--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/plotGenomeCoverage.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,132 @@
+#! /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.
+#
+
+from optparse import OptionParser
+from commons.core.parsing.FastaParser import FastaParser
+from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+from SMART.Java.Python.misc.Progress import Progress
+from SMART.Java.Python.misc.RPlotter import RPlotter
+from SMART.Java.Python.misc.Utils import *
+
+
+class GetGenomeCoverage(object):
+
+    def __init__(self, verbosity = 1):
+        self.verbosity       = verbosity
+        self.inputContainer  = None
+        self.referenceParser = None
+        self.outputFileName  = None
+        self.genomeSize      = None
+        self.coverage        = {}
+        self.distribution    = {}
+
+
+    def setInputFile(self, fileName, format):
+        self.inputContainer = TranscriptContainer(fileName, format, self.verbosity)
+
+
+    def setOutputFile(self, fileName):
+        self.outputFileName = fileName
+
+
+    def setReference(self, fileName):
+        self.referenceParser = FastaParser(fileName, self.verbosity)
+
+
+    def getReferenceSizes(self):
+        self.genomeSize = 0
+        for chromosome in self.referenceParser.getRegions():
+            self.genomeSize += self.referenceParser.getSizeOfRegion(chromosome)
+    
+
+    def getCoverage(self):
+        progress = Progress(self.inputContainer.getNbTranscripts(), "Reading reads", self.verbosity)
+        for transcript in self.inputContainer.getIterator():
+            chromosome = transcript.getChromosome()
+            if chromosome not in self.coverage:
+                self.coverage[chromosome] = {}
+            for exon in transcript.getExons():
+                for pos in range(exon.getStart(), exon.getEnd() + 1):
+                    if pos not in self.coverage[chromosome]:
+                        self.coverage[chromosome][pos] = 1
+                    else:
+                        self.coverage[chromosome][pos] += 1
+            progress.inc()
+        progress.done()
+
+    
+    def getDistribution(self):
+        nbNucleotides = sum([len(self.coverage[chromosome].keys()) for chromosome in self.coverage])
+        progress      = Progress(nbNucleotides, "Building distribution", self.verbosity)
+        for chromosome in self.coverage:
+            for num in self.coverage[chromosome].values():
+                if num not in self.distribution:
+                    self.distribution[num] = 1
+                else:
+                    self.distribution[num] += 1
+                progress.inc()
+        progress.done()
+        self.distribution[0] = self.genomeSize - nbNucleotides
+                
+
+    def plotDistribution(self):
+        plotter = RPlotter(self.outputFileName, self.verbosity)
+        plotter.setFill(0)
+        plotter.addLine(self.distribution)
+        plotter.plot()
+        print "min/avg/med/max reads per base: %d/%.2f/%.1f/%d" % getMinAvgMedMax(self.distribution)
+
+
+    def run(self):
+        self.getReferenceSizes()
+        self.getCoverage()
+        self.getDistribution()
+        self.plotDistribution()
+        
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Plot Genome Coverage v1.0.1: Get the coverage of a genome. [Category: Personal]"
+
+    parser = OptionParser(description = description)
+    parser.add_option("-i", "--input",     dest="inputFileName",  action="store",               type="string", help="reads file [compulsory] [format: file in transcript format given by -f]")
+    parser.add_option("-f", "--format",    dest="format",         action="store",               type="string", help="format of file [compulsory] [format: transcript file format]")
+    parser.add_option("-r", "--reference", dest="reference",      action="store",               type="string", help="sequences file [compulsory] [format: file in FASTA format]")
+    parser.add_option("-o", "--output",    dest="outputFileName", action="store",               type="string", help="output file [compulsory] [format: output file in PNG format]")
+    parser.add_option("-v", "--verbosity", dest="verbosity",      action="store", default=1,    type="int",    help="trace level [format: int]")
+    (options, args) = parser.parse_args()
+
+    getGenomeCoverage = GetGenomeCoverage(options.verbosity)
+    getGenomeCoverage.setInputFile(options.inputFileName, options.format)
+    getGenomeCoverage.setOutputFile(options.outputFileName)
+    getGenomeCoverage.setReference(options.reference)
+    getGenomeCoverage.run()