--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/GetDistribution.py	Tue Apr 30 15:02:29 2013 -0400
@@ -0,0 +1,362 @@
+#! /usr/bin/env python
+#
+# Copyright INRA-URGI 2009-2012
+# 
+# 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 os
+from optparse import OptionParser
+from commons.core.parsing.ParserChooser import ParserChooser
+from commons.core.parsing.FastaParser import FastaParser
+from SMART.Java.Python.structure.Transcript import Transcript
+from commons.core.writer.Gff3Writer import Gff3Writer
+from SMART.Java.Python.misc.RPlotter import RPlotter
+from SMART.Java.Python.misc.MultipleRPlotter import MultipleRPlotter
+from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
+from SMART.Java.Python.misc.Progress import Progress
+
+TWOSTRANDS = {True: [1, -1], False: [0]}
+STRANDTOSTR = {1: "(+)", -1: "(-)", 0: ""}
+
+class GetDistribution(object):
+
+	def __init__(self, verbosity):
+		self.verbosity     = verbosity
+		self.sizes         = None
+		self.twoStrands    = False
+		self.start         = 1
+		self.names         = ["nbElements"]
+		self.average       = False
+		self.nbValues      = {}
+		self.height        = 300
+		self.width         = 600
+		self.colors        = None
+		self.gffFileName   = None
+		self.csvFileName   = None
+		self.yMin          = None
+		self.yMax          = None
+		self.chromosome    = None
+		self.merge         = False
+		self.nbTranscripts = None
+
+	def setInputFile(self, fileName, format):
+		chooser = ParserChooser(self.verbosity)
+		chooser.findFormat(format)
+		self.parser = chooser.getParser(fileName)
+
+	def setReferenceFile(self, fileName):
+		if fileName == None:
+			return
+		fastaParser = FastaParser(fileName, self.verbosity)
+		self.chromosomes = fastaParser.getRegions()
+		self.sizes       = dict([region, fastaParser.getSizeOfRegion(region)] for region in self.chromosomes)
+		self.maxSize     = max(self.sizes.values())
+
+	def setRegion(self, chromosome, start, end):
+		if chromosome == None:
+			return
+		self.maxSize     = options.end
+		self.sizes       = {chromosome: end}
+		self.chromosomes = [chromosome]
+		self.chromosome  = chromosome
+		self.start       = start
+		self.end         = end
+
+	def setOutputFile(self, fileName):
+		self.outputFileName = fileName
+
+	def setNbBins(self, nbBins):
+		self.nbBins = nbBins
+
+	def set2Strands(self, twoStrands):
+		self.twoStrands = twoStrands
+
+	def setNames(self, names):
+		self.names = names
+
+	def setAverage(self, average):
+		self.average = average
+
+	def setNormalization(self, normalization):
+		self.normalization = normalization
+	
+	def setImageSize(self, height, width):
+		self.height = height
+		self.width  = width
+
+	def setYLimits(self, yMin, yMax):
+		self.yMin = yMin
+		self.yMax = yMax
+
+	def setColors(self, colors):
+		self.colors = colors
+
+	def writeGff(self, fileName):
+		self.gffFileName = fileName
+
+	def writeCsv(self, fileName):
+		self.csvFileName = fileName
+
+	def mergePlots(self, merge):
+		self.merge = merge
+
+	def _estimateSizes(self):
+		progress = UnlimitedProgress(10000, "Reading input for chromosome size estimate", self.verbosity)
+		self.sizes = {}
+		for self.nbTranscripts, transcript in enumerate(self.parser.getIterator()):
+			chromosome = transcript.getChromosome()
+			start      = transcript.getStart()
+			self.sizes[chromosome] = max(start, self.sizes.get(chromosome, 0))
+			progress.inc()
+		progress.done()
+
+	def _computeSliceSize(self):
+		if self.nbBins == 0:
+			return
+		tmp1           = int(max(self.sizes.values()) / float(self.nbBins))
+		tmp2           = 10 ** (len("%d" % (tmp1))-2)
+		self.sliceSize = max(1, int((tmp1 / tmp2) * tmp2))
+		if self.verbosity > 0:
+			print "choosing bin size of %d" % (self.sliceSize)
+
+	def _initBins(self):
+		self.bins = {}
+		for chromosome in self.sizes:
+			self.bins[chromosome] = {}
+			for name in self.names:
+				self.bins[chromosome][name] = {}
+				for strand in TWOSTRANDS[self.twoStrands]:
+					if self.nbBins == 0:
+						self.bins[chromosome][name][strand] = {}
+					else:
+						self.bins[chromosome][name][strand] = dict([(i * self.sliceSize + 1, 0.0) for i in range(self.start / self.sliceSize, self.sizes[chromosome] / self.sliceSize + 1)])
+
+	def _populateBins(self):
+		if self.nbTranscripts == None:
+			progress = UnlimitedProgress(10000, "Counting data", self.verbosity)
+		else:
+			progress = Progress(self.nbTranscripts, "Counting data", self.verbosity)
+		for transcript in self.parser.getIterator():
+			if transcript.__class__.__name__ == "Mapping":
+				transcript = transcript.getTranscript()
+			progress.inc()
+			chromosome = transcript.getChromosome()
+			start      = transcript.getStart()
+			if self.chromosome and (chromosome != self.chromosome or start < self.start or start > self.end):
+				continue
+			strand = transcript.getDirection() if self.twoStrands else 0
+			if self.nbBins != 0:
+				bin = (start / self.sliceSize) * self.sliceSize + 1
+			else:
+				bin = start
+			for name in self.names:
+				value = float(transcript.tags.get(name, 1))
+				self.bins[chromosome][name][strand][bin] = self.bins[chromosome][name][strand].get(bin, 0) + value
+				self.nbValues[name] = self.nbValues.get(name, 0) + value
+		progress.done()
+
+	def _normalize(self):
+		average = float(sum(self.nbValues)) / len(self.nbValues.keys())
+		factors = dict([name, float(average) / self.nbValues[name]] for name in self.nbValues)
+		for chromosome in self.bins:
+			for name in self.bins[chromosome]:
+				for strand in self.bins[chromosome][name]:
+					for bin in self.bins[chromosome][name][strand]:
+						self.bins[chromosome][name][strand][bin] *= factors[name]
+
+	def _computeAverage(self):
+		for chromosome in self.bins:
+			for name in self.bins[chromosome]:
+				for strand in self.bins[chromosome][name]:
+					for bin in self.bins[chromosome][name][strand]:
+						self.bins[chromosome][name][strand][bin] = float(self.bins[chromosome][name][strand][bin]) / self.sliceSize
+
+	def _getPlotter(self, chromosome):
+		plot = RPlotter("%s_%s.png" % (os.path.splitext(self.outputFileName)[0], chromosome), self.verbosity)
+		plot.setImageSize(self.width, self.height)
+		if self.sizes[chromosome] <= 1000:
+			unit  = "nt."
+			ratio = 1.0
+		elif self.sizes[chromosome] <= 1000000:
+			unit  = "kb"
+			ratio = 1000.0
+		else:
+			unit  = "Mb"
+			ratio = 1000000.0
+		if self.yMin != None:
+			plot.setMinimumY(self.yMin)
+		if self.yMax != None:
+			plot.setMaximumY(self.yMax)
+		plot.setXLabel("Position on %s (in %s)" % (chromosome.replace("_", " "), unit))
+		plot.setLegend(True)
+		for i, name in enumerate(self.bins[chromosome]):
+			for strand in self.bins[chromosome][name]:
+				fullName = "%s %s" % (name.replace("_", " ")[:6], STRANDTOSTR[strand])
+				factor = 1 if strand == 0 else strand
+				correctedLine = dict([(key / ratio, value * factor) for key, value in self.bins[chromosome][name][strand].iteritems()])
+				plot.addLine(correctedLine, fullName, self.colors[i] if self.colors else None)
+		return plot
+
+	def _plot(self):
+		if self.merge:
+			multiplePlot = MultipleRPlotter(self.outputFileName, self.verbosity)
+			multiplePlot.setImageSize(self.width, self.height * len(self.bins.keys()))
+		progress = Progress(len(self.bins.keys()), "Plotting", options.verbosity)
+		for chromosome in sorted(self.bins.keys()):
+			plot = self._getPlotter(chromosome)
+			if self.merge:
+				multiplePlot.addPlot(plot)
+			else:
+				plot.plot()
+			progress.inc()
+		if self.merge:
+			multiplePlot.plot()
+		progress.done()
+
+	def _writeCsv(self):
+		if self.verbosity > 1:
+			print "Writing CSV file..."
+		csvHandle = open(self.csvFileName, "w")
+		csvHandle.write("chromosome;tag;strand")
+		if self.nbBins != 0:
+			xValues = range(self.start / self.sliceSize, max(self.sizes.values()) / self.sliceSize + 1)
+			for value in xValues:
+				csvHandle.write(";%d-%d" % (value * self.sliceSize + 1, (value+1) * self.sliceSize))
+			csvHandle.write("\n")
+		else:
+			xValues = []
+			for chromosome in self.bins:
+				for name in self.bins[chromosome]:
+					for strand in self.bins[chromosome][name]:
+						for bin in self.bins[chromosome][name][strand]:
+							xValues.extend(self.bins[chromosome][name][strand].keys())
+			xValues = sorted(list(set(xValues)))
+			for value in xValues:
+				csvHandle.write(";%d" % (value))
+			csvHandle.write("\n")
+		for chromosome in self.bins:
+			csvHandle.write("%s" % (chromosome))
+			for name in self.bins[chromosome]:
+				csvHandle.write(";%s" % (name))
+				for strand in self.bins[chromosome][name]:
+					csvHandle.write(";%s" % (STRANDTOSTR[strand]))
+					for bin in xValues:
+						csvHandle.write(";%.2f" % (self.bins[chromosome][name][strand].get(bin, 0)))
+					csvHandle.write("\n")
+				csvHandle.write(";")
+			csvHandle.write(";")
+		csvHandle.close()
+		if self.verbosity > 1:
+			print "...done"
+		
+	def _writeGff(self):
+		if self.verbosity > 1:
+			print "Writing GFF file..."
+		writer = Gff3Writer(self.gffFileName, self.verbosity)
+		cpt    = 1
+		for chromosome in self.bins:
+			for name in self.bins[chromosome]:
+				for strand in self.bins[chromosome][name]:
+					for bin in self.bins[chromosome][name][strand]:
+						transcript = Transcript()
+						transcript.setChromosome(chromosome)
+						transcript.setStart(bin)
+						if self.nbBins > 0:
+							transcript.setEnd(bin + self.sliceSize)
+						else:
+							transcript.setEnd(self.start)
+						transcript.setDirection(1 if strand == 0 else strand)
+						transcript.setTagValue("ID", "region%d" % (cpt))
+						cpt += 1
+		writer.write()
+		if self.verbosity > 1:
+			print "...done"
+
+	def run(self):
+		if self.sizes == None:
+			self._estimateSizes()
+		self._computeSliceSize()
+		self._initBins()
+		self._populateBins()
+		if self.normalization:
+			self._normalize()
+		if self.average:
+			self._computeAverage()
+		self._plot()
+		if self.csvFileName != None:
+			self._writeCsv()
+		if self.gffFileName != None:
+			self._writeGff()
+
+
+if __name__ == "__main__":
+
+	description = "Get Distribution v1.0.2: Get the distribution of the genomic coordinates on a genome. [Category: Visualization]"
+
+	parser = OptionParser(description = description)
+	parser.add_option("-i", "--input",       dest="inputFileName",     action="store",                            type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
+	parser.add_option("-f", "--format",      dest="format",            action="store",                            type="string", help="format of the input file [compulsory] [format: transcript file format]")
+	parser.add_option("-o", "--output",      dest="outputFileName",    action="store",                            type="string", help="output file [compulsory] [format: output file in GFF3 format]")
+	parser.add_option("-r", "--reference",   dest="referenceFileName", action="store",      default=None,         type="string", help="file containing the genome [format: file in FASTA format]")
+	parser.add_option("-b", "--nbBins",      dest="nbBins",            action="store",      default=1000,         type="int",    help="number of bins [default: 1000] [format: int]")
+	parser.add_option("-2", "--bothStrands", dest="bothStrands",       action="store_true", default=False,                       help="plot one curve per strand [format: bool] [default: false]")
+	parser.add_option("-c", "--chromosome",  dest="chromosome",        action="store",      default=None,         type="string", help="plot only a chromosome [format: string]")
+	parser.add_option("-s", "--start",       dest="start",             action="store",      default=None,         type="int",    help="start from a given region [format: int]")
+	parser.add_option("-e", "--end",         dest="end",               action="store",      default=None,         type="int",    help="end from a given region [format: int]")
+	parser.add_option("-y", "--yMin",        dest="yMin",              action="store",      default=None,         type="int",    help="minimum value on the y-axis to plot [format: int]")
+	parser.add_option("-Y", "--yMax",        dest="yMax",              action="store",      default=None,         type="int",    help="maximum value on the y-axis to plot [format: int]")
+	parser.add_option("-x", "--csv",         dest="csv",               action="store",      default=None,                        help="write a .csv file [format: output file in CSV format] [default: None]")
+	parser.add_option("-g", "--gff",         dest="gff",               action="store",      default=None,                        help="also write GFF3 file [format: output file in GFF format] [default: None]")
+	parser.add_option("-H", "--height",      dest="height",            action="store",      default=300,          type="int",    help="height of the graphics [format: int] [default: 300]")
+	parser.add_option("-W", "--width",       dest="width",             action="store",      default=600,          type="int",    help="width of the graphics [format: int] [default: 1000]")
+	parser.add_option("-a", "--average",     dest="average",           action="store_true", default=False,                       help="plot average (instead of sum) [default: false] [format: boolean]")
+	parser.add_option("-n", "--names",       dest="names",             action="store",      default="nbElements", type="string", help="name for the tags (separated by commas and no space) [default: None] [format: string]")
+	parser.add_option("-l", "--color",       dest="colors",            action="store",      default=None,         type="string", help="color of the lines (separated by commas and no space) [format: string]")
+	parser.add_option("-z", "--normalize",   dest="normalize",         action="store_true", default=False,                       help="normalize data (when panels are different) [format: bool] [default: false]")
+	parser.add_option("-m", "--merge",       dest="mergePlots",        action="store_true", default=False,                       help="merge all plots in one figure [format: bool] [default: false]")
+	parser.add_option("-v", "--verbosity",   dest="verbosity",         action="store",      default=1,            type="int",    help="trace level [default: 1] [format: int]")
+	(options, args) = parser.parse_args()
+
+	gt = GetDistribution(options.verbosity)
+	gt.setInputFile(options.inputFileName, options.format)
+	gt.setOutputFile(options.outputFileName)
+	gt.setReferenceFile(options.referenceFileName)
+	gt.setNbBins(int(options.nbBins))
+	gt.set2Strands(options.bothStrands)
+	gt.setRegion(options.chromosome, options.start, options.end)
+	gt.setNormalization(options.normalize)
+	gt.setAverage(options.average)
+	gt.setYLimits(options.yMin, options.yMax)
+	gt.writeCsv(options.csv)
+	gt.writeGff(options.gff)
+	gt.setImageSize(options.height, options.width)
+	gt.setNames(options.names.split(","))
+	gt.setColors(None if options.colors == None else options.colors.split(","))
+	gt.setNormalization(options.normalize)
+	gt.mergePlots(options.mergePlots)
+	gt.run()
+