.gitignore

@@ -53,6 +53,7 @@ coverage.xml
 
 # Sphinx documentation
 docs/_build/
+**/doc/_build/
 
 #Data files
 *.wig
@@ -61,3 +62,10 @@ docs/_build/
 *.png
 *.out
 
+NOTES
+*~
+
+#Test output ignore
+tests/testoutput.txt
+tests/testoutput_genes.txt
+

.travis.yml

@@ -6,8 +6,8 @@ matrix:
       dist: trusty
       sudo: required
       python: 2.7
-      before_install: "sudo apt-get install -y -f python python-dev python-pip pkg-config python-wxgtk2.8 libpng-dev libjpeg8-dev libfreetype6-dev"
-      install: "pip install --upgrade pip setuptools numpy scipy pillow matplotlib pytest"
+      before_install: "sudo apt-get install -y -f python python-dev python-pip pkg-config libpng-dev libjpeg8-dev libfreetype6-dev"
+      install: "pip install --upgrade pip setuptools numpy scipy pillow matplotlib pytest statsmodels"
 
 DISPLAY: 0.0
 notifications:

CHANGELOG.md

 # Change log
 All notable changes to this project will be documented in this file.
 
+## Version 2.3.2 2018-11-09
+- TRANSIT:	
+  - Minor bug fixes related to changing parameters in TPP GUI
+
+## Version 2.3.1 2018-10-19
+- TRANSIT:	
+  - Removed dependence on PyPubSub (can run Transit in command-line mode without it, but needed for GUI)
+
+	
+## Version 2.3.0 2018-10-10
+- TRANSIT:	
+  - Added calculation of Pathway Enrichment as post-processing for resampling, to determine if conditionally essential genes over-represent a particular functional category or pathway (such as for GO terms)
+- Added ANOVA analysis for identifying genes with significant variability of counts across multiple conditions
+  - Updated Documentation - especially for "Quality Control/TnSeq Statistics"; also added more command-line examples under "Analysis Methods"
+  - Fixed bugs (including TrackView in the GUI)
+  - Upgraded dependencies, including wxPython 4.0 (required)
+	
+
+
+## Version 2.2.0 - 2018-06-04
+- TRANSIT:
+    - 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.
+    - Fixed bug in packaging of TPP, causing problem with console mode in new setuptools.
+    - Miscellaneous bugs fixes 
+
 	
 
 ## Version 2.1.0 - 2017-06-23

README.md

-
-
-
-# TRANSIT 2.2.1
+# TRANSIT 2.3.2
 
 
 [![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.
-- Improved speed of TPP.
-- Added Barseq functionality to TPP.
-- Fixed bug with creating resampling histograms on GUI mode.
-- Miscellaneous code improvements.
-
-
-**Version 2.1.1 changes (July, 2017)**
-- Miscellaneous bug fixes
-
-
-**Version 2.1.0 changes (June, 2017)**
-- Added tooltips next to most parameters to explain their functionality.
-- Added Quality Control window, with choice for normalization method.
-- Added more normalization options to the HMM method.
-- Added LOESS correction functionality back to TRANSIT
-- Added ability to scale Track View based on mean-count of the window.
-- Added ability to scale individual tracks in Track View.
-- Added ability to add tracks of features to Track View.
-- Better status messages for TrackView
-- TPP can now accept empty primer prefix (in case reads have been trimmed).
-- TPP can now process reads obtained using Mme1 enzyme and protocol.
-- TPP can now pass flags to BWA.
-- Lots of bug fixes.
-
-
-**Version 2.0.2 changes (August, 2016)**
-- Added support for for custom primers in TPP.
-- Added support for annotations in GFF3 format.
-- Ability to specify pseudocounts in resampling.
-- Misc. Bug fixes
-- **New [mailing list](https://groups.google.com/forum/#!forum/tnseq-transit/join)**
-
-
-**New in Version 2.0+**
- - Support for Tn5 datasets.
- - New analysis methods.
- - New way to export normalized datasets.
-
-
-
 Welcome! This is the distribution for the TRANSIT and TPP tools developed by the Ioerger Lab.
 
 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.
 
+[Changelog](https://github.com/mad-lab/transit/blob/master/CHANGELOG.md)
+
 
 ## Features
 TRANSIT offers a variety of features including:
@@ -86,20 +30,16 @@ TRANSIT offers a variety of features including:
 
 
 
+## Support
 
-
-## Mailing List
-
-You can join our mailing list to get announcements of new versions, discuss any bugs, or request features! Just head over to the following site and enter your email address:
-
-https://groups.google.com/forum/#!forum/tnseq-transit/join
+For any questions or comments, please contact Dr. Thomas Ioerger, ioerger@cs.tamu.edu.
 
 
 
 
 ## Instructions
 
-For full instructions on how to install and run TRANSIT (and the optional pre-processor, TPP), please see the documentation included in this distribution ("doc" folder) or visit the following web page:
+For full instructions on how to install and run TRANSIT (and the optional pre-processor, TPP), please see the documentation included in this distribution ("src/pytransit/doc" folder) or visit the following web page:
 
 
 http://saclab.tamu.edu/essentiality/transit/transit.html

VERSION

-version: 2.2.0-6-g2c24-mod
+version: 2.2.1-9-ge742-mod

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', 'wxpython'],
+    install_requires=['setuptools', 'numpy~=1.15', 'scipy~=1.1', 'matplotlib~=2.2', 'pillow~=5.0', 'statsmodels~=0.9'],
 
     #dependency_links = [
     #	"git+https://github.com/wxWidgets/wxPython.git#egg=wxPython"

src/pytpp/tpp_gui.py

@@ -99,7 +99,7 @@ if hasWx:
             sizer3 = wx.BoxSizer(wx.HORIZONTAL)
             label3 = wx.StaticText(panel, label='Choose a reference genome (FASTA):',size=(330,-1))
             sizer3.Add(label3,0,wx.ALIGN_CENTER_VERTICAL,0)
-            self.picker3 = wx.lib.filebrowsebutton.FileBrowseButton(panel, id=wx.ID_ANY, dialogTitle='Please select the reference genome', fileMode=wx.OPEN, fileMask='*.fna;*.fasta;*.fa', size=(400,30), startDirectory=os.path.dirname(vars.ref), initialValue=vars.ref, labelText='')
+            self.picker3 = wx.lib.filebrowsebutton.FileBrowseButton(panel, id=wx.ID_ANY, dialogTitle='Please select the reference genome', fileMode=wx.FD_OPEN, fileMask='*.fna;*.fasta;*.fa', size=(400,30), startDirectory=os.path.dirname(vars.ref), initialValue=vars.ref, labelText='')
             sizer3.Add(self.picker3, proportion=1, flag=wx.EXPAND|wx.ALL, border=5)
             sizer3.Add(TPPIcon(panel, wx.ID_ANY, bmp, "Select a reference genome in FASTA format."), flag=wx.CENTER, border=0)
             sizer3.Add((10, 1), 0, wx.EXPAND)
@@ -109,7 +109,7 @@ if hasWx:
             sizer1 = wx.BoxSizer(wx.HORIZONTAL)
             label1 = wx.StaticText(panel, label='Choose the Fastq file for read 1:',size=(330,-1))
             sizer1.Add(label1,0,wx.ALIGN_CENTER_VERTICAL,0)
-            self.picker1 = wx.lib.filebrowsebutton.FileBrowseButton(panel, id=wx.ID_ANY, dialogTitle='Please select the .fastq file for read 1', fileMode=wx.OPEN, fileMask='*.fastq;*.fq;*.reads;*.fasta;*.fa;*.fastq.gz', size=(400,30), startDirectory=os.path.dirname(vars.fq1), initialValue=vars.fq1, labelText='',changeCallback=self.OnChanged2)
+            self.picker1 = wx.lib.filebrowsebutton.FileBrowseButton(panel, id=wx.ID_ANY, dialogTitle='Please select the .fastq file for read 1', fileMode=wx.FD_OPEN, fileMask='*.fastq;*.fq;*.reads;*.fasta;*.fa;*.fastq.gz', size=(400,30), startDirectory=os.path.dirname(vars.fq1), initialValue=vars.fq1, labelText='',changeCallback=self.OnChanged2)
             sizer1.Add(self.picker1, proportion=1, flag=wx.EXPAND|wx.ALL, border=5)
             sizer1.Add(TPPIcon(panel, wx.ID_ANY, bmp, "Select a file containing the reads in .FASTQ (or compressed FASTQ) format."), flag=wx.CENTER, border=0)
             sizer1.Add((10, 1), 0, wx.EXPAND)
@@ -120,7 +120,7 @@ if hasWx:
             sizer2 = wx.BoxSizer(wx.HORIZONTAL)
             label2 = wx.StaticText(panel, label='Choose the Fastq file for read 2:',size=(330,-1))
             sizer2.Add(label2,0,wx.ALIGN_CENTER_VERTICAL,0)
-            self.picker2 = wx.lib.filebrowsebutton.FileBrowseButton(panel, id=wx.ID_ANY, dialogTitle='Please select the .fastq file for read 2', fileMode=wx.OPEN, fileMask='*.fastq;*.fq;*.reads;*.fasta;*.fa;*.fastq.gz', size=(400,30), startDirectory=os.path.dirname(vars.fq2), initialValue=vars.fq2, labelText='', changeCallback=self.OnChanged2)
+            self.picker2 = wx.lib.filebrowsebutton.FileBrowseButton(panel, id=wx.ID_ANY, dialogTitle='Please select the .fastq file for read 2', fileMode=wx.FD_OPEN, fileMask='*.fastq;*.fq;*.reads;*.fasta;*.fa;*.fastq.gz', size=(400,30), startDirectory=os.path.dirname(vars.fq2), initialValue=vars.fq2, labelText='', changeCallback=self.OnChanged2)
             sizer2.Add(self.picker2, proportion=1, flag=wx.EXPAND|wx.ALL, border=5)
             sizer2.Add(TPPIcon(panel, wx.ID_ANY, bmp, "Select a file containing the pair-end reads in .FASTQ (or compressed FASTQ) format. Optional."), flag=wx.CENTER, border=0)
             sizer2.Add((10, 1), 0, wx.EXPAND)
@@ -207,7 +207,7 @@ The Mme1 protocol generally assumes reads do NOT include the primer prefix, and
             label0 = wx.StaticText(panel, label='BWA executable:',size=(330,-1))
             sizer0.Add(label0,0,wx.ALIGN_CENTER_VERTICAL,0)
 
-            self.picker0 = wx.lib.filebrowsebutton.FileBrowseButton(panel, id = wx.ID_ANY, size=(400,30), dialogTitle='Path to BWA', fileMode=wx.OPEN, fileMask='bwa*', startDirectory=os.path.dirname(vars.bwa), initialValue=vars.bwa, labelText='')
+            self.picker0 = wx.lib.filebrowsebutton.FileBrowseButton(panel, id = wx.ID_ANY, size=(400,30), dialogTitle='Path to BWA', fileMode=wx.FD_OPEN, fileMask='bwa*', startDirectory=os.path.dirname(vars.bwa), initialValue=vars.bwa, labelText='')
 
              
             sizer0.Add(self.picker0, proportion=1, flag=wx.EXPAND|wx.ALL, border=5)
@@ -235,7 +235,7 @@ The Mme1 protocol generally assumes reads do NOT include the primer prefix, and
             self.barseq_select.SetSelection(0)
             sizer9.Add(self.barseq_select, proportion=0.5, flag=wx.EXPAND|wx.ALL, border=5) ## 
 
-            self.picker9 = wx.lib.filebrowsebutton.FileBrowseButton(panel, id=wx.ID_ANY, dialogTitle='Please select the Barseq catalog filename', fileMode=wx.OPEN, size=(400,30), startDirectory=os.path.dirname(vars.fq2), initialValue="", labelText='', ) # no need for this: changeCallback=self.OnChanged9 ; initialValue set below ; no file mask
+            self.picker9 = wx.lib.filebrowsebutton.FileBrowseButton(panel, id=wx.ID_ANY, dialogTitle='Please select the Barseq catalog filename', fileMode=wx.FD_OPEN, size=(400,30), startDirectory=os.path.dirname(vars.fq2), initialValue="", labelText='', ) # no need for this: changeCallback=self.OnChanged9 ; initialValue set below ; no file mask
             sizer9.Add(self.picker9, proportion=1, flag=wx.EXPAND|wx.ALL, border=5)
 
             if vars.barseq_catalog_in!=None:
@@ -306,7 +306,8 @@ The Mme1 protocol generally assumes reads do NOT include the primer prefix, and
 #
 
         def OnChangePrimerPrefix(self, event):
-            self.transposon.SetValue("[Custom]")
+            #self.transposon.SetValue("[Custom]")
+            pass
 
 #
 
@@ -348,7 +349,7 @@ The Mme1 protocol generally assumes reads do NOT include the primer prefix, and
               defaultDir=".",
               defaultFile="",
               wildcard="*.wig",
-              style=wx.OPEN | wx.MULTIPLE | wx.CHANGE_DIR
+              style=wx.FD_OPEN | wx.FD_MULTIPLE | wx.FD_CHANGE_DIR
               )
           if dlg.ShowModal() == wx.ID_OK:
               paths = dlg.GetPaths()

src/pytpp/tpp_tools.py

@@ -233,7 +233,8 @@ def extract_staggered(infile,outfile,vars):
   lenADAP = len(ADAPTER2)
 
   #P,Q = 5,10 # 1-based inclusive positions to look for start of Tn prefix
-  P,Q = 0,15
+  #P,Q = 0,15
+  P,Q = 0,50 # relax this, because it has caused problems for various users; shouldn't matter, if prefix is long enough to make random occurences unlikely
   if vars.barseq_catalog_out!=None: Q = 100 # relax for barseq
 
   vars.tot_tgtta = 0
@@ -424,7 +425,9 @@ def template_counts(ref,sam,bcfile,vars):
 
   sites = []
   for i in range(len(genome)-1):
-    if genome[i:i+2].upper()=="TA":
+    #if genome[i:i+2].upper()=="TA":
+    if vars.transposon=="Himar1" and genome[i:i+2].upper()!="TA": continue
+    else:
       pos = i+1
       h = hits.get(pos,[])
       f = filter(lambda x: x[0]=='F',h)
@@ -460,7 +463,8 @@ def read_counts(ref,sam,vars):
     genome = read_genome(ref)
     sites = {}
     for i in range(len(genome)-1):
-        if genome[i:i+2]=="TA" or vars.transposon=='Tn5':
+        #if genome[i:i+2]=="TA" or vars.transposon=='Tn5':
+        if vars.transposon=='Himar1' and genome[i:i+2]!="TA": continue
         pos = i+1
         sites[pos] = [pos,0,0,0,0,0,0]
 
@@ -980,7 +984,7 @@ def warning(s):
 
 
 
-def set_defaults(vars, protocol):
+def set_protocol_defaults(vars, protocol):
     #protocol = kwargs.get("protocol", "sassetti")
     if protocol == "sassetti":
         set_sassetti_defaults(vars)

src/pytransit/__init__.py

@@ -2,6 +2,6 @@
 __all__ = ["transit_tools", "tnseq_tools", "norm_tools", "stat_tools"]
 
 
-__version__ = "v2.2.1"
+__version__ = "v2.3.2"
 prefix = "[TRANSIT]"
 

src/pytransit/__main__.py

@@ -9,23 +9,11 @@ try:
 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
+    from pubsub import pub
     import wx.adv
 
 
@@ -60,6 +48,13 @@ def main(*args, **kwargs):
         sys.argv.remove("--debug")
         kwargs.pop("-debug")
 
+    if (not args and 'h' in kwargs):
+        print "For commandline mode, please use one of the known methods (or see documentation to add a new one):"
+        for m in all_methods:
+            print "\t - %s" % m
+        print "Usage: python %s <method>" % sys.argv[0]
+        sys.exit(0)
+
     # Check if running in GUI Mode
     if not (args or kwargs) and hasWx:
 

src/pytransit/analysis/__init__.py

@@ -17,6 +17,10 @@ import hmm
 import rankproduct
 import gi
 import utest
+import normalize
+import pathway_enrichment #08/22/2018 by Ivan
+import anova
+import tnseq_stats
 
 methods = {}
 methods["example"] = example.ExampleAnalysis()
@@ -28,16 +32,17 @@ methods["resampling"] = resampling.ResamplingAnalysis()
 methods["tn5gaps"] = tn5gaps.Tn5GapsAnalysis()
 methods["rankproduct"] = rankproduct.RankProductAnalysis()
 methods["utest"] = utest.UTestAnalysis()
-methods["gi"] = gi.GIAnalysis()
+methods["GI"] = gi.GIAnalysis()
+methods["anova"] = anova.AnovaAnalysis()
 #methods["mcce"] = mcce.MCCEAnalysis()
 #methods["mcce2"] = mcce2.MCCE2Analysis()
 #methods["motifhmm"] = motifhmm.MotifHMMAnalysis()
-
+methods["normalize"] = normalize.Normalize()
+methods["pathway_enrichment"]=pathway_enrichment.GSEAAnalysis()
+methods["tnseq_stats"]=tnseq_stats.TnseqStats()
 
 # EXPORT METHODS
 import norm
 export_methods = {}
 export_methods["norm"] = norm.NormAnalysis()
 
-
-

src/pytransit/analysis/anova.py

+import scipy
+import numpy
+import statsmodels.stats.multitest
+
+import time
+import sys
+import collections
+
+import base
+import pytransit
+import pytransit.transit_tools as transit_tools
+import pytransit.tnseq_tools as tnseq_tools
+import pytransit.norm_tools as norm_tools
+
+############# GUI ELEMENTS ##################
+
+short_name = "anova"
+long_name = "anova"
+short_desc = "Perform Anova analysis"
+long_desc = """Perform Anova analysis"""
+EOL = "\n"
+
+transposons = ["", ""]
+columns = []
+
+class AnovaAnalysis(base.TransitAnalysis):
+    def __init__(self):
+        base.TransitAnalysis.__init__(self, short_name, long_name, short_desc, long_desc, transposons, AnovaMethod)
+def main():
+    print("ANOVA example")
+
+class AnovaMethod(base.MultiConditionMethod):
+    """
+    anova
+    """
+    def __init__(self, combined_wig, metadata, annotation, normalization, output_file, ignored_conditions=set()):
+        base.MultiConditionMethod.__init__(self, short_name, long_name, short_desc, long_desc, combined_wig, metadata, annotation, output_file, normalization=normalization)
+        self.ignored_conditions = ignored_conditions
+
+    @classmethod
+    def fromargs(self, rawargs):
+        (args, kwargs) = transit_tools.cleanargs(rawargs)
+
+        if (kwargs.get('-help', False) or kwargs.get('h', False)):
+            print(AnovaMethod.usage_string())
+            sys.exit(0)
+
+        combined_wig = args[0]
+        annotation = args[1]
+        metadata = args[2]
+        output_file = args[3]
+        normalization = kwargs.get("n", "TTR")
+        ignored_conditions = set(kwargs.get("-ignore-conditions", "Unknown").split(","))
+
+        return self(combined_wig, metadata, annotation, normalization, output_file, ignored_conditions)
+
+    def wigs_to_conditions(self, conditionsByFile, filenamesInCombWig):
+        """
+            Returns list of conditions corresponding to given wigfiles.
+            ({FileName: Condition}, [FileName]) -> [Condition]
+            Condition :: [String]
+        """
+        return [conditionsByFile.get(f, "Unknown") for f in filenamesInCombWig]
+
+    def means_by_condition_for_gene(self, sites, conditions, data):
+        """
+            Returns a dictionary of {Condition: Mean} for each condition.
+            ([Site], [Condition]) -> {Condition: Number}
+            Site :: Number
+            Condition :: String
+        """
+        wigsByConditions = collections.defaultdict(lambda: [])
+        for i, c in enumerate(conditions):
+            wigsByConditions[c].append(i)
+
+        return { c: numpy.mean(data[wigIndex][:, sites]) for (c, wigIndex) in wigsByConditions.items() }
+
+    def filter_by_conditions_blacklist(self, data, conditions, ignored_conditions):
+        """
+            Filters out wigfiles, with ignored conditions.
+            ([[Wigdata]], [Condition]) -> Tuple([[Wigdata]], [Condition])
+        """
+        d_filtered, cond_filtered = [], [];
+        for i, c in enumerate(conditions):
+          if c not in ignored_conditions:
+            d_filtered.append(data[i])
+            cond_filtered.append(conditions[i])
+
+        return (numpy.array(d_filtered), numpy.array(cond_filtered))
+
+    def read_samples_metadata(self, metadata_file):
+        """
+          Filename -> ConditionMap
+          ConditionMap :: {Filename: Condition}
+        """
+        wigFiles = []
+        conditionsByFile = {}
+        headersToRead = ["condition", "filename"]
+        with open(metadata_file) as mfile:
+            lines = mfile.readlines()
+            headIndexes = [i
+                    for h in headersToRead
+                    for i, c in enumerate(lines[0].split())
+                    if c.lower() == h]
+            for line in lines:
+                if line[0]=='#': continue
+                vals = line.split()
+                [condition, wfile] = vals[headIndexes[0]], vals[headIndexes[1]]
+                conditionsByFile[wfile] = condition
+        return conditionsByFile
+
+    def means_by_rv(self, data, RvSiteindexesMap, genes, conditions):
+        """
+            Returns Dictionary of mean values by condition
+            ([[Wigdata]], {Rv: SiteIndex}, [Gene], [Condition]) -> {Rv: {Condition: Number}}
+            Wigdata :: [Number]
+            SiteIndex :: Number
+            Gene :: {start, end, rv, gene, strand}
+            Condition :: String
+        """
+        MeansByRv = {}
+        for gene in genes:
+            Rv = gene["rv"]
+            if len(RvSiteindexesMap[gene["rv"]]) > 0: # skip genes with no TA sites
+                MeansByRv[Rv] = self.means_by_condition_for_gene(RvSiteindexesMap[Rv], conditions, data)
+        return MeansByRv
+
+    def group_by_condition(self, wigList, conditions):
+        """
+            Returns array of datasets, where each dataset corresponds to one condition.
+            ([[Wigdata]], [Condition]) -> [[DataForCondition]]
+            Wigdata :: [Number]
+            Condition :: String
+            DataForCondition :: [Number]
+        """
+        countsByCondition = collections.defaultdict(lambda: [])
+        for i, c in enumerate(conditions):
+          countsByCondition[c].append(wigList[i])
+
+        return [numpy.array(v).flatten() for v in countsByCondition.values()]
+
+    def run_anova(self, data, genes, MeansByRv, RvSiteindexesMap, conditions):
+        """
+            Runs Anova (grouping data by condition) and returns p and q values
+            ([[Wigdata]], [Gene], {Rv: {Condition: Mean}}, {Rv: [SiteIndex]}, [Condition]) -> Tuple([Number], [Number])
+            Wigdata :: [Number]
+            Gene :: {start, end, rv, gene, strand}
+            Mean :: Number
+            SiteIndex: Integer
+            Condition :: String
+        """
+        count = 0
+        self.progress_range(len(genes))
+
+        pvals,Rvs = [],[]
+        for gene in genes:
+            count += 1
+            Rv = gene["rv"]
+            if Rv in MeansByRv:
+                countsvec = self.group_by_condition(map(lambda wigData: wigData[RvSiteindexesMap[Rv]], data), conditions)
+                stat,pval = scipy.stats.f_oneway(*countsvec)
+                pvals.append(pval)
+                Rvs.append(Rv)
+
+            # Update progress
+            text = "Running Anova Method... %5.1f%%" % (100.0*count/len(genes))
+            self.progress_update(text, count)
+
+        pvals = numpy.array(pvals)
+        mask = numpy.isfinite(pvals)
+        qvals = numpy.full(pvals.shape, numpy.nan)
+        qvals[mask] = statsmodels.stats.multitest.fdrcorrection(pvals[mask])[1] # BH, alpha=0.05
+
+        p,q = {},{}
+        for i,rv in enumerate(Rvs):
+            p[rv],q[rv] = pvals[i],qvals[i]
+        return (p, q)
+
+    def Run(self):
+        self.transit_message("Starting Anova analysis")
+        start_time = time.time()
+
+        self.transit_message("Getting Data")
+        (sites, data, filenamesInCombWig) = tnseq_tools.read_combined_wig(self.combined_wig)
+
+        self.transit_message("Normalizing using: %s" % self.normalization)
+        (data, factors) = norm_tools.normalize_data(data, self.normalization)
+
+        conditions = self.wigs_to_conditions(
+            self.read_samples_metadata(self.metadata),
+            filenamesInCombWig)
+        data, conditions = self.filter_by_conditions_blacklist(data, conditions, self.ignored_conditions)
+
+        genes = tnseq_tools.read_genes(self.annotation_path)
+
+        TASiteindexMap = {TA: i for i, TA in enumerate(sites)}
+        RvSiteindexesMap = tnseq_tools.rv_siteindexes_map(genes, TASiteindexMap)
+        MeansByRv = self.means_by_rv(data, RvSiteindexesMap, genes, conditions)
+
+        self.transit_message("Running Anova")
+        pvals,qvals = self.run_anova(data, genes, MeansByRv, RvSiteindexesMap, conditions)
+
+        self.transit_message("Adding File: %s" % (self.output))
+        file = open(self.output,"w")
+        conditionsList = list(set(conditions))
+        vals = "Rv Gene TAs".split() + conditionsList + "pval padj".split()
+        file.write('\t'.join(vals)+EOL)
+        for gene in genes:
+            Rv = gene["rv"]
+            if Rv in MeansByRv:
+              vals = ([Rv, gene["gene"], str(len(RvSiteindexesMap[Rv]))] +
+                      ["%0.1f" % MeansByRv[Rv][c] for c in conditionsList] +
+                      ["%f" % x for x in [pvals[Rv], qvals[Rv]]])
+              file.write('\t'.join(vals)+EOL)
+        file.close()
+        self.transit_message("Finished Anova analysis")
+
+    @classmethod
+    def usage_string(self):
+        return """python %s anova <combined wig file> <annotation .prot_table> <samples_metadata file> <output file> [Optional Arguments]
+
+        Optional Arguments:
+        -n <string>         :=  Normalization method. Default: -n TTR
+        --ignore-conditions <cond1,cond2> :=  Comma seperated list of conditions to ignore, for the analysis. Default --ignore-conditions Unknown
+
+        """ % (sys.argv[0])
+
+
+
+if __name__ == "__main__":
+    main()
+

src/pytransit/analysis/base.py

@@ -9,26 +9,13 @@ try:
 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
+    from pubsub import pub
     import wx.adv
 
-   
 import traceback
 import datetime
 import pytransit.transit_tools as transit_tools
@@ -68,10 +55,7 @@ class TransitGUIBase:
     def status_message(self, text, time=-1):
         #TODO: write docstring
         if self.wxobj:
-            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()
 
 #
@@ -203,6 +187,26 @@ class AnalysisGUI:
     def Enable(self):
         self.panel.Enable()
 
+#
+
+    def GlobalEnable(self):
+        pass
+
+#
+
+    def GlobalHide(self):
+        pass
+
+#
+
+    def GlobalShow(self):
+        pass
+
+#
+
+    def GlobalDisable(self):
+        pass
+
 #
 
     def definePanel(self, wxobj):
@@ -366,30 +370,21 @@ class AnalysisMethod:
         data = {"path":path, "type":filetype, "date": datetime.datetime.today().strftime("%B %d, %Y %I:%M%p")}
 
         if self.wxobj:
-            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 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 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)
@@ -398,10 +393,7 @@ class AnalysisMethod:
     def progress_range(self, count):
         #TODO: write docstring
         if self.wxobj:
-            if WX_VERSION > 2:
             wx.CallAfter(pub.sendMessage, "progressrange", msg=count)
-            else:
-                wx.CallAfter(pub.sendMessage, "progressrange", count)
             wx.Yield()
 
 #
@@ -409,10 +401,7 @@ class AnalysisMethod:
     def status_message(self, text, time=-1):
         #TODO: write docstring
         if self.wxobj:
-            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()
 
 #
@@ -512,6 +501,21 @@ class QuadConditionMethod(AnalysisMethod):
         self.ignoreCodon = ignoreCodon
         self.NTerminus = NTerminus
         self.CTerminus = CTerminus
+#
+
+class MultiConditionMethod(AnalysisMethod):
+    '''
+    Class to be inherited by analysis methods that compare essentiality between multiple conditions (e.g Anova).
+    '''
+
+    def __init__(self, short_name, long_name, short_desc, long_desc, combined_wig, metadata, annotation_path, output, normalization=None, LOESS=False, ignoreCodon=True, wxobj=None):
+        AnalysisMethod.__init__(self, short_name, long_name, short_desc, long_desc, output,
+                annotation_path, wxobj)
+        self.combined_wig = combined_wig
+        self.metadata = metadata
+        self.normalization = normalization
+        self.LOESS = LOESS
+        self.ignoreCodon = ignoreCodon
 
 #
 

src/pytransit/analysis/binomial.py

@@ -8,25 +8,11 @@ try:
 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
-
+    from pubsub import pub
 
 import os
 import time

src/pytransit/analysis/example.py

@@ -8,26 +8,13 @@ try:
 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
+    from pubsub import pub
     import wx.adv
 
-
 import os
 import time
 import math

src/pytransit/analysis/gi.py

@@ -8,26 +8,13 @@ try:
 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
+    from pubsub import pub
     import wx.adv
 
-
 import os
 import time
 import ntpath
@@ -56,7 +43,7 @@ long_desc = """Method for determining genetic interactions based on changes in e
 NOTE: This method requires 4 groups of datasets. Use the main interface to add datasets for the two strain backgrounds under the first condition. A window will allow you to add the datasets under the second condition.
 """
 
-transposons = ["himar1", "tn5"]
+transposons = []
 columns = ["Orf","Name","Number of TA Sites","Mean count (Strain A Condition 1)","Mean count (Strain A Condition 2)","Mean count (Strain B Condition 1)","Mean count (Strain B Condition 2)", "Mean logFC (Strain A)", "Mean logFC (Strain B)", "Mean delta logFC","Lower Bound delta logFC","Upper Bound delta logFC", "Prob. of delta-logFC being within ROPE", "Adjusted Probability (BFDR)", "Is HDI outside ROPE?", "Type of Interaction"]
 
 
@@ -419,21 +406,12 @@ if hasWx:
             name = transit_tools.basename(fullpath)
             (density, meanrd, nzmeanrd, nzmedianrd, maxrd, totalrd, skew, kurtosis) = tnseq_tools.get_wig_stats(fullpath)
 
-            if WX_VERSION > 3:
             self.list_ctrl.InsertItem(self.index_ctrl, name)
             self.list_ctrl.SetItem(self.index_ctrl, 1, "%1.1f" % (totalrd))
             self.list_ctrl.SetItem(self.index_ctrl, 2, "%2.1f" % (density*100))
             self.list_ctrl.SetItem(self.index_ctrl, 3, "%1.1f" % (meanrd))
             self.list_ctrl.SetItem(self.index_ctrl, 4, "%d" % (maxrd))
             self.list_ctrl.SetItem(self.index_ctrl, 5, "%s" % (fullpath))
-            else:
-                self.list_ctrl.InsertStringItem(self.index_ctrl, name)
-                self.list_ctrl.SetStringItem(self.index_ctrl, 1, "%1.1f" % (totalrd))
-                self.list_ctrl.SetStringItem(self.index_ctrl, 2, "%2.1f" % (density*100))
-                self.list_ctrl.SetStringItem(self.index_ctrl, 3, "%1.1f" % (meanrd))
-                self.list_ctrl.SetStringItem(self.index_ctrl, 4, "%d" % (maxrd))
-                self.list_ctrl.SetStringItem(self.index_ctrl, 5, "%s" % (fullpath))
-                self.list_ctrl.Select(self.index_ctrl)
             self.list_ctrl.Select(self.index_ctrl)
             self.index_ctrl+=1
 
@@ -443,21 +421,12 @@ if hasWx:
             name = transit_tools.basename(fullpath)
             (density, meanrd, nzmeanrd, nzmedianrd, maxrd, totalrd, skew, kurtosis) = tnseq_tools.get_wig_stats(fullpath)
 
-            if WX_VERSION > 3:
             self.list_exp.InsertItem(self.index_exp, name)
             self.list_exp.SetItem(self.index_exp, 1, "%1.1f" % (totalrd))
             self.list_exp.SetItem(self.index_exp, 2, "%2.1f" % (density*100))
             self.list_exp.SetItem(self.index_exp, 3, "%1.1f" % (meanrd))
             self.list_exp.SetItem(self.index_exp, 4, "%d" % (maxrd))
             self.list_exp.SetItem(self.index_exp, 5, "%s" % (fullpath))
-            else:
-                self.list_exp.InsertStringItem(self.index_exp, name)
-                self.list_exp.SetStringItem(self.index_exp, 1, "%1.1f" % (totalrd))
-                self.list_exp.SetStringItem(self.index_exp, 2, "%2.1f" % (density*100))
-                self.list_exp.SetStringItem(self.index_exp, 3, "%1.1f" % (meanrd))
-                self.list_exp.SetStringItem(self.index_exp, 4, "%d" % (maxrd))
-                self.list_exp.SetStringItem(self.index_exp, 5, "%s" % (fullpath))
-
             self.list_exp.Select(self.index_exp)
             self.index_exp+=1
 
@@ -517,9 +486,10 @@ class GIMethod(base.QuadConditionMethod):
         self.samples = samples
         self.includeZeros = includeZeros
         self.rope = rope
-        self.doBFDR = False
-        self.doFWER = False 
-
+        self.doBFDR = True # TRI
+        self.doFWER = True # TRI
+        self.NTerminus = NTerminus
+        self.CTerminus = CTerminus
 
     @classmethod
     def fromGUI(self, wxobj):
@@ -620,7 +590,7 @@ class GIMethod(base.QuadConditionMethod):
 
         normalization = kwargs.get("n", "TTR")
         samples = int(kwargs.get("s", 10000))
-        rope = int(kwargs.get("-rope", 0.5))
+        rope = float(kwargs.get("-rope", 0.5)) # fixed! changed int to float
         replicates = kwargs.get("r", "Sum")
         includeZeros = kwargs.get("iz", False)
 
@@ -680,10 +650,10 @@ class GIMethod(base.QuadConditionMethod):
                 data[j] = stat_tools.loess_correction(position, data[j])
 
         # Get Gene objects for each condition
-        G_A1 = tnseq_tools.Genes([], self.annotation_path, data=data[:Na1], position=position)
-        G_B1 = tnseq_tools.Genes([], self.annotation_path, data=data[Na1:(Na1+Nb1)], position=position)
-        G_A2 = tnseq_tools.Genes([], self.annotation_path, data=data[(Na1+Nb1):(Na1+Nb1+Na2)], position=position)
-        G_B2 = tnseq_tools.Genes([], self.annotation_path, data=data[(Na1+Nb1+Na2):], position=position)
+        G_A1 = tnseq_tools.Genes([], self.annotation_path, data=data[:Na1], position=position,nterm=self.NTerminus,cterm=self.CTerminus)
+        G_B1 = tnseq_tools.Genes([], self.annotation_path, data=data[Na1:(Na1+Nb1)], position=position,nterm=self.NTerminus,cterm=self.CTerminus)
+        G_A2 = tnseq_tools.Genes([], self.annotation_path, data=data[(Na1+Nb1):(Na1+Nb1+Na2)], position=position,nterm=self.NTerminus,cterm=self.CTerminus)
+        G_B2 = tnseq_tools.Genes([], self.annotation_path, data=data[(Na1+Nb1+Na2):], position=position,nterm=self.NTerminus,cterm=self.CTerminus)
 
         means_list_a1 = []
         means_list_b1 = []

src/pytransit/analysis/griffin.py

@@ -8,23 +8,11 @@ try:
 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
+    from pubsub import pub
     import wx.adv
 
 

src/pytransit/analysis/gumbel.py

@@ -8,26 +8,13 @@ try:
 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
+    from pubsub import pub
     import wx.adv
 
-
 import os
 import time
 import math

src/pytransit/analysis/hmm.py

@@ -8,26 +8,13 @@ try:
 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
+    from pubsub import pub
     import wx.adv
 
-
 import os
 import time
 import math

src/pytransit/analysis/norm.py

@@ -8,26 +8,13 @@ try:
 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
+    from pubsub import pub
     import wx.adv
 
-
 import os
 import time
 import math