--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/RestrictFromCoverage.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,224 @@
+#! /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, struct, time, random
+from optparse import OptionParser
+from commons.core.parsing.ParserChooser import ParserChooser
+from commons.core.writer.Gff3Writer import Gff3Writer
+from SMART.Java.Python.structure.Transcript import Transcript
+from SMART.Java.Python.structure.Interval import Interval
+from SMART.Java.Python.ncList.NCList import NCList
+from SMART.Java.Python.ncList.NCListCursor import NCListCursor
+from SMART.Java.Python.ncList.NCListFilePickle import NCListFilePickle, NCListFileUnpickle
+from SMART.Java.Python.ncList.FileSorter import FileSorter
+from SMART.Java.Python.misc.Progress import Progress
+from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
+from SMART.Java.Python.misc import Utils
+try:
+    import cPickle as pickle
+except:
+    import pickle
+
+REFERENCE = 0
+QUERY = 1
+TYPES = (REFERENCE, QUERY)
+TYPETOSTRING = {0: "reference", 1: "query"}
+
+class RestrictFromCoverage(object):
+
+    def __init__(self, verbosity = 1):
+        self._verbosity               = verbosity
+        self._randomNumber            = random.randint(0, 100000)
+        self._nbWritten               = 0
+        self._nbLines                 = dict([type, 0]  for type in TYPES)
+        self._splittedFileNames       = dict([type, {}] for type in TYPES)
+        self._nbElementsPerChromosome = dict([type, {}] for type in TYPES)
+        self._nbElements              = dict([type, 0]  for type in TYPES)
+        
+    def __del__(self):
+        pass
+
+    def _close(self):
+        self._writer.close()
+        
+    def setInputFileName(self, fileName, format, type):
+        chooser = ParserChooser(self._verbosity)
+        chooser.findFormat(format)
+        parser = chooser.getParser(fileName)
+        sortedFileName = "%s_%d_%d_sorted.pkl" % (os.path.splitext(fileName)[0], self._randomNumber, type)
+        if self._verbosity > 2:
+            print "Preparing %s file..." % (TYPETOSTRING[type])
+        startTime = time.time()
+        fs = FileSorter(parser, self._verbosity-1)
+        fs.perChromosome(True)
+        fs.setOutputFileName(sortedFileName)
+        fs.sort()
+        self._nbLines[type]                 = fs.getNbElements()
+        self._splittedFileNames[type]       = fs.getOutputFileNames()
+        self._nbElementsPerChromosome[type] = fs.getNbElementsPerChromosome()
+        self._nbElements[type]              = fs.getNbElements()
+        endTime = time.time()
+        if self._verbosity > 2:
+            print "    ...done (%ds)" % (endTime - startTime)
+            
+    def setOutputFileName(self, outputFileName):
+        self._writer = Gff3Writer(outputFileName)
+
+    def setPercent(self, minPercent, maxPercent):
+        self._minPercent = minPercent
+        self._maxPercent = maxPercent
+
+    def setNbNucleotides(self, minNb, maxNb):
+        self._minNucleotides = minNb
+        self._maxNucleotides = maxNb
+
+    def setOverlap(self, minOverlap, maxOverlap):
+        self._minOverlap = minOverlap
+        self._maxOverlap = maxOverlap
+
+    def setStrands(self, boolean):
+        self._twoStrands = boolean
+
+    def _compareChromosome(self, chromosome):
+        firstOverlap = 0
+        parser1      = NCListFileUnpickle(self._splittedFileNames[QUERY][chromosome],     self._verbosity)
+        parser2      = NCListFileUnpickle(self._splittedFileNames[REFERENCE][chromosome], self._verbosity)
+        progress     = Progress(self._nbElementsPerChromosome[QUERY][chromosome], "Analyzing %s" % (chromosome), self._verbosity)
+        for transcript1 in parser1.getIterator():
+            firstOverlap = self._compareList(transcript1, parser2)
+            parser2.setInitAddress(firstOverlap)
+            progress.inc()
+        progress.done()
+
+    def _compareList(self, transcript1, parser2):
+        values = []
+        for exon in transcript1.getExons():
+            values.append([0.0] * exon.getSize())
+        firstOverlap = None
+        for transcript2 in parser2.getIterator():
+            address       = parser2.getCurrentTranscriptAddress()
+            nbElements    = float(transcript2.getTagValue("nbElements"))    if "nbElements"    in transcript2.getTagNames() else 1.0
+            nbOccurrences = float(transcript2.getTagValue("nbOccurrences")) if "nbOccurrences" in transcript2.getTagNames() else 1.0
+            nbElements   /= nbOccurrences
+            if transcript2.getStart() > transcript1.getEnd():
+                if firstOverlap == None:
+                    firstOverlap = address
+                if self._checkValues(values):
+                    self._printTranscript(transcript1)
+                return firstOverlap
+            elif transcript1.overlapWith(transcript2):
+                if firstOverlap == None:
+                    firstOverlap = address
+                values = self._compareTranscript(transcript1, transcript2, values, nbElements)
+        if self._checkValues(values):
+            self._printTranscript(transcript1)
+            return firstOverlap
+    
+    def _compareTranscript(self, transcript1, transcript2, values, nbElements):
+        if not transcript1.overlapWith(transcript2) or ((self._twoStrands) and transcript1.getDirection() != transcript2.getDirection()):
+            return values
+        for id1, exon1 in enumerate(transcript1.getExons()):
+            for exon2 in transcript2.getExons():
+                values[id1] = map(sum, zip(values[id1], self._compareExon(exon1, exon2, nbElements)))
+        return values
+        
+    def _compareExon(self, exon1, exon2, nbElements):
+        array = [0.0] * exon1.getSize()
+        if not exon1.overlapWith(exon2) or ((self._twoStrands) and exon1.getDirection() != exon2.getDirection()):
+            return array
+        for pos in range(max(exon1.getStart(), exon2.getStart()) - exon1.getStart(), min(exon1.getEnd(), exon2.getEnd()) - exon1.getStart()+1):
+            array[pos] += nbElements
+        return array
+
+    def _filter(self, value):
+        if self._minOverlap and self._maxOverlap:
+            return self._minOverlap <= value <= self._maxOverlap
+        if self._minOverlap:
+            return self._minOverlap <= value
+        if self._maxOverlap:
+            return value <= self._maxOverlap
+        return True
+
+    def _checkValues(self, values):
+        nbValues    = sum(map(len, values))
+        nbPosValues = sum(map(len, [filter(self._filter, valuePart) for valuePart in values]))
+        ratio       = float(nbPosValues) / nbValues * 100
+        if self._minNucleotides and nbPosValues < self._minNucleotides:
+            return False
+        if self._maxNucleotides and nbPosValues > self._maxNucleotides:
+            return False
+        if self._minPercent and ratio < self._minPercent:
+            return False
+        if self._maxPercent and ratio > self._maxPercent:
+            return False
+        return True
+
+    def _printTranscript(self, transcript):
+        self._writer.addTranscript(transcript)
+        self._nbWritten += 1
+
+    def run(self):
+        for chromosome in sorted(self._splittedFileNames[QUERY].keys()):
+            self._compareChromosome(chromosome)
+        self._close()
+        if self._verbosity > 0:
+            print "# queries: %d" % (self._nbElements[QUERY])
+            print "# refs:    %d" % (self._nbElements[REFERENCE])
+            print "# written: %d (%d%%)" % (self._nbWritten, 0 if self._nbElements[QUERY] == 0 else round(float(self._nbWritten) / self._nbElements[QUERY] * 100))
+        
+
+if __name__ == "__main__":
+    description = "Restrict From Coverage v1.0.0: Select the elements from the first set which have a given coverage. [Category: Data Comparison]"
+
+    parser = OptionParser(description = description)
+    parser.add_option("-i", "--input1",           dest="inputFileName1", action="store",                     type="string", help="input file 1 [compulsory] [format: file in transcript format given by -f]")
+    parser.add_option("-f", "--format1",          dest="format1",        action="store",                     type="string", help="format of file 1 [compulsory] [format: transcript file format]")
+    parser.add_option("-j", "--input2",           dest="inputFileName2", action="store",                     type="string", help="input file 2 [compulsory] [format: file in transcript format given by -g]")
+    parser.add_option("-g", "--format2",          dest="format2",        action="store",                     type="string", help="format of file 2 [compulsory] [format: transcript file format]")
+    parser.add_option("-o", "--output",           dest="output",         action="store",      default=None,  type="string", help="output file [compulsory] [format: output file in GFF3 format]")
+    parser.add_option("-n", "--minNucleotides",   dest="minNucleotides", action="store",      default=None,  type="int",    help="minimum number of nucleotides overlapping to declare an overlap [format: int]")
+    parser.add_option("-N", "--maxNucleotides",   dest="maxNucleotides", action="store",      default=None,  type="int",    help="maximum number of nucleotides overlapping to declare an overlap [format: int]")
+    parser.add_option("-p", "--minPercent",       dest="minPercent",     action="store",      default=None,  type="int",    help="minimum percentage of nucleotides overlapping to declare an overlap [format: int]")
+    parser.add_option("-P", "--maxPercent",       dest="maxPercent",     action="store",      default=None,  type="int",    help="maximum percentage of nucleotides overlapping to declare an overlap [format: int]")
+    parser.add_option("-e", "--minOverlap",       dest="minOverlap",     action="store",      default=None,  type="int",    help="minimum number of elements from 2nd file to declare an overlap [format: int]")
+    parser.add_option("-E", "--maxOverlap",       dest="maxOverlap",     action="store",      default=None,  type="int",    help="maximum number of elements from 2nd file to declare an overlap [format: int]")
+    parser.add_option("-s", "--strands",          dest="strands",        action="store_true", default=False,                help="consider the two strands separately [format: bool] [default: false]")
+    parser.add_option("-v", "--verbosity",        dest="verbosity",      action="store",      default=1,     type="int",    help="trace level [format: int]")
+    (options, args) = parser.parse_args()
+
+    rfc = RestrictFromCoverage(options.verbosity)
+    rfc.setInputFileName(options.inputFileName1, options.format1, QUERY)
+    rfc.setInputFileName(options.inputFileName2, options.format2, REFERENCE)
+    rfc.setOutputFileName(options.output)
+    rfc.setNbNucleotides(options.minNucleotides, options.maxNucleotides)
+    rfc.setPercent(options.minPercent, options.maxPercent)
+    rfc.setOverlap(options.minOverlap, options.maxOverlap)
+    rfc.setStrands(options.strands)
+    rfc.run()