--- a/SMART/Java/Python/GetReadDistribution.py	Fri Dec 13 10:37:16 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,303 +0,0 @@
-#! /usr/bin/env python
-#
-# Copyright INRA-URGI 2009-2010
-# 
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software. You can use,
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info".
-# 
-# As a counterpart to the access to the source code and rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty and the software's author, the holder of the
-# economic rights, and the successive licensors have only limited
-# liability.
-# 
-# In this respect, the user's attention is drawn to the risks associated
-# with loading, using, modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean that it is complicated to manipulate, and that also
-# therefore means that it is reserved for developers and experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or
-# data to be ensured and, more generally, to use and operate it in the
-# same conditions as regards security.
-# 
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-#
-import random, os, glob, subprocess
-from commons.core.parsing.ParserChooser import ParserChooser
-from commons.core.parsing.GffParser import GffParser
-from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
-from SMART.Java.Python.misc.Progress import Progress
-from SMART.Java.Python.misc import Utils
-from commons.core.LoggerFactory import LoggerFactory
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-
-LOG_DEPTH      = "smart"
-DEFAULT_REGION = "_all_"
-MULTIPLE_STR   = {1: "", 1000: " (in kbp)", 1000000: " (in Gbp)"}
-
-class GetReadDistribution(object):
-
-	def __init__(self, verbosity = 0):
-		self.xLab         = ""
-		self.yLab         = "# reads"
-		self.verbosity    = verbosity
-		self.number       = random.randint(0, 100000)
-		self.log          = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self.verbosity)
-		self.parsers      = {}
-		self.distribution = {}
-		self.factors      = {}
-		self.regions      = None
-		self.tmpDatName   = None
-		self.tmpRName     = None
-		self.quorum       = 1
-		self.strands      = False
-		self.width        = 800
-		self.height       = 300
-		self.arial        = False
-
-	def setNames(self, names):
-		self.names = names
-
-	def setInputFiles(self, fileNames, format):
-		chooser = ParserChooser(self.verbosity)
-		chooser.findFormat(format)
-		for cpt, fileName in enumerate(fileNames):
-			self.parsers[self.names[cpt]] = chooser.getParser(fileName)
-
-	def setOutputFileName(self, fileName):
-		self.outputFileName = fileName
-
-	def setLabs(self, xLab, yLab):
-		self.xLab = xLab
-		self.yLab = yLab
-
-	def setBinSize(self, binSize):
-		self.binSize = binSize
-
-	def setColors(self, colors):
-		self.colors = colors
-
-	def setFactors(self, factors):
-		if factors == None:
-			self.factors = dict([name, 1.0] for name in self.names)
-		else:
-			self.factors = dict(zip(self.names, factors))
-
-	def setMultiple(self, boolean):
-		self.multiple = boolean
-	
-	def setImageSize(self, width, height):
-		if width != None:
-			self.width = width
-		if height != None:
-			self.height = height
-
-	def setQuorum(self, quorum):
-		self.quorum = quorum
-
-	def setRegionsFile(self, fileName):
-		if fileName != None:
-			self._loadRegions(fileName)
-
-	def setBothStrands(self, strands):
-		self.strands = strands
-
-	def setArial(self, arial):
-		self.arial = arial
-
-	def _checkOptions(self):
-		if not self.parsers:
-			self.logAndRaise("ERROR: Missing input file names")
-
-	def _logAndRaise(self, errorMsg):
-		self.log.error(errorMsg)
-		raise Exception(errorMsg)
-
-	def _loadRegions(self, fileName):
-		self.regions = {}
-		parser       = GffParser(fileName, self.verbosity)
-		for transcript in parser.getIterator():
-			chromosome = transcript.getChromosome()
-			start      = transcript.getStart()
-			end        = transcript.getEnd()
-			name       = transcript.getName()
-			if chromosome not in self.regions:
-				self.regions[chromosome] = {}
-			if start not in self.regions[chromosome]:
-				self.regions[chromosome][start] = {}
-			if end not in self.regions[chromosome][start]:
-				self.regions[chromosome][start][end] = []
-			self.regions[chromosome][start][end].append(name)
-
-	def _getRegions(self, transcript):
-		if self.regions == None:
-			return [DEFAULT_REGION]
-		chromosome = transcript.getChromosome()
-		start      = transcript.getStart()
-		end        = transcript.getEnd()
-		if chromosome not in self.regions:
-			return []
-		names = []
-		for loadedStart in sorted(self.regions[chromosome].keys()):
-			if loadedStart > end:
-				return names
-			for loadedEnd in reversed(sorted(self.regions[chromosome][loadedStart].keys())):
-				if loadedEnd < start:
-					break
-				names.extend(self.regions[chromosome][loadedStart][loadedEnd])
-		return names
-
-	def _parse(self, name):
-		progress = UnlimitedProgress(10000, "Reading file '%s'" % (name), self.verbosity)
-		for transcript in self.parsers[name].getIterator():
-			if transcript.__class__.__name__ == "Mapping":
-				transcript = transcript.getTranscript()
-			regions = self._getRegions(transcript)
-			for region in regions:
-				if region not in self.distribution:
-					self.distribution[region] = {}
-				if name not in self.distribution[region]:
-					self.distribution[region][name] = {}
-				chromosome  = transcript.getChromosome()
-				nbElements  = float(transcript.getTagValue("nbElements")) if "nbElements" in transcript.getTagNames() else 1
-				nbElements *= self.factors.get(name, 1)
-				strand      = transcript.getDirection() if self.strands else 1
-				if chromosome not in self.distribution[region][name]:
-					self.distribution[region][name][chromosome] = {}
-				if strand not in self.distribution[region][name][chromosome]:
-					self.distribution[region][name][chromosome][strand] = {}
-				previousBin = None
-				for exon in transcript.getExons():
-					for pos in range(exon.getStart(), exon.getEnd()+1):
-						bin = pos / self.binSize
-						if bin != previousBin:
-							self.distribution[region][name][chromosome][strand][bin] = self.distribution[region][name][chromosome][strand].get(bin, 0) + nbElements
-							previousBin = bin
-			progress.inc()
-		progress.done()
-
-	def _checkQuorum(self, region):
-		if self.quorum == None:
-			return True
-		return max([max([max([max(self.distribution[region][name][chromosome][strand].values()) for strand in self.distribution[region][name][chromosome]]) for chromosome in self.distribution[region][name]]) for name in self.distribution[region]])
-
-	def _writeData(self, region):
-		self.tmpDatName = "tmpFile%d.dat" % (self.number)
-		handle          = open(self.tmpDatName, "w")
-		handle.write("Chr\tPos\tStrand\tCount\tSample\n")
-		for name in self.distribution[region]:
-			for chromosome in sorted(self.distribution[region][name].keys()):
-				for strand in sorted(self.distribution[region][name][chromosome].keys()):
-					for pos in sorted(self.distribution[region][name][chromosome][strand].keys()):
-						handle.write("%s\t%d\t%d\t%d\t\"%s\"\n" % (chromosome, pos * self.binSize, strand, self.distribution[region][name][chromosome][strand].get(pos, 0) * strand, name))
-		handle.close()
-
-	def _findMultiple(self, region):
-		if not self.multiple:
-			return 1
-		maxPosition = max([max([max([max(self.distribution[region][name][chromosome][strand].keys()) for strand in self.distribution[region][name][chromosome]]) for chromosome in self.distribution[region][name]]) for name in self.distribution[region]]) * self.binSize
-		if maxPosition > 2000000:
-			return 1000000
-		elif maxPosition > 2000:
-			return 1000
-		return 1
-
-	def _writeScript(self, region):
-		self.tmpRName = "tmpFile%d.R" % (self.number)
-		fileName      = self.outputFileName if region == DEFAULT_REGION else "%s_%s.png" % (os.path.splitext(self.outputFileName)[0], region)
-		colors        = "scale_fill_brewer(palette=\"Set1\") + scale_color_brewer(palette=\"Set1\")" if self.colors == None else "scale_fill_manual(values = c(%s)) + scale_color_manual(values = c(%s))" % (", ".join(["\"%s\"" % (color) for color in self.colors]), ", ".join(["\"%s\"" % (color) for color in self.colors]))
-		title         = "" if region == DEFAULT_REGION else " + labs(title = \"Distribution of %s\") " % (region)
-		facet         = "Sample ~ Chr" if region == DEFAULT_REGION else "Sample ~ ."
-		handle        = open(self.tmpRName, "w")
-		multiple      = self._findMultiple(region)
-		arial         = ", text = element_text(family=\"Arial\", size=20)" if self.arial else ""
-		if self.arial:
-			handle.write("library(extrafont)\nloadfonts()\n")
-		handle.write("library(ggplot2)\n")
-		handle.write("data <- read.table(\"%s\", header = T)\n" % (self.tmpDatName))
-		handle.write("data$Sample <- factor(data$Sample, levels=c(%s))\n" % (", ".join(["\"%s\"" % (name) for name in self.names])))
-		handle.write("png(\"%s\", width = %d, height = %d)\n" % (fileName, self.width, self.height))
-		handle.write("ggplot(data, aes(x = Pos/%d, y = Count, fill = Sample, color = Sample)) %s + geom_bar(stat = \"identity\") + facet_grid(%s, space=\"free\") + xlab(\"%s%s\") + ylab(\"%s\") + %s + theme(legend.position = \"none\", panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank()%s)\n" % (multiple, title, facet, self.xLab, MULTIPLE_STR[multiple], self.yLab, colors, arial))
-		handle.write("dev.off()\n")
-
-	def _runR(self):
-		rCommand = os.environ["SMARTRPATH"] if "SMARTRPATH" in os.environ else "R"
-		command  = "\"%s\" CMD BATCH %s" % (rCommand, self.tmpRName)
-		status   = subprocess.call(command, shell=True)
-		if status != 0:
-			raise Exception("Problem with the execution of script file %s, status is: %s" % (self.tmpRName, status))
-
-	def _plot(self):
-		progress = Progress(len(self.distribution), "Plotting data", self.verbosity)
-		for region in self.distribution:
-			if not self._checkQuorum(region):
-				self.log.info("Not displaying '%s' for it contains insufficient data." % (region))
-			else:
-				self._writeData(region)
-				self._writeScript(region)
-				self._runR()
-			progress.inc()
-		progress.done()
-
-	def _cleanFiles(self):
-		for fileName in (self.tmpDatName, self.tmpRName):
-			if fileName != None and os.path.exists(fileName):
-				os.remove(fileName)
-				for otherFileName in glob.glob("%s*" % (fileName)):
-					os.remove(otherFileName)
-
-	def run(self):
-		LoggerFactory.setLevel(self.log, self.verbosity)
-		self._checkOptions()
-		self.log.info("START Get Read Distribution")
-		for name in self.names:
-			self._parse(name)
-		self._plot()
-		self._cleanFiles()
-		self.log.info("END Get Read Distribution")
-
-
-if __name__ == "__main__":
-	description = "Usage: GetReadDistribution.py [options]\n\nGet Read Distribution v1.0.1: Get the distribution of a set of reads. [Category: Personal]\n"
-	epilog = ""
-	parser = RepetOptionParser(description = description, epilog = epilog)
-	parser.add_option("-i", "--input",     dest="inputFileNames",  action="store",      default=None,      type="string", help="input files, separated by commas [compulsory] [format: string]")
-	parser.add_option("-f", "--format",    dest="format",          action="store",      default=None,      type="string", help="format of the input [compulsory] [format: transcript or sequence file format]")
-	parser.add_option("-n", "--names",     dest="names",           action="store",      default=None,      type="string", help="name of the input data, separated by commas [compulsory] [format: string]")
-	parser.add_option("-o", "--output",    dest="outputFileName",  action="store",      default=None,      type="string", help="output file [format: output file in PNG format]")
-	parser.add_option("-s", "--binSize",   dest="binSize",         action="store",      default=10000,     type="int",    help="bin size [format: int] [default: 10000]")
-	parser.add_option("-l", "--xLabel",    dest="xLab",            action="store",      default="",        type="string", help="x-axis label name [format: string]")
-	parser.add_option("-L", "--yLabel",    dest="yLab",            action="store",      default="# reads", type="string", help="y-axis label name [format: string] [default: Reads]")
-	parser.add_option("-c", "--colors",    dest="colors",          action="store",      default=None,      type="string", help="colors of the bars, separated by commas  [format: string]")
-	parser.add_option("-a", "--factors",   dest="factors",         action="store",      default=None,      type="string", help="normalization factors, separated by commas  [format: string]")
-	parser.add_option("-r", "--regions",   dest="regionsFileName", action="store",      default=None,      type="string", help="regions to plot [format: transcript file in GFF format]")
-	parser.add_option("-2", "--strands",   dest="strands",         action="store_true", default=False,                    help="plot negative strands on the negative x-axis [format: boolean] [default: False]")
-	parser.add_option("-m", "--multiple",  dest="multiple",        action="store_true", default=False,                    help="use human readable genomic positions (k, G) [format: boolean] [default: False]")
-	parser.add_option("-q", "--quorum",    dest="quorum",          action="store",      default=1,         type="int",    help="minimum number of intervals to plot a region [format: int] [default: 1]")
-	parser.add_option("-z", "--width",     dest="width",           action="store",      default=800,       type="int",    help="width of the image [format: int] [default: 800]")
-	parser.add_option("-Z", "--height",    dest="height",          action="store",      default=300,       type="int",    help="height of the image [format: int] [default: 300]")
-	parser.add_option("-A", "--arial",     dest="arial",           action="store_true", default=False,                    help="use Arial font [format: boolean] [default: false]")
-	parser.add_option("-v", "--verbosity", dest="verbosity",       action="store",      default=1,         type="int",    help="trace level [format: int]")
-	options = parser.parse_args()[0]
-	iGetReadDistribution = GetReadDistribution(options.verbosity)
-	iGetReadDistribution.setNames(options.names.split(","))
-	iGetReadDistribution.setInputFiles(options.inputFileNames.split(","), options.format)
-	iGetReadDistribution.setOutputFileName(options.outputFileName)
-	iGetReadDistribution.setLabs(options.xLab, options.yLab)
-	iGetReadDistribution.setBinSize(options.binSize)
-	iGetReadDistribution.setColors(None if options.colors == None else options.colors.split(","))
-	iGetReadDistribution.setFactors(None if options.factors == None else map(float, options.factors.split(",")))
-	iGetReadDistribution.setRegionsFile(options.regionsFileName)
-	iGetReadDistribution.setMultiple(options.multiple)
-	iGetReadDistribution.setQuorum(options.quorum)
-	iGetReadDistribution.setImageSize(options.width, options.height)
-	iGetReadDistribution.setBothStrands(options.strands)
-	iGetReadDistribution.setArial(options.arial)
-	iGetReadDistribution.run()
-

--- a/SMART/Java/Python/GetReadSizes.py	Fri Dec 13 10:37:16 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,282 +0,0 @@
-#! /usr/bin/env python
-#
-# Copyright INRA-URGI 2009-2010
-# 
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software. You can use,
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info".
-# 
-# As a counterpart to the access to the source code and rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty and the software's author, the holder of the
-# economic rights, and the successive licensors have only limited
-# liability.
-# 
-# In this respect, the user's attention is drawn to the risks associated
-# with loading, using, modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean that it is complicated to manipulate, and that also
-# therefore means that it is reserved for developers and experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or
-# data to be ensured and, more generally, to use and operate it in the
-# same conditions as regards security.
-# 
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-#
-import random, os, glob, subprocess
-from commons.core.parsing.ParserChooser import ParserChooser
-from commons.core.parsing.GffParser import GffParser
-from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
-from SMART.Java.Python.misc.Progress import Progress
-from SMART.Java.Python.misc import Utils
-from commons.core.LoggerFactory import LoggerFactory
-from commons.core.utils.RepetOptionParser import RepetOptionParser
-
-LOG_DEPTH      = "smart"
-DEFAULT_REGION = "_all_"
-
-class GetReadSizes(object):
-
-	def __init__(self, verbosity = 0):
-		self.xLab       = "Size"
-		self.yLab       = "# reads"
-		self.verbosity  = verbosity
-		self.number     = random.randint(0, 100000)
-		self.log        = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self.verbosity)
-		self.parsers    = {}
-		self.sizes      = {}
-		self.factors    = {}
-		self.regions    = None
-		self.percentage = False
-		self.tmpDatName = None
-		self.tmpRName   = None
-		self.width      = 800
-		self.height     = 300
-		self.arial      = False
-
-	def setNames(self, names):
-		self.names = names
-
-	def setInputFiles(self, fileNames, format):
-		chooser = ParserChooser(self.verbosity)
-		chooser.findFormat(format)
-		for cpt, fileName in enumerate(fileNames):
-			self.parsers[self.names[cpt]] = chooser.getParser(fileName)
-		if not self.factors:
-			self.factors = dict([name, 1.0] for name in self.names)
-
-	def setOutputFileName(self, fileName):
-		self.outputFileName = fileName
-
-	def setLabs(self, xLab, yLab):
-		self.xLab = xLab
-		self.yLab = yLab
-
-	def setSizes(self, minSize, maxSize):
-		self.minSize = minSize
-		self.maxSize = maxSize
-
-	def setColors(self, colors):
-		self.colors = colors
-
-	def setFactors(self, factors):
-		if factors:
-			self.factors = dict(zip(self.names, factors))
-
-	def setRegionsFile(self, fileName):
-		if fileName != None:
-			self._loadRegions(fileName)
-
-	def setPercentage(self, percentage):
-		self.percentage = percentage
-		self.xLab = "% reads"
-
-	def setImageSize(self, width, height):
-		if width != None:
-			self.width = width
-		if height != None:
-			self.height = height
-
-	def setArial(self, arial):
-		self.arial = arial
-
-	def _checkOptions(self):
-		if not self.parsers:
-			self.logAndRaise("ERROR: Missing input file names")
-
-	def _logAndRaise(self, errorMsg):
-		self.log.error(errorMsg)
-		raise Exception(errorMsg)
-
-	def _loadRegions(self, fileName):
-		self.regions = {}
-		parser       = GffParser(fileName, self.verbosity)
-		for transcript in parser.getIterator():
-			chromosome = transcript.getChromosome()
-			start      = transcript.getStart()
-			end        = transcript.getEnd()
-			name       = transcript.getName()
-			if chromosome not in self.regions:
-				self.regions[chromosome] = {}
-			if start not in self.regions[chromosome]:
-				self.regions[chromosome][start] = {}
-			if end not in self.regions[chromosome][start]:
-				self.regions[chromosome][start][end] = []
-			self.regions[chromosome][start][end].append(name)
-
-	def _getRegions(self, transcript):
-		if self.regions == None:
-			return [DEFAULT_REGION]
-		chromosome = transcript.getChromosome()
-		start      = transcript.getStart()
-		end        = transcript.getEnd()
-		if chromosome not in self.regions:
-			return []
-		names = []
-		for loadedStart in sorted(self.regions[chromosome].keys()):
-			if loadedStart > end:
-				return names
-			for loadedEnd in reversed(sorted(self.regions[chromosome][loadedStart].keys())):
-				if loadedEnd < start:
-					break
-				names.extend(self.regions[chromosome][loadedStart][loadedEnd])
-		return names
-
-	def _parse(self, name):
-		progress = UnlimitedProgress(10000, "Reading file '%s'" % (name), self.verbosity)
-		for transcript in self.parsers[name].getIterator():
-			if transcript.__class__.__name__ == "Mapping":
-				transcript = transcript.getTranscript()
-			regions = self._getRegions(transcript)
-			for region in regions:
-				if region not in self.sizes:
-					self.sizes[region] = {}
-				if name not in self.sizes[region]:
-					self.sizes[region][name] = {}
-				size = transcript.getSize()
-				if (self.minSize == None or size >= self.minSize) and (self.maxSize == None or size <= self.maxSize):
-					nbElements                     = float(transcript.getTagValue("nbElements")) if "nbElements" in transcript.getTagNames() else 1
-					nbElements                    *= self.factors.get(name, 1)
-					self.sizes[region][name][size] = self.sizes[region][name].get(size, 0) + nbElements
-			progress.inc()
-		progress.done()
-		if self.minSize == None:
-			self.minSize = min([min(self.sizes[region][name].keys()) for name in self.names for region in region])
-		if self.maxSize == None:
-			self.maxSize = max([max(self.sizes[region][name].keys()) for name in self.names for region in region])
-
-	def _checkQuorum(self, region):
-		return (max([sum(self.sizes[region][name].values()) for name in self.sizes[region]]) > 0)
-
-	def _computePercentage(self):
-		for region in self.sizes:
-			for name in self.sizes[region]:
-				if self.sizes[region][name]:
-					sumData = float(sum(self.sizes[region][name].values()))
-					for size in self.sizes[region][name]:
-						self.sizes[region][name][size] = self.sizes[region][name][size] / sumData * 100
-
-	def _writeData(self, region):
-		self.tmpDatName = "tmpFile%d.dat" % (self.number)
-		handle          = open(self.tmpDatName, "w")
-		handle.write("Size\tCount\tSample\n")
-		for name in self.sizes[region]:
-			for size in sorted(self.sizes[region][name].keys()):
-				handle.write("%d\t%d\t\"%s\"\n" % (size, self.sizes[region][name].get(size, 0), name))
-		handle.close()
-
-	def _writeScript(self, region):
-		self.tmpRName = "tmpFile%d.R" % (self.number)
-		fileName      = self.outputFileName if region == DEFAULT_REGION else "%s_%s.png" % (os.path.splitext(self.outputFileName)[0], region)
-		colors        = "scale_fill_brewer(palette=\"Set1\")" if self.colors == None else "scale_fill_manual(values = c(%s))" % (", ".join(["\"%s\"" % (color) for color in self.colors]))
-		title         = "" if region == DEFAULT_REGION else " + labs(title = \"Sizes of %s\")" % (region)
-		handle        = open(self.tmpRName, "w")
-		arial         = ", text = element_text(family=\"Arial\", size=20)" if self.arial else ""
-		if self.arial:
-			handle.write("library(extrafont)\nloadfonts()\n")
-		handle.write("library(ggplot2)\n")
-		handle.write("data <- read.table(\"%s\", header = T)\n" % (self.tmpDatName))
-		handle.write("data$Sample <- factor(data$Sample, levels=c(%s))\n" % (", ".join(["\"%s\"" % (name) for name in self.names])))
-		handle.write("data$Size <- factor(data$Size, levels=c(%s))\n" % (", ".join(["%d" % (size) for size in range(self.minSize, self.maxSize+1)])))
-		handle.write("png(\"%s\", width = %d, height = %d)\n" % (fileName, self.width, self.height))
-		handle.write("ggplot(data, aes(x = Size, y = Count, fill = Size)) %s + geom_bar(stat = \"identity\") + facet_grid(. ~ Sample, space=\"free_x\") + xlab(\"%s\") + ylab(\"%s\") + %s + theme(legend.position = \"none\", panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank()%s)\n" % (title, self.xLab, self.yLab, colors, arial))
-		handle.write("dev.off()\n")
-
-	def _runR(self):
-		rCommand = os.environ["SMARTRPATH"] if "SMARTRPATH" in os.environ else "R"
-		command  = "\"%s\" CMD BATCH %s" % (rCommand, self.tmpRName)
-		status   = subprocess.call(command, shell=True)
-		if status != 0:
-			raise Exception("Problem with the execution of script file %s, status is: %s" % (self.tmpRName, status))
-
-	def _plot(self):
-		progress = Progress(len(self.sizes), "Plotting data", self.verbosity)
-		for region in self.sizes:
-			if not self._checkQuorum(region):
-				self.log.info("Not displaying '%s' for it contains no data." % (region))
-			else:
-				self._writeData(region)
-				self._writeScript(region)
-				self._runR()
-			progress.inc()
-		progress.done()
-
-	def _cleanFiles(self):
-		for fileName in (self.tmpDatName, self.tmpRName):
-			if fileName != None and os.path.exists(fileName):
-				os.remove(fileName)
-				for otherFileName in glob.glob("%s*" % (fileName)):
-					os.remove(otherFileName)
-
-	def run(self):
-		LoggerFactory.setLevel(self.log, self.verbosity)
-		self._checkOptions()
-		self.log.info("START Get Read Sizes")
-		for name in self.names:
-			self._parse(name)
-		if self.percentage:
-			self._computePercentage()
-		self._plot()
-		self._cleanFiles()
-		self.log.info("END Get Read Sizes")
-
-
-if __name__ == "__main__":
-	description = "Usage: GetReadSizes.py [options]\n\nGet Read Sizes v1.0.1: Get the sizes of a set of reads. [Category: Personal]\n"
-	epilog = ""
-	parser = RepetOptionParser(description = description, epilog = epilog)
-	parser.add_option("-i", "--input",     dest="inputFileNames",  action="store",      default=None,     type="string", help="input files, separated by commas [compulsory] [format: string]")
-	parser.add_option("-f", "--format",    dest="format",          action="store",      default=None,     type="string", help="format of the input [compulsory] [format: transcript or sequence file format]")
-	parser.add_option("-n", "--names",     dest="names",           action="store",      default=None,     type="string", help="name of the input data, separated by commas [compulsory] [format: string]")
-	parser.add_option("-o", "--output",    dest="outputFileName",  action="store",      default=None,      type="string", help="output file [format: output file in PNG format]")
-	parser.add_option("-s", "--minSize",   dest="minSize",         action="store",      default=None,      type="int",    help="minimum size [format: int]")
-	parser.add_option("-S", "--maxSize",   dest="maxSize",         action="store",      default=None,      type="int",    help="maximum size [format: int]")
-	parser.add_option("-l", "--xLabel",    dest="xLab",            action="store",      default="Size",    type="string", help="x-axis label name [format: string] [default: Size]")
-	parser.add_option("-L", "--yLabel",    dest="yLab",            action="store",      default="# reads", type="string", help="y-axis label name [format: string] [default: Reads]")
-	parser.add_option("-c", "--colors",    dest="colors",          action="store",      default=None,      type="string", help="colors of the bars, separated by commas  [format: string]")
-	parser.add_option("-a", "--factors",   dest="factors",         action="store",      default=None,      type="string", help="normalization factors, separated by commas  [format: string]")
-	parser.add_option("-r", "--regions",   dest="regionsFileName", action="store",      default=None,      type="string", help="regions to plot [format: transcript file in GFF format]")
-	parser.add_option("-p", "--percent",   dest="percentage",      action="store_true", default=False,                    help="compute percentage instead [format: boolean] [default: false]")
-	parser.add_option("-z", "--width",     dest="width",           action="store",      default=800,       type="int",    help="width of the image [format: int] [default: 800]")
-	parser.add_option("-Z", "--height",    dest="height",          action="store",      default=300,       type="int",    help="height of the image [format: int] [default: 300]")
-	parser.add_option("-A", "--arial",     dest="arial",           action="store_true", default=False,                    help="use Arial font [format: boolean] [default: false]")
-	parser.add_option("-v", "--verbosity", dest="verbosity",       action="store",      default=1,         type="int",    help="trace level [format: int]")
-	options = parser.parse_args()[0]
-	iGetReadSizes = GetReadSizes(options.verbosity)
-	iGetReadSizes.setNames(options.names.split(","))
-	iGetReadSizes.setInputFiles(options.inputFileNames.split(","), options.format)
-	iGetReadSizes.setOutputFileName(options.outputFileName)
-	iGetReadSizes.setSizes(options.minSize, options.maxSize)
-	iGetReadSizes.setColors(None if options.colors == None else options.colors.split(","))
-	iGetReadSizes.setFactors(None if options.factors == None else map(float, options.factors.split(",")))
-	iGetReadSizes.setRegionsFile(options.regionsFileName)
-	iGetReadSizes.setPercentage(options.percentage)
-	iGetReadSizes.setImageSize(options.width, options.height)
-	iGetReadSizes.setLabs(options.xLab, options.yLab)
-	iGetReadSizes.setArial(options.arial)
-	iGetReadSizes.run()