--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Python/clusterizeBySlidingWindows.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,344 @@
+#! /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 re
+from commons.core.writer.WriterChooser import WriterChooser
+"""
+Cluster the data into regions (defined by size and overlap with next region) and keep only highest peaks.
+"""
+
+import os, os.path
+from optparse import OptionParser
+from SMART.Java.Python.structure.Transcript import Transcript
+from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+from SMART.Java.Python.misc.RPlotter import RPlotter
+from SMART.Java.Python.misc.Progress import Progress
+from commons.core.writer.Gff3Writer import Gff3Writer
+
+class ClusterizeBySlidingWindows(object):
+
+    def __init__(self, verbosity = 0):
+        self.verbosity = verbosity
+        self.strands   = (0, )
+        self.normalize = False
+        self.plot      = None
+        self.excel     = None
+        self.outputFileName = ''
+        self.defaultValue = None
+
+    def __del__(self):
+        pass
+
+    def setInputFile(self, fileName, format):
+        self.parser = TranscriptContainer(fileName, format, self.verbosity)
+
+    def setOutputFileName(self, fileName, format="gff", title="S-MART", feature="transcript", featurePart="exon"):
+        writerChooser = WriterChooser(self.verbosity)
+        writerChooser.findFormat(format)
+        self.writer = writerChooser.getWriter(fileName)
+        self.writer.setTitle(title)
+        self.writer.setFeature(feature)
+        self.writer.setFeaturePart(featurePart)
+#        self.outputFileName = fileName
+#        self.outputFormat = format
+
+    def setWindowSize(self, size):
+        self.size = size
+
+    def setWindowOverlap(self, overlap):
+        self.overlap = overlap
+
+    def setTag(self, tag):
+        self.tag = tag
+
+    def setOperation(self, operation):
+        self.operation = operation
+
+    def setBothStrands(self, bothStrands):
+        if bothStrands:
+            self.strands = (-1, 1)
+
+    def setNormalize(self, normalize):
+        self.normalize = normalize
+
+    def setPlot(self, plot):
+        self.plot = plot
+
+    def setExcel(self, excel):
+        self.excel = excel
+
+    def setOutputTag(self, tag):
+        self.outputTagName = tag
+        
+    def setDefaultValue(self, defaultValue):
+        self.defaultValue = defaultValue
+
+    def checkOptions(self):
+#        if self.operation != None:
+#            raise Exception("Trying to combine the values without specifying tag! Aborting...")
+        if self.operation != None and self.operation not in ("sum", "avg", "med", "min", "max"):
+            raise Exception("Do not understand tag '%s'! Aborting..." % (self.operation))
+
+    def getChromosomeSizes(self):
+        self.sizes = {}
+        progress = Progress(self.parser.getNbTranscripts(), "Getting sizes in genome", self.verbosity)
+        for transcript in self.parser.getIterator():
+            self.sizes[transcript.getChromosome()] = max(transcript.getStart(), self.sizes.get(transcript.getChromosome(), 0))
+            progress.inc()
+        progress.done()
+
+    def getBinsFromPos(self, pos):
+        bin = (pos - 1) / (self.size - self.overlap)
+        if bin >= 1 and pos <= bin * (self.size - self.overlap) + self.overlap:
+            return (bin - 1, bin)
+        return (bin, )
+
+    def getPosFromBin(self, bin):
+        return (bin * (self.size - self.overlap) + 1, bin * (self.size - self.overlap) + self.size)
+
+    def initializeBins(self):
+        self.binsPerStrand        = {}
+        self.sumsPerStrand        = {}
+        self.valuesPerStrand      = {}
+        self.toBePlottedPerStrand = {}
+        for strand in self.strands:
+            self.binsPerStrand[strand]        = {}
+            self.sumsPerStrand[strand]        = {}
+            self.valuesPerStrand[strand]      = {}
+            self.toBePlottedPerStrand[strand] = {}
+            for chromosome in self.sizes:
+                binRange = range(self.getBinsFromPos(self.sizes[chromosome])[-1] + 1)
+                self.binsPerStrand[strand][chromosome]        = dict([[i, 0]   for i in binRange])
+                self.sumsPerStrand[strand][chromosome]        = dict([[i, 0.0] for i in binRange])
+                self.valuesPerStrand[strand][chromosome]      = dict([[i, []]  for i in binRange])
+                self.toBePlottedPerStrand[strand][chromosome] = dict([[i, 0] for i in binRange])
+
+    def getNbElements(self, transcript):
+        nbOccurrences = 1 if "nbOccurrences" not in transcript.getTagNames() else transcript.getTagValue("nbOccurrences")
+        nbElements    = 1 if "nbElements"    not in transcript.getTagNames() else transcript.getTagValue("nbElements")
+        nbOccurrences = float(nbOccurrences)
+        nbElements = float(nbElements)
+        nbElements /= float(nbOccurrences)
+        return nbElements
+
+    def setBins(self):
+        progress = Progress(self.parser.getNbTranscripts(), "Setting bins", self.verbosity)
+        for transcript in self.parser.getIterator():
+            nbElements = self.getNbElements(transcript)
+            strand     = transcript.getDirection() if len(self.strands) == 2 else 0
+            for bin in self.getBinsFromPos(transcript.getStart()):
+                self.binsPerStrand[strand][transcript.getChromosome()][bin] += nbElements
+                if self.tag != None:
+                    if self.tag not in transcript.getTagNames():
+                        if self.defaultValue is None:
+                            raise Exception("Tag %s undefined in transcript %s" % (self.tag, transcript))
+                        value = self.defaultValue
+                    else:
+                        value = float(transcript.getTagValue(self.tag))
+                    self.sumsPerStrand[strand][transcript.getChromosome()][bin] += value
+                    self.valuesPerStrand[strand][transcript.getChromosome()][bin].append(value)
+            progress.inc()
+        progress.done()
+
+    def aggregateData(self):
+        if self.operation == "sum":
+            self.computeSumData()
+        elif self.operation == "avg":
+            self.computeAvgData()
+        elif self.operation == "med":
+            self.computeMedData()
+        elif self.operation == "min":
+            self.computeMinData()
+        elif self.operation == "max":
+            self.computeMaxData()
+        elif self.operation == "GCpercent":
+            self.computeGCPercent()
+        else:
+            self.toBePlottedPerStrand = self.binsPerStrand
+
+    def computeSumData(self):
+        self.toBePlottedPerStrand = self.sumsPerStrand
+
+    def computeAvgData(self):
+        for strand in self.strands:
+            for chromosome in self.binsPerStrand[strand]:
+                for bin in self.binsPerStrand[strand][chromosome]:
+                    if self.binsPerStrand[strand][chromosome][bin] != 0:
+                        self.toBePlottedPerStrand[strand][chromosome][bin] = float(self.sumsPerStrand[strand][chromosome][bin]) / self.binsPerStrand[strand][chromosome][bin]
+
+    def computeMedData(self):
+        for strand in self.strands:
+            for chromosome in self.binsPerStrand[strand]:
+                for bin in self.binsPerStrand[strand][chromosome]:
+                    if self.valuesPerStrand[strand][chromosome][bin]:
+                        self.valuesPerStrand[strand][chromosome][bin].sort()
+                        size = len(self.valuesPerStrand[strand][chromosome][bin])
+                        if size % 2 == 1:
+                            self.toBePlottedPerStrand[strand][chromosome][bin] = self.valuesPerStrand[strand][chromosome][bin][(size - 1) / 2]
+                        else:
+                            self.toBePlottedPerStrand[strand][chromosome][bin] = (self.valuesPerStrand[strand][chromosome][bin][size / 2 - 1] + self.valuesPerStrand[strand][chromosome][bin][size / 2]) / 2.0
+
+    def computeMinData(self):
+        for strand in self.strands:
+            for chromosome in self.binsPerStrand[strand]:
+                for bin in self.binsPerStrand[strand][chromosome]:
+                    if self.valuesPerStrand[strand][chromosome][bin]:
+                        self.toBePlottedPerStrand[strand][chromosome][bin] = min(self.valuesPerStrand[strand][chromosome][bin])
+
+    def computeMaxData(self):
+        for strand in self.strands:
+            for chromosome in self.binsPerStrand[strand]:
+                for bin in self.binsPerStrand[strand][chromosome]:
+                    if self.valuesPerStrand[strand][chromosome][bin]:
+                        self.toBePlottedPerStrand[strand][chromosome][bin] = max(self.valuesPerStrand[strand][chromosome][bin])
+                        
+    def computeGCPercent(self):
+        for strand in self.strands:
+            for chromosome in self.binsPerStrand[strand]:
+                for bin in self.binsPerStrand[strand][chromosome]:
+                    if self.valuesPerStrand[strand][chromosome][bin]:
+                        subSequence = self.valuesPerStrand[strand][chromosome][bin]
+                        NPercent = 100 * (subSequence.countNt("N") / float(subSequence.getSize()))
+                        if NPercent >= 50:
+                            currentGCpercent = "NA"
+                        else:
+                            currentGCpercent = subSequence.getGCpercentageInSequenceWithoutCountNInLength()
+                        
+                        self.toBePlottedPerStrand[strand][chromosome][bin] = currentGCpercent
+        #TODO: see if a map method could be used for the various "compute" methods 
+        #return currentGCpercent, NPercent
+        
+    def plotData(self):
+        if self.plot != None:
+            for strand in self.strands:
+                adjunct = ""
+                if strand != 0:
+                    adjunct = "Strand%d" % (strand)
+                for chromosome in self.toBePlottedPerStrand[strand]:
+                    if len(self.toBePlottedPerStrand[strand][chromosome].keys()) > 0:
+                        plotter = RPlotter(self.plot, self.verbosity)
+                        plotter.setFill(0)
+                        plotter.addLine(self.toBePlottedPerStrand[strand][chromosome], chromosome)
+                        plotter.plot()
+
+    def writeExcel(self):
+        if self.excel != None:
+            excelFile = open(self.excel, "w")
+            for strand in self.strands:
+                maxBin = max([max(self.toBePlottedPerStrand[strand][chromosome].keys()) for chromosome in self.binsPerStrand[strand]])
+                for bin in range(0, maxBin + 1):
+                    excelFile.write(",%d-%d" % self.getPosFromBin(bin))
+                excelFile.write("\n")
+                for chromosome in self.toBePlottedPerStrand[strand]:
+                    excelFile.write("%s" % (chromosome))
+                    for bin in self.toBePlottedPerStrand[strand][chromosome]:
+                        excelFile.write(",%f" % (self.toBePlottedPerStrand[strand][chromosome][bin]))
+                    excelFile.write("\n")
+            excelFile.close()
+
+    def printRegions(self):
+        cpt           = 1
+        tagOp         = "nb"
+        tagName       = "Elements"
+        outputTagName = "nbElements"
+        if self.operation != None:
+            tagOp = self.operation.lower()
+        if self.tag != None:
+            tagName = self.tag.title()
+        if self.outputTagName != None:
+            outputTagName = self.outputTagName
+            
+     
+        #writer = Gff3Writer(self.outputFileName, self.verbosity)
+        
+        for strand in self.strands:
+            for chromosome in self.toBePlottedPerStrand[strand]:
+                for bin in self.toBePlottedPerStrand[strand][chromosome]:
+                    transcript = Transcript()
+                    transcript.setName("region%d" % cpt)
+                    transcript.setChromosome(chromosome)
+                    transcript.setStart(self.getPosFromBin(bin)[0])
+                    transcript.setEnd(self.getPosFromBin(bin)[1])
+                    transcript.setDirection(1 if strand == 0 else strand)
+                    transcript.setTagValue(outputTagName, self.binsPerStrand[strand][chromosome][bin])
+                    transcript.setTagValue("%s%s" % (tagOp, tagName), str(self.toBePlottedPerStrand[strand][chromosome][bin]))
+                    self.writer.addTranscript(transcript)
+                    cpt += 1
+        self.writer.close()
+
+    def run(self):
+        self.checkOptions()
+        self.getChromosomeSizes()
+        self.initializeBins()
+        self.setBins()
+        self.aggregateData()
+        if self.excel:
+            self.writeExcel()
+        if self.plot:
+            self.plotData()
+        self.printRegions()
+
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Clusterize by Sliding Windows v1.0.1: Produces a GFF3 file that clusters a list of transcripts using a sliding window. [Category: Sliding Windows]"
+
+    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", "--inputFormat", dest="inputFormat",    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 transcript format given by -u]")
+    parser.add_option("-u", "--outputFormat", dest="outputFormat",  action="store",     default="gff",  type="string", help="format of the output file [format: transcript file format]")
+    parser.add_option("-s", "--size",        dest="size",           action="store",                     type="int",    help="size of the regions [compulsory] [format: int]")
+    parser.add_option("-e", "--overlap",     dest="overlap",        action="store",                     type="int",    help="overlap between two consecutive regions [compulsory] [format: int]")
+    parser.add_option("-m", "--normalize",   dest="normalize",      action="store_true", default=False,                help="normalize the number of reads per cluster by the number of mappings per read [format: bool] [default: false]")
+    parser.add_option("-g", "--tag",         dest="tag",            action="store",      default=None,  type="string", help="use a given tag as input (instead of summing number of features) [format: string]")    
+    parser.add_option("-r", "--operation",   dest="operation",      action="store",      default=None,  type="string", help="combine tag value with given operation [format: choice (sum, avg, med, min, max)]")
+    parser.add_option("-d", "--defaultValue",dest="defaultValue",   action="store",                     type="float",    help="default value for input tag [format: float]")
+    parser.add_option("-w", "--write",       dest="writeTag",       action="store",      default=None,  type="string", help="print the result in the given tag (default usually is 'nbElements') [format: string]")    
+    parser.add_option("-2", "--strands",     dest="strands",        action="store_true", default=False,                help="consider the two strands separately [format: bool] [default: false]")
+    parser.add_option("-p", "--plot",        dest="plot",           action="store",      default=None,  type="string", help="plot regions to the given file [format: output file in PNG format]")
+    parser.add_option("-x", "--excel",       dest="excel",          action="store",      default=None,  type="string", help="write an Excel file to the given file [format: output file in Excel format]")
+    parser.add_option("-v", "--verbosity",   dest="verbosity",      action="store",      default=1,     type="int",    help="trace level [format: int] [default: 1]")
+    (options, args) = parser.parse_args()
+
+    cbsw = ClusterizeBySlidingWindows(options.verbosity)
+    cbsw.setInputFile(options.inputFileName, options.inputFormat)
+    cbsw.setOutputFileName(options.outputFileName, options.outputFormat)
+    cbsw.setWindowSize(options.size)
+    cbsw.setWindowOverlap(options.overlap)
+    cbsw.setTag(options.tag)
+    cbsw.setDefaultValue(options.defaultValue)
+    cbsw.setOperation(options.operation)
+    cbsw.setOutputTag(options.writeTag)
+    cbsw.setBothStrands(options.strands)
+    cbsw.setPlot(options.plot)
+    cbsw.setExcel(options.excel)
+    cbsw.run()