--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Python/getDistribution.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,291 @@
+#! /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.
+#
+"""Get the repartition of some elements in a chromosomes"""
+
+import os
+from optparse import OptionParser
+from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+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.Progress import Progress
+from math import *
+
+def divideKeyDict(dictionary, ratio):
+    return dict([(key / ratio, dictionary[key]) for key in dictionary])
+
+
+def setTranscript(chromosome, direction, start, end, name, value):
+    transcript = Transcript()
+    transcript.setChromosome(chromosome)
+    transcript.setDirection(direction)
+    transcript.setStart(start)
+    transcript.setEnd(end)
+    transcript.setName(name)
+    transcript.setTagValue("nbElements", value)
+    return transcript
+
+
+
+if __name__ == "__main__":
+    
+    magnifyingFactor = 1000
+    
+    # parse command line
+    description = "Get Distribution v1.0.1: 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 [compulsory] [format: file in FASTA format]")
+    parser.add_option("-n", "--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("-w", "--raw",         dest="raw",               action="store_true", default=False,                      help="plot raw number of occurrences instead of density [format: bool] [default: false]")
+    parser.add_option("-x", "--csv",         dest="csv",               action="store_true", default=False,                      help="write a .csv file [format: bool]")
+    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("-g", "--gff",         dest="gff",               action="store_true", default=False,                      help="also write GFF3 file [format: bool] [default: false]")
+    parser.add_option("-H", "--height",      dest="height",            action="store",      default=None,        type="int",    help="height of the graphics [format: int] [default: 300]")
+    parser.add_option("-W", "--width",       dest="width",             action="store",      default=None,        type="int",    help="width of the graphics [format: int] [default: 1000]")
+    parser.add_option("-v", "--verbosity",   dest="verbosity",         action="store",      default=1,           type="int",    help="trace level [default: 1] [format: int]")
+    parser.add_option("-l", "--log",         dest="log",               action="store_true", default=False,                      help="write a log file [format: bool]")
+    parser.add_option("-D", "--directory",   dest="working_Dir",       action="store",      default=os.getcwd(), type="string", help="the directory to store the results [format: directory]")
+    (options, args) = parser.parse_args()
+
+    sizes = {}
+    if options.referenceFileName != None:
+        # get the sizes of the chromosomes
+        referenceHandle = open(options.referenceFileName)
+        name            = None
+        size            = 0
+        maxSize         = 0
+        for line in referenceHandle:
+            line = line.strip()
+            if line == "": continue
+            if line[0] == ">":
+                if name != None:
+                    if options.verbosity > 10:
+                        print name
+                    sizes[name] = size
+                    maxSize     = max(maxSize, size)
+                    size        = 0
+                name = line[1:]
+            else:
+                size += len(line)
+        sizes[name] = size
+        maxSize     = max(maxSize, size)
+        if options.verbosity > 1:
+            print "done"
+        start = 0
+        end   = maxSize
+    else:
+        if options.chromosome == None or options.start == None or options.end == None:
+            raise Exception("Missing chromosome or start and end positions, or reference file")
+        maxSize                   = options.end
+        sizes[options.chromosome] = options.end
+        start                     = options.start
+        end                       = options.end
+
+    
+    tmp1      = int(maxSize / float(options.nbBins))
+    tmp2      = 10 ** (len("%d" % (tmp1))-2)
+    sliceSize = int((tmp1 / tmp2) * tmp2)
+    
+    bins      = dict()
+    binsPlus  = dict()
+    binsMinus = dict()
+    for chromosome in sizes:
+        bins[chromosome]      = dict([(i * sliceSize + 1, 0) for i in range(start / sliceSize, sizes[chromosome] / sliceSize + 1)])
+        binsPlus[chromosome]  = dict([(i * sliceSize + 1, 0) for i in range(start / sliceSize, sizes[chromosome] / sliceSize + 1)])
+        binsMinus[chromosome] = dict([(i * sliceSize + 1, 0) for i in range(start / sliceSize, sizes[chromosome] / sliceSize + 1)])
+
+    parser   = TranscriptContainer(options.inputFileName, options.format, options.verbosity)
+    progress = Progress(parser.getNbTranscripts(), "Parsing %s" % (options.inputFileName), options.verbosity)
+    maxSlice = 0
+    # count the number of reads
+    for transcript in parser.getIterator():
+        if options.chromosome == None or (transcript.getChromosome() == options.chromosome and transcript.getStart() >= start and transcript.getStart() <= end):
+            if transcript.getDirection() == 1:
+                binsPlus[transcript.getChromosome()][(transcript.getStart() / sliceSize) * sliceSize + 1] += 1
+            else:
+                binsMinus[transcript.getChromosome()][(transcript.getStart() / sliceSize) * sliceSize + 1] += 1
+            bins[transcript.getChromosome()][(transcript.getStart() / sliceSize) * sliceSize + 1] += 1
+            maxSlice = max(maxSlice, transcript.getStart() / sliceSize)
+        progress.inc()
+    progress.done()
+
+    # compute densities
+    densityPlus = dict()
+    for chromosome in bins:
+        densityPlus[chromosome] = dict([(bin, 0) for bin in binsPlus[chromosome]])
+        for bin in binsPlus[chromosome]:
+            densityPlus[chromosome][bin] = float(binsPlus[chromosome][bin]) / sliceSize * magnifyingFactor
+        # correct densities for first and last bins
+        if start % sliceSize != 0:
+            densityPlus[chromosome][(start / sliceSize) * sliceSize + 1] = float(binsPlus[chromosome][(start / sliceSize) * sliceSize + 1]) / (sliceSize - (start % sliceSize)) * magnifyingFactor
+        if sizes[chromosome] % sliceSize != 0:
+            densityPlus[chromosome][(sizes[chromosome] / sliceSize) * sliceSize + 1] = float(binsPlus[chromosome][(sizes[chromosome] / sliceSize) * sliceSize + 1]) / (sizes[chromosome] % sliceSize) * magnifyingFactor
+    densityMinus = dict()
+    for chromosome in binsMinus:
+        densityMinus[chromosome] = dict([(bin, 0) for bin in binsMinus[chromosome]])
+        for bin in binsMinus[chromosome]:
+            densityMinus[chromosome][bin] = float(binsMinus[chromosome][bin]) / sliceSize * magnifyingFactor
+        # correct densities for first and last bins
+        if start % sliceSize != 0:
+            densityMinus[chromosome][(start / sliceSize) * sliceSize + 1] = float(binsMinus[chromosome][(start / sliceSize) * sliceSize + 1]) / (sliceSize - (start % sliceSize)) * magnifyingFactor
+        if sizes[chromosome] % sliceSize != 0:
+            densityMinus[chromosome][(sizes[chromosome] / sliceSize) * sliceSize + 1] = float(binsMinus[chromosome][(sizes[chromosome] / sliceSize) * sliceSize + 1]) / (sizes[chromosome] % sliceSize) * magnifyingFactor
+    density = dict()
+    for chromosome in bins:
+        density[chromosome] = dict([(bin, 0) for bin in bins[chromosome]])
+        for bin in bins[chromosome]:
+            density[chromosome][bin] = densityPlus[chromosome][bin] + densityMinus[chromosome][bin]
+
+    for chromosome in densityMinus:
+        for bin in densityMinus[chromosome]:
+            densityMinus[chromosome][bin] *= -1
+        for bin in binsMinus[chromosome]:
+            binsMinus[chromosome][bin] *= -1
+
+    for chromosome in density:
+        maxX = max(bins[chromosome].keys())
+        if maxX <= 1000:
+            unit  = "nt."
+            ratio = 1.0
+        elif maxX <= 1000000:
+            unit  = "kb"
+            ratio = 1000.0
+        else:
+            unit  = "Mb"
+            ratio = 1000000.0
+        outputFileName = "%s_%s" % (options.outputFileName, chromosome)
+        if options.start != None and options.end != None:
+            outputFileName += ":%d-%d" % (options.start, options.end)
+        outputFileName += ".png"
+        plotter = RPlotter(outputFileName, options.verbosity)
+        plotter.setXLabel("Position on %s (in %s)" % (chromosome.replace("_", " "), unit))
+        plotter.setYLabel("# reads")
+        if options.bothStrands:
+            plotter.setImageSize(1000, 300)
+        else:
+            plotter.setImageSize(1000, 200)
+        if options.height != None:
+            plotter.setHeight(options.height)
+        if options.width != None:
+            plotter.setWidth(options.width)
+        if options.yMax != None:
+            plotter.setMinimumY(options.yMin)
+        if options.yMax != None:
+            plotter.setMaximumY(options.yMax)
+        if options.bothStrands :
+            if options.raw:
+                plotter.addLine(divideKeyDict(binsPlus[chromosome], ratio))
+            else:
+                plotter.addLine(divideKeyDict(densityPlus[chromosome], ratio))
+            if options.raw:
+                plotter.addLine(divideKeyDict(binsMinus[chromosome], ratio))
+            else:
+                plotter.addLine(divideKeyDict(densityMinus[chromosome], ratio))
+        else:
+            if options.raw:
+                plotter.addLine(divideKeyDict(bins[chromosome], ratio))
+            else:
+                plotter.addLine(divideKeyDict(density[chromosome], ratio))
+        plotter.plot()
+        
+    if options.csv:
+        outputFileName = "%s" % (options.outputFileName)
+        if options.chromosome != None:
+            outputFileName += "_%s" % (options.chromosome)
+        if options.start != None and options.end != None:
+            outputFileName += ":%d-%d" % (options.start, options.end)
+        outputFileName += ".csv"
+        csvHandle = open(outputFileName, "w")
+        for slice in range(start / sliceSize, maxSlice + 1):
+            csvHandle.write(";%d-%d" % (slice * sliceSize + 1, (slice+1) * sliceSize))
+        csvHandle.write("\n")
+        if options.bothStrands:
+            for chromosome in densityPlus:
+                if len(densityPlus[chromosome]) > 0:
+                    csvHandle.write("%s [+]" % (chromosome))
+                    for slice in sorted(densityPlus[chromosome].keys()):
+                        csvHandle.write(";%.2f" % (densityPlus[chromosome][slice]))
+                    csvHandle.write("\n")            
+                if len(densityMinus[chromosome]) > 0:
+                    csvHandle.write("%s [-]" % (chromosome))
+                    for slice in sorted(densityPlus[chromosome].keys()):
+                        csvHandle.write(";%.2f" % (-densityMinus[chromosome][slice]))
+                    csvHandle.write("\n")            
+        else:
+            for chromosome in density:
+                if len(density[chromosome]) > 0:
+                    csvHandle.write(chromosome)
+                    for slice in sorted(density[chromosome].keys()):
+                        csvHandle.write(";%.2f" % (density[chromosome][slice]))
+                    csvHandle.write("\n")
+        csvHandle.close()
+             
+    if options.gff:
+        chromosome = "" if options.chromosome == None                         else options.chromosome.capitalize()
+        start      = "" if options.start      == None                         else "%d" % (options.start)
+        end        = "" if options.end        == None                         else "%d" % (options.end)
+        link1      = "" if options.start      == None and options.end == None else ":"
+        link2      = "" if options.start      == None and options.end == None else "-"
+        writer     = Gff3Writer("%s%s%s%s%s.gff3" % (options.outputFileName, link1, start, link2, end), options.verbosity)
+        cpt = 1
+        if options.raw:
+            valuesPlus  = binsPlus
+            valuesMinus = binsMinus
+            values      = bins
+        else:
+            valuesPlus  = densityPlus
+            valuesMinus = densityMinus
+            values      = density
+        if options.bothStrands:
+            for chromosome in values:
+                for slice in valuesPlus[chromosome]:
+                    writer.addTranscript(setTranscript(chromosome, 1, slice, slice + sliceSize, "region%d" % (cpt), valuesPlus[chromosome][slice]))
+                    cpt += 1
+                for slice in valuesMinus[chromosome]:
+                    writer.addTranscript(setTranscript(chromosome, -1, slice, slice + sliceSize, "region%d" % (cpt), - valuesMinus[chromosome][slice]))
+                    cpt += 1
+        else:
+            for chromosome in values:
+                for slice in values[chromosome]:
+                    writer.addTranscript(setTranscript(chromosome, 1, slice, slice + sliceSize, "region%d" % (cpt), values[chromosome][slice]))
+                    cpt += 1
+        writer.write()
+
+