--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/ComputeCoverage.py	Tue Apr 30 15:02:29 2013 -0400
@@ -0,0 +1,142 @@
+#! /usr/bin/env python
+#
+# Copyright INRA-URGI 2009-2011
+# 
+# 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, random
+from optparse import OptionParser, OptionGroup
+from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+from SMART.Java.Python.misc.Progress import Progress
+from commons.core.writer.Gff3Writer import Gff3Writer
+
+
+class CoverageComputer(object):
+
+	def __init__(self, verbosity = 0):
+		self.verbosity	     = verbosity
+		self.queryReader	 = None
+		self.referenceReader = None
+		self.outputWriter	 = None
+		self.introns		 = False
+		self.nbNucleotides   = 0
+		self.nbCovered	     = 0
+
+	def setInputQueryFile(self, fileName, format):
+		self.queryReader = TranscriptContainer(fileName, format, self.verbosity-1)
+
+	def setInputReferenceFile(self, fileName, format):
+		self.referenceReader = TranscriptContainer(fileName, format, self.verbosity-1)
+
+	def includeIntrons(self, boolean):
+		self.introns = boolean
+
+	def setOutputFileName(self, fileName, title="S-MART", feature="transcript", featurePart="exon"):
+		self.outputWriter = Gff3Writer(fileName, self.verbosity-1)
+		self.outputWriter.setTitle(title)
+		self.outputWriter.setFeature(feature)
+		self.outputWriter.setFeaturePart(featurePart)
+
+	def readReference(self):
+		self.coveredRegions = {}
+		progress = Progress(self.referenceReader.getNbTranscripts(), "Reading reference file", self.verbosity-1)
+		for transcript in self.referenceReader.getIterator():
+			chromosome = transcript.getChromosome()
+			if chromosome not in self.coveredRegions:
+				self.coveredRegions[chromosome] = {}
+			if self.introns:
+				transcript.removeExons()
+			for exon in transcript.getExons():
+				for position in range(exon.getStart(), exon.getEnd()+1):
+					self.coveredRegions[chromosome][position] = 1
+			progress.inc()
+		progress.done()
+
+	def readQuery(self):
+		progress = Progress(self.queryReader.getNbTranscripts(), "Reading query file", self.verbosity-1)
+		for transcript in self.queryReader.getIterator():
+			progress.inc()
+			chromosome = transcript.getChromosome()
+			if chromosome not in self.coveredRegions:
+				continue
+			if self.introns:
+				transcript.removeExons()
+			for exon in transcript.getExons():
+				for position in range(exon.getStart(), exon.getEnd()+1):
+					self.nbNucleotides += 1
+					self.nbCovered     += self.coveredRegions[chromosome].get(position, 0)
+		progress.done()
+
+	def write(self):
+		progress = Progress(self.queryReader.getNbTranscripts(), "Writing output file", self.verbosity-1)
+		for transcript in self.queryReader.getIterator():
+			chromosome = transcript.getChromosome()
+			if self.introns:
+				transcript.removeExons()
+			size	 = transcript.getSize()
+			coverage = 0
+			for exon in transcript.getExons():
+				for position in range(exon.getStart(), exon.getEnd()+1):
+					coverage += self.coveredRegions[chromosome].get(position, 0)
+			transcript.setTagValue("coverage", 0 if size == 0 else float(coverage) / size * 100)
+			self.outputWriter.addTranscript(transcript)
+			progress.inc()
+		progress.done()
+
+	def sumUp(self):
+		print "%d nucleotides in query, %d (%.f%%) covered" % (self.nbNucleotides, self.nbCovered, 0 if self.nbNucleotides == 0 else float(self.nbCovered) / self.nbNucleotides * 100)
+
+	def run(self):
+		self.readReference()
+		self.readQuery()
+		if self.outputWriter != None:
+			self.write()
+		self.sumUp()
+
+
+if __name__ == "__main__":
+	
+	# parse command line
+	description = "Compute Coverage v1.0.1: Compute the coverage of a set with respect to another set. [Category: Personal]"
+
+	parser = OptionParser(description = description)
+	parser.add_option("-i", "--input1",	   dest="inputFileName1", action="store",                     type="string", help="input query file [compulsory] [format: file in transcript format given by -f]")
+	parser.add_option("-f", "--format1",   dest="format1",        action="store",                     type="string", help="format of the first file [compulsory] [format: transcript file format]")
+	parser.add_option("-j", "--input2",	   dest="inputFileName2", action="store",                     type="string", help="input reference file [compulsory] [format: file in transcript format given by -f]")
+	parser.add_option("-g", "--format2",   dest="format2",        action="store",                     type="string", help="format of the second file [compulsory] [format: transcript file format]")
+	parser.add_option("-t", "--introns",   dest="introns",        action="store_true", default=False,                help="also include introns [format: boolean] [default: false]")
+	parser.add_option("-o", "--output",	   dest="outputFileName", action="store",	   default=None,  type="string", help="output file [format: output file in GFF3 format]")
+	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()
+
+	computer = CoverageComputer(options.verbosity)
+	computer.setInputQueryFile(options.inputFileName1, options.format1)
+	computer.setInputReferenceFile(options.inputFileName2, options.format2)
+	computer.includeIntrons(options.introns)
+	computer.setOutputFileName(options.outputFileName)
+	computer.run()
+