--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/GetReadDistribution.py	Thu May 02 09:56:47 2013 -0400
@@ -0,0 +1,303 @@
+#! /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()
+