+        pub.subscribe
+
+    if WX_VERSION == 4:
+        from wx.lib.pubsub import pub
+        pub.subscribe
+        import wx.adv
+
 
 import os
 import time
@@ -35,8 +48,9 @@ import pytransit.stat_tools as stat_tools
 ############# GUI ELEMENTS ##################
 
 short_name = "griffin"
-long_name = "Basic frequentist analysis of essentiality using gaps."
-description = "Analysis of gaps used in Griffin et al. 2011"
+long_name = "Griffin"
+short_desc = "Basic frequentist analysis of essentiality using gaps."
+long_desc = "Analysis of gaps used in Griffin et al. 2011"
 transposons = ["himar1"]
 columns = ["Orf","Name","Desc","k","n","r","s","t","Expected Run","p-value", "p-adjusted"]
 
@@ -46,7 +60,7 @@ columns = ["Orf","Name","Desc","k","n","r","s","t","Expected Run","p-value", "p-
 
 class GriffinAnalysis(base.TransitAnalysis):
     def __init__(self):
-        base.TransitAnalysis.__init__(self, short_name, long_name, description, transposons, GriffinMethod, GriffinGUI, [GriffinFile])
+        base.TransitAnalysis.__init__(self, short_name, long_name, short_desc, long_desc, transposons, GriffinMethod, GriffinGUI, [GriffinFile])
 
 
 ################## FILE ###################
@@ -83,8 +97,8 @@ class GriffinGUI(base.AnalysisGUI):
 
         griffinSection = wx.BoxSizer( wx.VERTICAL )
 
-        griffinLabel = wx.StaticText( griffinPanel, wx.ID_ANY, u"griffin Options", wx.DefaultPosition, wx.DefaultSize, 0 )
-        griffinLabel.Wrap( -1 )
+        griffinLabel = wx.StaticText( griffinPanel, wx.ID_ANY, u"griffin Options", wx.DefaultPosition, (120,-1), 0 )
+        griffinLabel.SetFont( wx.Font( 10, wx.DEFAULT, wx.NORMAL, wx.BOLD) )
         griffinSection.Add( griffinLabel, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
 
         griffinSizer1 = wx.BoxSizer( wx.HORIZONTAL )
@@ -126,7 +140,7 @@ class GriffinMethod(base.SingleConditionMethod):
                 NTerminus=0.0,
                 CTerminus=0.0, wxobj=None):
 
-        base.SingleConditionMethod.__init__(self, short_name, long_name, description, ctrldata, annotation_path, output_file, replicates=replicates, normalization=normalization, LOESS=LOESS, ignoreCodon=ignoreCodon, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
+        base.SingleConditionMethod.__init__(self, short_name, long_name, short_desc, long_desc, ctrldata, annotation_path, output_file, replicates=replicates, normalization=normalization, LOESS=LOESS, ignoreCodon=ignoreCodon, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
         self.minread = minread
 
 
@@ -249,9 +263,8 @@ class GriffinMethod(base.SingleConditionMethod):
                 pval = 1.0 - tnseq_tools.GumbelCDF(gene.r, u, B)
                 results.append([gene, exprun, pval])
 
-            text = "Running Griffin Method... %2.0f%%" % (100.0*(count+1)/(N))
+            text = "Running Griffin Method... %5.1f%%" % (100.0*(count+1)/(N))
             self.progress_update(text, count)
-            self.transit_message_inplace(text)
             count+=1
 
 

src/pytransit/analysis/gumbel.py

@@ -2,18 +2,31 @@ import sys
 
 try:
     import wx
+    WX_VERSION = int(wx.version()[0])
     hasWx = True
-    #Check if wx is the newest 3.0+ version:
-    try:
-        from wx.lib.pubsub import pub
-        pub.subscribe
-        newWx = True
-    except AttributeError as e:
-        from wx.lib.pubsub import Publisher as pub
-        newWx = False
+
 except Exception as e:
     hasWx = False
-    newWx = False
+    WX_VERSION = 0
+    print "EXCEPTION:", str(e)
+
+if hasWx:
+    import wx.xrc
+    from wx.lib.buttons import GenBitmapTextButton
+
+    #Imports depending on version:
+    if WX_VERSION == 2:
+        from wx.lib.pubsub import Publisher as pub
+
+    if WX_VERSION == 3:
+        from wx.lib.pubsub import pub
+        pub.subscribe
+
+    if WX_VERSION == 4:
+        from wx.lib.pubsub import pub
+        pub.subscribe
+        import wx.adv
+
 
 import os
 import time
@@ -34,8 +47,9 @@ import pytransit.stat_tools as stat_tools
 ############# GUI ELEMENTS ##################
 
 short_name = "gumbel"
-long_name = "Bayesian analysis of essentiality based on long gaps."
-description = """Bayesian methods of analyzing longest runs of non-insertions in a row. Estimates the parameters using the MCMC sampling, and estimates posterior probabilities of essentiality. 
+long_name = "Gumbel"
+short_desc = "Bayesian analysis of essentiality based on long gaps."
+long_desc = """Bayesian methods of analyzing longest runs of non-insertions in a row. Estimates the parameters using the MCMC sampling, and estimates posterior probabilities of essentiality. 
 
 Reference: DeJesus et al. (2013; Bioinformatics)"""
 transposons = ["himar1"]
@@ -46,7 +60,7 @@ columns = ["Orf","Name","Desc","k","n","r","s","zbar", "Call"]
 
 class GumbelAnalysis(base.TransitAnalysis):
     def __init__(self):
-        base.TransitAnalysis.__init__(self, short_name, long_name, description, transposons, GumbelMethod, GumbelGUI, [GumbelFile])
+        base.TransitAnalysis.__init__(self, short_name, long_name, short_desc, long_desc, transposons, GumbelMethod, GumbelGUI, [GumbelFile])
 
 
 ################## FILE ###################
@@ -88,8 +102,9 @@ class GumbelGUI(base.AnalysisGUI):
 
         gumbelSection = wx.BoxSizer( wx.VERTICAL )
 
-        gumbelLabel = wx.StaticText( gumbelPanel, wx.ID_ANY, u"Gumbel Options", wx.DefaultPosition, wx.DefaultSize, 0 )
-        gumbelLabel.Wrap( -1 )
+        gumbelLabel = wx.StaticText( gumbelPanel, wx.ID_ANY, u"Gumbel Options", wx.DefaultPosition, (130,20))
+    
+        gumbelLabel.SetFont( wx.Font( 10, wx.DEFAULT, wx.NORMAL, wx.BOLD) )
         gumbelSection.Add( gumbelLabel, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
 
         mainSizer1 = wx.BoxSizer( wx.VERTICAL )
@@ -140,6 +155,8 @@ class GumbelGUI(base.AnalysisGUI):
 
 ########## METHOD #######################
 
+EXACT = 20
+
 ALPHA = 1
 BETA = 1
 class GumbelMethod(base.SingleConditionMethod):
@@ -162,7 +179,7 @@ class GumbelMethod(base.SingleConditionMethod):
                 NTerminus=0.0,
                 CTerminus=0.0, wxobj=None):
 
-        base.SingleConditionMethod.__init__(self, short_name, long_name, description, ctrldata, annotation_path, output_file, replicates=replicates, normalization=normalization, LOESS=LOESS, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
+        base.SingleConditionMethod.__init__(self, short_name, long_name, short_desc, long_desc, ctrldata, annotation_path, output_file, replicates=replicates, normalization=normalization, LOESS=LOESS, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
         self.samples = samples
         self.burnin = burnin
         self.trim = trim
@@ -170,8 +187,7 @@ class GumbelMethod(base.SingleConditionMethod):
       
 
         self.cache_nn = {}
- 
-
+        self.cache_expruns = {}
 
     @classmethod
     def fromGUI(self, wxobj):
@@ -365,6 +381,10 @@ class GumbelMethod(base.SingleConditionMethod):
         
         SIG = numpy.array([self.sigmoid(g.s, g.t) * scipy.stats.norm.pdf(g.r, mu_r*g.s, sigma_r) for g in G if self.good_orf(g)])
 
+#        idxG,idxN = -1,0
+#        for i in range(len(G)):
+#          if G[i].name=="glf": idxG = i
+#          if ii_good[i]==True: idxN += 1 # could do sum(ii_good[:idxG])
 
         i = 1; count = 0;
         while i < self.samples:
@@ -393,6 +413,7 @@ class GumbelMethod(base.SingleConditionMethod):
                     phi_sample[i] = phi_new
                     Z_sample[:,i] = Z
                     i+=1
+
             except ValueError as e:
                 self.transit_message("Error: %s" % e) 
                 self.transit_message("This is likely to have been caused by poor data (e.g. too sparse).") 
@@ -400,12 +421,12 @@ class GumbelMethod(base.SingleConditionMethod):
                 self.transit_message("Quitting.") 
                 return
 
+#            print i,phi_new,w1,G[idxG].name,N[idxN],R[idxN],Z[idxN]
             
             phi_old = phi_new
             #Update progress
-            text = "Running Gumbel Method... %2.0f%%" % (100.0*(count+1)/(self.samples+self.burnin))
+            text = "Running Gumbel Method... %5.1f%%" % (100.0*(count+1)/(self.samples+self.burnin))
             self.progress_update(text, count)
-            self.transit_message_inplace(text)
 
 
         ZBAR = numpy.apply_along_axis(numpy.mean, 1, Z_sample)
@@ -476,28 +497,44 @@ class GumbelMethod(base.SingleConditionMethod):
     def good_orf(self, gene):
         return (gene.n >= 3 and gene.t >= 150)
 
+    def ExpectedRuns_cached(self,n,q):
+        if (n,q) not in self.cache_expruns: self.cache_expruns[(n,q)] = tnseq_tools.ExpectedRuns(n,q)
+        return self.cache_expruns[(n,q)]
+
     def classify(self, n,r,p):
         if n == 0: return 0
-        q = 1-p; B = 1/math.log(1/p); u = math.log(n*q,1/p);
-        pval = 1 - scipy.stats.gumbel_r.cdf(r,u,B)
+        q = 1-p; B = 1/math.log(1/p); u = math.log(n*q,1/p) 
+        BetaGamma = B*tnseq_tools.getGamma()
+        if n<EXACT: # estimate more accurately based on expected run len, using exact calc for small genes
+          exprun = self.ExpectedRuns_cached(n,p)
+          u = exprun-BetaGamma # u is mu of Gumbel (mean=mu+gamma*beta); matching of moments
+        pval = 1 - scipy.exp(scipy.stats.gumbel_r.logcdf(r,u,B))
         if pval < 0.05: return(1)
         else: return(0)
 
-    def F_non(self, p, N, R):
-        q = 1.0 - p
+    def F_non(self, p, N, R): # pass in P_nonins as p
+        q = 1.0 - p; 
+        BetaGamma = tnseq_tools.getGamma()/math.log(1/p)
         total = numpy.log(scipy.stats.beta.pdf(p,ALPHA,BETA))
         mu = numpy.log(N*q) / numpy.log(1/p)
+        for i in range(len(N)): # estimate more accurately based on expected run len, using exact calc for small genes
+          if N[i]<EXACT: mu[i] = self.ExpectedRuns_cached(int(N[i]),p)-BetaGamma
         sigma = 1/math.log(1/p);
-        total+= numpy.sum(numpy.log(scipy.stats.gumbel_r.pdf(R, mu, sigma)))
+        #for i in range(len(N)): print '\t'.join([str(x) for x in N[i],R[i],self.ExpectedRuns_cached(int(N[i]),q),mu[i],scipy.stats.gumbel_r.pdf(R[i], mu[i], sigma)])
+        total += numpy.sum(scipy.stats.gumbel_r.logpdf(R, mu, sigma))
         return(total)
     
     def sample_Z(self, p, w1, N, R, S, T, mu_s, sigma_s, SIG):
         G = len(N)
         q = 1.0-p
-        mu = numpy.log(N*q) / numpy.log(1.0/p)
+        BetaGamma = tnseq_tools.getGamma()/math.log(1/p)
+        mu = numpy.log(N*q) / numpy.log(1/p)
+        for i in range(len(N)): # estimate more accurately based on expected run len, using exact calc for small genes
+          if N[i]<EXACT: mu[i] = self.ExpectedRuns_cached(int(N[i]),p)-BetaGamma
         sigma = 1.0/math.log(1.0/p);
-        h0 = ((scipy.stats.gumbel_r.pdf(R,mu,sigma)) * scipy.stats.norm.pdf(S, mu_s*R, sigma_s)  * (1-w1))
+        h0 = ((scipy.exp(scipy.stats.gumbel_r.logpdf(R,mu,sigma))) * scipy.stats.norm.pdf(S, mu_s*R, sigma_s)  * (1-w1))
         h1 = SIG * w1
+        h1 += 1e-10; h0 += 1e-10 # to prevent div-by-zero; if neither class is probable, p(z1) should be ~0.5
         p_z1 = h1/(h0+h1)
         return scipy.stats.binom.rvs(1, p_z1, size=G)
 

src/pytransit/analysis/hmm.py

@@ -2,18 +2,31 @@ import sys
 
 try:
     import wx
+    WX_VERSION = int(wx.version()[0])
     hasWx = True
-    #Check if wx is the newest 3.0+ version:
-    try:
-        from wx.lib.pubsub import pub
-        pub.subscribe
-        newWx = True
-    except AttributeError as e:
-        from wx.lib.pubsub import Publisher as pub
-        newWx = False
+
 except Exception as e:
     hasWx = False
-    newWx = False
+    WX_VERSION = 0
+    print "EXCEPTION:", str(e)
+
+if hasWx:
+    import wx.xrc
+    from wx.lib.buttons import GenBitmapTextButton
+
+    #Imports depending on version:
+    if WX_VERSION == 2:
+        from wx.lib.pubsub import Publisher as pub
+
+    if WX_VERSION == 3:
+        from wx.lib.pubsub import pub
+        pub.subscribe
+
+    if WX_VERSION == 4:
+        from wx.lib.pubsub import pub
+        pub.subscribe
+        import wx.adv
+
 
 import os
 import time
@@ -35,8 +48,9 @@ import pytransit.stat_tools as stat_tools
 ############# GUI ELEMENTS ##################
 
 short_name = "hmm"
-long_name = "Analysis of genomic regions using a Hidden Markov Model"
-description = """Analysis of essentiality in the entire genome using a Hidden Markov Model. Capable of determining regions with different levels of essentiality representing Essential, Growth-Defect, Non-Essential and Growth-Advantage regions.
+long_name = "HMM"
+short_desc = "Analysis of genomic regions using a Hidden Markov Model"
+long_desc = """Analysis of essentiality in the entire genome using a Hidden Markov Model. Capable of determining regions with different levels of essentiality representing Essential, Growth-Defect, Non-Essential and Growth-Advantage regions.
 
 Reference: DeJesus et al. (2013; BMC Bioinformatics)
 """
@@ -49,7 +63,7 @@ columns_genes = ["Orf","Name","Description","Total Sites","Num. ES","Num. GD","N
 
 class HMMAnalysis(base.TransitAnalysis):
     def __init__(self):
-        base.TransitAnalysis.__init__(self, short_name, long_name, description, transposons, HMMMethod, HMMGUI, [HMMSitesFile, HMMGenesFile])
+        base.TransitAnalysis.__init__(self, short_name, long_name, short_desc, long_desc, transposons, HMMMethod, HMMGUI, [HMMSitesFile, HMMGenesFile])
 
 
 ################## FILE ###################
@@ -121,8 +135,8 @@ class HMMGUI(base.AnalysisGUI):
 
         hmmSection = wx.BoxSizer( wx.VERTICAL )
 
-        hmmLabel = wx.StaticText( hmmPanel, wx.ID_ANY, u"HMM Options", wx.DefaultPosition, wx.DefaultSize, 0 )
-        hmmLabel.Wrap( -1 )
+        hmmLabel = wx.StaticText( hmmPanel, wx.ID_ANY, u"HMM Options", wx.DefaultPosition, (110,-1), 0 )
+        hmmLabel.SetFont( wx.Font( 10, wx.DEFAULT, wx.NORMAL, wx.BOLD) )
         hmmSection.Add( hmmLabel, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
 
         hmmSizer1 = wx.BoxSizer( wx.VERTICAL )
@@ -143,7 +157,7 @@ class HMMGUI(base.AnalysisGUI):
 
 
         # LOESS
-        (self.wxobj.hmmLoessCheck, loessCheckSizer) = self.defineCheckBox(hmmPanel, labelText="Correct for Genome Positional Bias", widgetCheck=False, widgetSize=(230,-1), tooltipText="Check to correct read-counts for possible regional biase using LOESS. Clicking on the button below will plot a preview, which is helpful to visualize the possible bias in the counts.")
+        (self.wxobj.hmmLoessCheck, loessCheckSizer) = self.defineCheckBox(hmmPanel, labelText="Correct for Genome Positional Bias", widgetCheck=False, widgetSize=(-1,-1), tooltipText="Check to correct read-counts for possible regional biase using LOESS. Clicking on the button below will plot a preview, which is helpful to visualize the possible bias in the counts.")
         hmmSizer1.Add( loessCheckSizer, 0, wx.EXPAND, 5 )
 
         # LOESS Button
@@ -187,7 +201,7 @@ class HMMMethod(base.SingleConditionMethod):
                 NTerminus=0.0,
                 CTerminus=0.0, wxobj=None):
 
-        base.SingleConditionMethod.__init__(self, short_name, long_name, description, ctrldata, annotation_path, output_file, replicates=replicates, normalization=normalization, LOESS=LOESS, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
+        base.SingleConditionMethod.__init__(self, short_name, long_name, short_desc, long_desc, ctrldata, annotation_path, output_file, replicates=replicates, normalization=normalization, LOESS=LOESS, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
 
         try:
             T = len([1 for line in open(ctrldata[0]).readlines() if not line.startswith("#")])
@@ -460,8 +474,8 @@ class HMMMethod(base.SingleConditionMethod):
             if numpy.sum(alpha[:,t]) == 0:
                 alpha[:,t] = 0.0000000000001
            
-            self.progress_update("hmm", self.count)
-            self.transit_message_inplace("Running HMM Method... %1.1f%%" % (100.0*self.count/self.maxiterations))
+            text = "Running HMM Method... %1.1f%%" % (100.0*self.count/self.maxiterations)
+            self.progress_update(text, self.count)
             self.count+=1
             #print t, O[:,t], alpha[:,t]
 
@@ -490,8 +504,8 @@ class HMMMethod(base.SingleConditionMethod):
             if C.any():
                 beta[:,t] = beta[:,t] * C[t]
 
-            self.progress_update("hmm", self.count)
-            self.transit_message_inplace("Running HMM Method... %1.1f%%" % (100.0*self.count/self.maxiterations))
+            text = "Running HMM Method... %1.1f%%" % (100.0*self.count/self.maxiterations)
+            self.progress_update(text, self.count)
             self.count+=1
 
         return(beta)
@@ -515,20 +529,21 @@ class HMMMethod(base.SingleConditionMethod):
             nus = delta[:, t-1] + A
             delta[:,t] = nus.max(1) + numpy.log(b_o)
             Q[:,t] = nus.argmax(1)
-            self.progress_update("hmm", self.count)
-            self.transit_message_inplace("Running HMM Method... %1.1f%%" % (100.0*self.count/self.maxiterations))
+            text = "Running HMM Method... %5.1f%%" % (100.0*self.count/self.maxiterations)
+            self.progress_update(text, self.count)
             self.count+=1
 
         Q_opt = [int(numpy.argmax(delta[:,T-1]))]
         for t in xrange(T-2, -1, -1):
             Q_opt.insert(0, Q[Q_opt[0],t+1])
-            self.progress_update("hmm", self.count)
-            self.transit_message_inplace("Running HMM Method... %1.1f%%" % (100.0*self.count/self.maxiterations))
+
+            text = "Running HMM Method... %5.1f%%" % (100.0*self.count/self.maxiterations)
+            self.progress_update(text, self.count)
             self.count+=1
 
         numpy.seterr(divide='warn')
-        self.progress_update("hmm", self.count)
-        self.transit_message_inplace("Running HMM Method... %1.1f%%" % (100.0*self.count/self.maxiterations))
+        text = "Running HMM Method... %5.1f%%" % (100.0*self.count/self.maxiterations)
+        self.progress_update(text, self.count)
 
         return((Q_opt, delta, Q))
 

src/pytransit/analysis/norm.py

 import sys
+
 try:
     import wx
+    WX_VERSION = int(wx.version()[0])
     hasWx = True
-    #Check if wx is the newest 3.0+ version:
-    try:
-        from wx.lib.pubsub import pub
-        pub.subscribe
-        newWx = True
-    except AttributeError as e:
-        from wx.lib.pubsub import Publisher as pub
-        newWx = False
+
 except Exception as e:
     hasWx = False
-    newWx = False
+    WX_VERSION = 0
+    print "EXCEPTION:", str(e)
+
+if hasWx:
+    import wx.xrc
+    from wx.lib.buttons import GenBitmapTextButton
+
+    #Imports depending on version:
+    if WX_VERSION == 2:
+        from wx.lib.pubsub import Publisher as pub
+
+    if WX_VERSION == 3:
+        from wx.lib.pubsub import pub
+        pub.subscribe
+
+    if WX_VERSION == 4:
+        from wx.lib.pubsub import pub
+        pub.subscribe
+        import wx.adv
+
 
 import os
 import time
@@ -32,8 +46,9 @@ import pytransit.stat_tools as stat_tools
 ############# Description ##################
 
 short_name = "norm"
-long_name = "Normalization method"
-description = "Method for normalizing datasets and outputting into CombinedWig file."
+long_name = "Normalization"
+short_desc = "Normalization method"
+long_desc = "Method for normalizing datasets and outputting into CombinedWig file."
 transposons = ["himar1", "tn5"]
 columns = ["Position","Reads","Genes"]
 
@@ -42,7 +57,7 @@ columns = ["Position","Reads","Genes"]
 
 class NormAnalysis(base.TransitAnalysis):
     def __init__(self):
-        base.TransitAnalysis.__init__(self, short_name, long_name, description, transposons, NormMethod, NormGUI, [NormFile])
+        base.TransitAnalysis.__init__(self, short_name, long_name, short_desc, long_desc, transposons, NormMethod, NormGUI, [NormFile])
 
 
 ################## FILE ###################
@@ -83,7 +98,7 @@ class NormMethod(base.SingleConditionMethod):
                 NTerminus=0.0,
                 CTerminus=0.0, wxobj=None):
 
-        base.SingleConditionMethod.__init__(self, short_name, long_name, description, ctrldata, annotation_path, output_file, replicates=replicates, normalization=normalization, LOESS=LOESS, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
+        base.SingleConditionMethod.__init__(self, short_name, long_name, short_desc, long_desc, ctrldata, annotation_path, output_file, replicates=replicates, normalization=normalization, LOESS=LOESS, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
 
 
     @classmethod

src/pytransit/analysis/rankproduct.py

@@ -2,18 +2,30 @@ import sys
 
 try:
     import wx
+    WX_VERSION = int(wx.version()[0])
     hasWx = True
-    #Check if wx is the newest 3.0+ version:
-    try:
-        from wx.lib.pubsub import pub
-        pub.subscribe
-        newWx = True
-    except AttributeError as e:
-        from wx.lib.pubsub import Publisher as pub
-        newWx = False
+
 except Exception as e:
     hasWx = False
-    newWx = False
+    WX_VERSION = 0
+    print "EXCEPTION:", str(e)
+
+if hasWx:
+    import wx.xrc
+    from wx.lib.buttons import GenBitmapTextButton
+
+    #Imports depending on version:
+    if WX_VERSION == 2:
+        from wx.lib.pubsub import Publisher as pub
+
+    if WX_VERSION == 3:
+        from wx.lib.pubsub import pub
+        pub.subscribe
+
+    if WX_VERSION == 4:
+        from wx.lib.pubsub import pub
+        pub.subscribe
+        import wx.adv
 
 
 import os
@@ -36,8 +48,9 @@ import pytransit.stat_tools as stat_tools
 ############# GUI ELEMENTS ##################
 
 short_name = "rankproduct"
-long_name = "Rank Product test for determining conditional essentiality."
-description = "Differential Comparison based on ranks"
+long_name = "Rank Product"
+short_desc = "Rank Product test for determining conditional essentiality."
+long_desc = "Differential Comparison based on ranks"
 transposons = ["himar1", "tn5"]
 columns = ["Orf","Name","Desc","Sites","Mean Ctrl","Mean Exp","log2FC","Obs RP","Expected RP","q-value"]
 
@@ -47,7 +60,7 @@ columns = ["Orf","Name","Desc","Sites","Mean Ctrl","Mean Exp","log2FC","Obs RP",
 
 class RankProductAnalysis(base.TransitAnalysis):
     def __init__(self):
-        base.TransitAnalysis.__init__(self, short_name, long_name, description, transposons, RankProductMethod, RankProductGUI, [RankProductFile])
+        base.TransitAnalysis.__init__(self, short_name, long_name, short_desc, long_desc, transposons, RankProductMethod, RankProductGUI, [RankProductFile])
 
 
 ################## FILE ###################
@@ -68,8 +81,8 @@ class RankProductGUI(base.AnalysisGUI):
     
         rankproductSizer = wx.BoxSizer( wx.VERTICAL )
 
-        rankproductLabel = wx.StaticText( rankproductPanel, wx.ID_ANY, u"rankproduct Options", wx.DefaultPosition, wx.DefaultSize, 0 )
-        rankproductLabel.Wrap( -1 )
+        rankproductLabel = wx.StaticText( rankproductPanel, wx.ID_ANY, u"rankproduct Options", wx.DefaultPosition, (160,-1), 0 )
+        rankproductLabel.SetFont( wx.Font( 10, wx.DEFAULT, wx.NORMAL, wx.BOLD) )
         rankproductSizer.Add( rankproductLabel, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
 
         rankproductLabelSizer = wx.BoxSizer( wx.VERTICAL )
@@ -127,7 +140,7 @@ class RankProductMethod(base.DualConditionMethod):
                 NTerminus=0.0,
                 CTerminus=0.0, wxobj=None):
 
-        base.DualConditionMethod.__init__(self, short_name, long_name, description, ctrldata, expdata, annotation_path, output_file, normalization=normalization, replicates=replicates, LOESS=LOESS, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
+        base.DualConditionMethod.__init__(self, short_name, long_name, short_desc, long_desc, ctrldata, expdata, annotation_path, output_file, normalization=normalization, replicates=replicates, LOESS=LOESS, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
 
         self.samples = samples
         self.adaptive = adaptive
@@ -308,8 +321,10 @@ class RankProductMethod(base.DualConditionMethod):
             q_paper = e_val/float(rankRP[i])
  
             data.append([gene.orf, gene.name, gene.desc, gene.n, meanctrl, meanexp, log2fc, obsRP[i], e_val, q_paper, pval])
-            self.progress_update("rankproduct", count)
-            self.transit_message_inplace("Running rankproduct Method... %1.1f%%" % (100.0*count/Ngenes))
+            
+            # Update Progress
+            text = "Running rankproduct Method... %5.1f%%" % (100.0*count/Ngenes)
+            self.progress_update(text, count)
 
 
         #

src/pytransit/analysis/resampling.py

@@ -2,18 +2,30 @@ import sys
 
 try:
     import wx
+    WX_VERSION = int(wx.version()[0])
     hasWx = True
-    #Check if wx is the newest 3.0+ version:
-    try:
-        from wx.lib.pubsub import pub
-        pub.subscribe
-        newWx = True
-    except AttributeError as e:
-        from wx.lib.pubsub import Publisher as pub
-        newWx = False
+
 except Exception as e:
     hasWx = False
-    newWx = False
+    WX_VERSION = 0
+    print "EXCEPTION:", str(e)
+
+if hasWx:
+    import wx.xrc
+    from wx.lib.buttons import GenBitmapTextButton
+
+    #Imports depending on version:
+    if WX_VERSION == 2:
+        from wx.lib.pubsub import Publisher as pub
+
+    if WX_VERSION == 3:
+        from wx.lib.pubsub import pub
+        pub.subscribe
+
+    if WX_VERSION == 4:
+        from wx.lib.pubsub import pub
+        pub.subscribe
+        import wx.adv
    
 
 import os
@@ -37,15 +49,16 @@ import pytransit.stat_tools as stat_tools
 ############# GUI ELEMENTS ##################
 
 short_name = "resampling"
-long_name = "Resampling test of conditional essentiality between two conditions"
-description = """Method for determining conditional essentiality based on resampling (i.e. permutation test). Identifies significant changes in mean read-counts for each gene after normalization."""
+long_name = "Resampling (Permutation test)"
+short_desc = "Resampling test of conditional essentiality between two conditions"
+long_desc = """Method for determining conditional essentiality based on resampling (i.e. permutation test). Identifies significant changes in mean read-counts for each gene after normalization."""
 
 transposons = ["himar1", "tn5"]
 columns = ["Orf","Name","Desc","Sites","Mean Ctrl","Mean Exp","log2FC", "Sum Ctrl", "Sum Exp", "Delta Mean","p-value","Adj. p-value"]
 
 class ResamplingAnalysis(base.TransitAnalysis):
     def __init__(self):
-        base.TransitAnalysis.__init__(self, short_name, long_name, description, transposons, ResamplingMethod, ResamplingGUI, [ResamplingFile])
+        base.TransitAnalysis.__init__(self, short_name, long_name, short_desc, long_desc, transposons, ResamplingMethod, ResamplingGUI, [ResamplingFile])
 
 
 
@@ -106,8 +119,8 @@ class ResamplingGUI(base.AnalysisGUI):
 
         resamplingSizer = wx.BoxSizer( wx.VERTICAL )
 
-        resamplingLabel = wx.StaticText( resamplingPanel, wx.ID_ANY, u"resampling Options", wx.DefaultPosition, wx.DefaultSize, 0 )
-        resamplingLabel.Wrap( -1 )
+        resamplingLabel = wx.StaticText( resamplingPanel, wx.ID_ANY, u"resampling Options", wx.DefaultPosition, (160,-1), 0 )
+        resamplingLabel.SetFont( wx.Font( 10, wx.DEFAULT, wx.NORMAL, wx.BOLD) )
         resamplingSizer.Add( resamplingLabel, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
 
         resamplingTopSizer = wx.BoxSizer( wx.HORIZONTAL )
@@ -139,7 +152,7 @@ class ResamplingGUI(base.AnalysisGUI):
 
 
         # LOESS Check
-        (self.wxobj.resamplingLoessCheck, loessCheckSizer) = self.defineCheckBox(resamplingPanel, labelText="Correct for Genome Positional Bias", widgetCheck=False, widgetSize=(230,-1), tooltipText="Check to correct read-counts for possible regional biase using LOESS. Clicking on the button below will plot a preview, which is helpful to visualize the possible bias in the counts.")
+        (self.wxobj.resamplingLoessCheck, loessCheckSizer) = self.defineCheckBox(resamplingPanel, labelText="Correct for Genome Positional Bias", widgetCheck=False, widgetSize=(-1,-1), tooltipText="Check to correct read-counts for possible regional biase using LOESS. Clicking on the button below will plot a preview, which is helpful to visualize the possible bias in the counts.")
         resamplingSizer.Add( loessCheckSizer, 0, wx.EXPAND, 5 )
 
         # LOESS Button
@@ -147,16 +160,16 @@ class ResamplingGUI(base.AnalysisGUI):
         resamplingSizer.Add( self.wxobj.resamplingLoessPrev, 0, wx.ALL|wx.CENTER, 5 )
 
         # Adaptive Check
-        (self.wxobj.resamplingAdaptiveCheckBox, adaptiveSizer) = self.defineCheckBox(resamplingPanel, labelText="Adaptive Resampling (Faster)", widgetCheck=False, widgetSize=(200,-1), tooltipText="Dynamically stops permutations early if it is unlikely the ORF will be significant given the results so far. Improves performance, though p-value calculations for genes that are not differentially essential will be less accurate.")
+        (self.wxobj.resamplingAdaptiveCheckBox, adaptiveSizer) = self.defineCheckBox(resamplingPanel, labelText="Adaptive Resampling (Faster)", widgetCheck=False, widgetSize=(-1,-1), tooltipText="Dynamically stops permutations early if it is unlikely the ORF will be significant given the results so far. Improves performance, though p-value calculations for genes that are not differentially essential will be less accurate.")
         resamplingSizer.Add( adaptiveSizer, 0, wx.EXPAND, 5 )
 
         # Histogram Check
-        (self.wxobj.resamplingHistogramCheckBox, histSizer) = self.defineCheckBox(resamplingPanel, labelText="Generate Resampling Histograms", widgetCheck=False, widgetSize=(225,-1), tooltipText="Creates .png images with the resampling histogram for each of the ORFs. Histogram images are created in a folder with the same name as the output file.")
+        (self.wxobj.resamplingHistogramCheckBox, histSizer) = self.defineCheckBox(resamplingPanel, labelText="Generate Resampling Histograms", widgetCheck=False, widgetSize=(-1,-1), tooltipText="Creates .png images with the resampling histogram for each of the ORFs. Histogram images are created in a folder with the same name as the output file.")
         resamplingSizer.Add(histSizer, 0, wx.EXPAND, 5 )
         
 
         # Zeros Check
-        (self.wxobj.resamplingZeroCheckBox, zeroSizer) = self.defineCheckBox(resamplingPanel, labelText="Include sites with all zeros", widgetCheck=True, widgetSize=(180,-1), tooltipText="Includes sites that are empty (zero) accross all datasets. Unchecking this may be useful for tn5 datasets, where all nucleotides are possible insertion sites and will have a large number of empty sites (significantly slowing down computation and affecting estimates).")
+        (self.wxobj.resamplingZeroCheckBox, zeroSizer) = self.defineCheckBox(resamplingPanel, labelText="Include sites with all zeros", widgetCheck=True, widgetSize=(-1,-1), tooltipText="Includes sites that are empty (zero) accross all datasets. Unchecking this may be useful for tn5 datasets, where all nucleotides are possible insertion sites and will have a large number of empty sites (significantly slowing down computation and affecting estimates).")
         resamplingSizer.Add(zeroSizer, 0, wx.EXPAND, 5 )
 
 
@@ -200,7 +213,7 @@ class ResamplingMethod(base.DualConditionMethod):
                 NTerminus=0.0,
                 CTerminus=0.0, wxobj=None):
 
-        base.DualConditionMethod.__init__(self, short_name, long_name, description, ctrldata, expdata, annotation_path, output_file, normalization=normalization, replicates=replicates, LOESS=LOESS, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
+        base.DualConditionMethod.__init__(self, short_name, long_name, short_desc, long_desc, ctrldata, expdata, annotation_path, output_file, normalization=normalization, replicates=replicates, LOESS=LOESS, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
 
         self.samples = samples
         self.adaptive = adaptive
@@ -392,9 +405,9 @@ class ResamplingMethod(base.DualConditionMethod):
             if self.doHistogram:
                 import matplotlib.pyplot as plt
                 if testlist:
-                    n, bins, patches = plt.hist(testlist, normed=1, facecolor='c', alpha=0.75, bins=100)
+                    n, bins, patches = plt.hist(testlist, density=1, facecolor='c', alpha=0.75, bins=100)
                 else:
-                    n, bins, patches = plt.hist([0,0], normed=1, facecolor='c', alpha=0.75, bins=100)
+                    n, bins, patches = plt.hist([0,0], density=1, facecolor='c', alpha=0.75, bins=100)
                 plt.xlabel('Delta Mean')
                 plt.ylabel('Probability')
                 plt.title('%s - Histogram of Delta Mean' % gene.orf)
@@ -410,8 +423,10 @@ class ResamplingMethod(base.DualConditionMethod):
             sum1 = numpy.sum(data1)
             sum2 = numpy.sum(data2)
             data.append([gene.orf, gene.name, gene.desc, gene.n, mean1, mean2, sum1, sum2, test_obs, log2FC, pval_2tail])
-            self.progress_update("resampling", count)
-            self.transit_message_inplace("Running Resampling Method... %1.1f%%" % (100.0*count/N))
+            
+            # Update progress
+            text = "Running Resampling Method... %5.1f%%" % (100.0*count/N)
+            self.progress_update(text, count)
 
 
         #

src/pytransit/analysis/tn5gaps.py

@@ -2,18 +2,31 @@ import sys
 
 try:
     import wx
+    WX_VERSION = int(wx.version()[0])
     hasWx = True
-    #Check if wx is the newest 3.0+ version:
-    try:
-        from wx.lib.pubsub import pub
-        pub.subscribe
-        newWx = True
-    except AttributeError as e:
-        from wx.lib.pubsub import Publisher as pub
-        newWx = False
+
 except Exception as e:
     hasWx = False
-    newWx = False
+    WX_VERSION = 0
+    print "EXCEPTION:", str(e)
+
+if hasWx:
+    import wx.xrc
+    from wx.lib.buttons import GenBitmapTextButton
+
+    #Imports depending on version:
+    if WX_VERSION == 2:
+        from wx.lib.pubsub import Publisher as pub
+
+    if WX_VERSION == 3:
+        from wx.lib.pubsub import pub
+        pub.subscribe
+
+    if WX_VERSION == 4:
+        from wx.lib.pubsub import pub
+        pub.subscribe
+        import wx.adv
+
 
 import os
 import time
@@ -35,8 +48,9 @@ import pytransit.stat_tools as stat_tools
 ############# GUI ELEMENTS ##################
 
 short_name = "tn5gaps"
-long_name = "Analysis of essentiality on gaps in entire genome (Tn5)."
-description = "A analysis method based on the extreme value (Gumbel) distribution that considers longest runs over the whole genome instead of individual genes."
+long_name = "Tn5 Gaps"
+short_desc = "Analysis of essentiality on gaps in entire genome (Tn5)."
+long_desc = "A analysis method based on the extreme value (Gumbel) distribution that considers longest runs over the whole genome instead of individual genes."
 transposons = ["tn5"]
 columns = ["Orf","Name","Desc","k","n","r","ovr","lenovr","pval","padj","call"]
 
@@ -46,7 +60,7 @@ columns = ["Orf","Name","Desc","k","n","r","ovr","lenovr","pval","padj","call"]
 
 class Tn5GapsAnalysis(base.TransitAnalysis):
     def __init__(self):
-        base.TransitAnalysis.__init__(self, short_name, long_name, description, transposons, Tn5GapsMethod, Tn5GapsGUI, [Tn5GapsFile])
+        base.TransitAnalysis.__init__(self, short_name, long_name, short_desc, long_desc, transposons, Tn5GapsMethod, Tn5GapsGUI, [Tn5GapsFile])
 
 
 ################## FILE ###################
@@ -81,8 +95,8 @@ class Tn5GapsGUI(base.AnalysisGUI):
 
         tn5GapsSection = wx.BoxSizer( wx.VERTICAL )
 
-        tn5GapsLabel = wx.StaticText( tn5GapsPanel, wx.ID_ANY, u"Tn5 Gaps Options", wx.DefaultPosition, wx.DefaultSize, 0 )
-        tn5GapsLabel.Wrap( -1 )
+        tn5GapsLabel = wx.StaticText( tn5GapsPanel, wx.ID_ANY, u"Tn5 Gaps Options", wx.DefaultPosition, (150,-1), 0 )
+        tn5GapsLabel.SetFont( wx.Font( 10, wx.DEFAULT, wx.NORMAL, wx.BOLD) )
         tn5GapsSection.Add( tn5GapsLabel, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
 
         mainSizer1 = wx.BoxSizer( wx.VERTICAL )   
@@ -139,7 +153,7 @@ class Tn5GapsMethod(base.SingleConditionMethod):
                 NTerminus=0.0,
                 CTerminus=0.0, wxobj=None):
 
-        base.SingleConditionMethod.__init__(self, short_name, long_name, description, ctrldata, annotation_path, output_file, replicates=replicates, normalization=normalization, LOESS=LOESS, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
+        base.SingleConditionMethod.__init__(self, short_name, long_name, short_desc, long_desc, ctrldata, annotation_path, output_file, replicates=replicates, normalization=normalization, LOESS=LOESS, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
         self.minread = minread
 
 
@@ -286,8 +300,10 @@ class Tn5GapsMethod(base.SingleConditionMethod):
                 curr_len = curr_val[7]
                 if inter_sz > curr_inter_sz:
                     results_per_gene[gene.orf] = [gene.orf, gene.name, gene.desc, gene.k, gene.n, gene.r, inter_sz, run_len, pval]
-            self.progress_update("tn5gaps", count)
-            self.transit_message_inplace("Running Tn5Gaps method... %1.1f%%" % (100.0*count/N))
+            
+            # Update Progress
+            text = "Running Tn5Gaps method... %1.1f%%" % (100.0*count/N) 
+            self.progress_update(text, count)
                 
         data = list(results_per_gene.values())
         exp_run_len = float(accum)/N