import sys
try:
import wx
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
import os
import time
import math
import random
import numpy
import scipy.stats
import datetime
import base
import pytransit.transit_tools as transit_tools
import pytransit.tnseq_tools as tnseq_tools
import pytransit.norm_tools as norm_tools
import pytransit.stat_tools as stat_tools
#method_name = "griffin"
############# GUI ELEMENTS ##################
short_name = "griffin"
long_name = "Basic frequentist analysis of essentiality using gaps."
description = "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"]
############# Analysis Method ##############
[docs]class GriffinAnalysis(base.TransitAnalysis):
def __init__(self):
base.TransitAnalysis.__init__(self, short_name, long_name, description, transposons, GriffinMethod, GriffinGUI, [GriffinFile])
################## FILE ###################
[docs]class GriffinFile(base.TransitFile):
def __init__(self):
base.TransitFile.__init__(self, "#Griffin", columns)
################## GUI ###################
[docs]class GriffinGUI(base.AnalysisGUI):
[docs] def definePanel(self, wxobj):
self.wxobj = wxobj
griffinPanel = wx.Panel( self.wxobj.optionsWindow, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, wx.TAB_TRAVERSAL )
griffinSection = wx.BoxSizer( wx.VERTICAL )
griffinLabel = wx.StaticText( griffinPanel, wx.ID_ANY, u"griffin Options", wx.DefaultPosition, wx.DefaultSize, 0 )
griffinLabel.Wrap( -1 )
griffinSection.Add( griffinLabel, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
griffinSizer1 = wx.BoxSizer( wx.HORIZONTAL )
griffinSection.Add( griffinSizer1, 1, wx.EXPAND, 5 )
griffinButton = wx.Button( griffinPanel, wx.ID_ANY, u"Run griffin", wx.DefaultPosition, wx.DefaultSize, 0 )
griffinSection.Add( griffinButton, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
griffinPanel.SetSizer( griffinSection )
griffinPanel.Layout()
griffinSection.Fit( griffinPanel )
#Connect events
griffinButton.Bind( wx.EVT_BUTTON, self.wxobj.RunMethod )
self.panel = griffinPanel
########## CLASS #######################
[docs]class GriffinMethod(base.SingleConditionMethod):
"""
griffin
"""
def __init__(self,
ctrldata,
annotation_path,
output_file,
minread=1,
replicates="Sum",
normalization=None,
LOESS=False,
ignoreCodon=True,
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)
self.minread = minread
[docs] @classmethod
def fromGUI(self, wxobj):
""" """
#Get Annotation file
annotationPath = wxobj.annotation
if not transit_tools.validate_annotation(annotationPath):
return None
#Get selected files
ctrldata = wxobj.ctrlSelected()
if not transit_tools.validate_control_datasets(ctrldata):
return None
#Validate transposon types
if not transit_tools.validate_transposons_used(ctrldata, transposons):
return None
#
minread = 1
#Read the parameters from the wxPython widgets
ignoreCodon = True
NTerminus = float(wxobj.globalNTerminusText.GetValue())
CTerminus = float(wxobj.globalCTerminusText.GetValue())
replicates = "Sum"
normalization = None
LOESS = False
#Get output path
name = transit_tools.basename(ctrldata[0])
defaultFileName = "griffin_output.dat"
defaultDir = os.getcwd()
output_path = wxobj.SaveFile(defaultDir, defaultFileName)
if not output_path: return None
output_file = open(output_path, "w")
return self(ctrldata,
annotationPath,
output_file,
minread,
replicates,
normalization,
LOESS,
ignoreCodon,
NTerminus,
CTerminus, wxobj)
[docs] @classmethod
def fromargs(self, rawargs):
(args, kwargs) = transit_tools.cleanargs(rawargs)
ctrldata = args[0].split(",")
annotationPath = args[1]
outpath = args[2]
output_file = open(outpath, "w")
minread = int(kwargs.get("m", 1))
replicates = kwargs.get("r", "Sum")
normalization = None
LOESS = False
ignoreCodon = not kwargs.get("sC", False)
NTerminus = float(kwargs.get("iN", 0.0))
CTerminus = float(kwargs.get("iC", 0.0))
return self(ctrldata,
annotationPath,
output_file,
minread,
replicates,
normalization,
LOESS,
ignoreCodon,
NTerminus,
CTerminus)
[docs] def Run(self):
self.transit_message("Starting Griffin Method")
start_time = time.time()
#Get orf data
self.transit_message("Getting Data")
(data, position) = transit_tools.get_validated_data(self.ctrldata, wxobj=self.wxobj)
(K,N) = data.shape
if self.normalization and self.normalization != "nonorm":
self.transit_message("Normalizing using: %s" % self.normalization)
(data, factors) = norm_tools.normalize_data(data, self.normalization, self.ctrldata, self.annotation_path)
G = tnseq_tools.Genes(self.ctrldata, self.annotation_path, minread=1, reps=self.replicates, ignoreCodon=self.ignoreCodon, nterm=self.NTerminus, cterm=self.CTerminus, data=data, position=position)
N = len(G)
self.progress_range(N)
count = 0
pins = G.global_theta()
pnon = 1.0 - pins
results = []
for gene in G:
if gene.n == 0:
results.append([gene, 0.0, 1.000])
else:
B = 1.0/math.log(1.0/pnon)
u = math.log(gene.n*pins, 1.0/pnon)
exprun = tnseq_tools.ExpectedRuns(gene.n, pnon)
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))
self.progress_update(text, count)
self.transit_message_inplace(text)
count+=1
pval = [row[-1] for row in results]
padj = stat_tools.BH_fdr_correction(pval)
for i in range(len(results)):
results[i].append(padj[i])
results.sort()
self.output.write("#Griffin\n")
if self.wxobj:
members = sorted([attr for attr in dir(self) if not callable(getattr(self,attr)) and not attr.startswith("__")])
memberstr = ""
for m in members:
memberstr += "%s = %s, " % (m, getattr(self, m))
self.output.write("#GUI with: ctrldata=%s, annotation=%s, output=%s\n" % (",".join(self.ctrldata).encode('utf-8'), self.annotation_path.encode('utf-8'), self.output.name.encode('utf-8')))
else:
self.output.write("#Console: python %s\n" % " ".join(sys.argv))
self.output.write("#Data: %s\n" % (",".join(self.ctrldata).encode('utf-8')))
self.output.write("#Annotation path: %s\n" % self.annotation_path.encode('utf-8'))
self.output.write("#Time: %s\n" % (time.time() - start_time))
self.output.write("#%s\n" % "\t".join(columns))
for (gene, exprun, pval, padj) in results:
self.output.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%1.1f\t%1.5f\t%1.5f\n" % (gene.orf, gene.name, gene.desc, gene.k, gene.n, gene.r, gene.s, gene.t, exprun, pval, padj))
self.output.close()
self.transit_message("") # Printing empty line to flush stdout
self.transit_message("Adding File: %s" % (self.output.name))
self.add_file(filetype="Griffin")
self.finish()
self.transit_message("Finished Griffin Method")
[docs] @classmethod
def usage_string(self):
return """python %s griffin <comma-separated .wig files> <annotation .prot_table> <output file> [Optional Arguments]
Optional Arguments:
-m <integer> := Smallest read-count to consider. Default: -m 1
-r <string> := How to handle replicates. Sum or Mean. Default: -r Sum
-sC := Include stop-codon (default is to ignore).
-iN <float> := Ignore TAs occuring at given fraction of the N terminus. Default: -iN 0.0
-iC <float> := Ignore TAs occuring at given fraction of the C terminus. Default: -iC 0.0
""" % (sys.argv[0])
if __name__ == "__main__":
(args, kwargs) = transit_tools.cleanargs(sys.argv)
G = GriffinMethod.fromargs(sys.argv[1:])
G.console_message("Printing the member variables:")
G.print_members()
print ""
print "Running:"
G.Run()