--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/CountLoci.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,230 @@
+#! /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, os.path, random
+from optparse import OptionParser
+from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+from commons.core.parsing.GffParser import GffParser
+from commons.core.writer.Gff3Writer import Gff3Writer
+from commons.core.writer.TranscriptWriter import TranscriptWriter
+from SMART.Java.Python.misc.Progress import Progress
+from SMART.Java.Python.misc.RPlotter import RPlotter
+from SMART.Java.Python.cleanGff import CleanGff
+from SMART.Java.Python.CompareOverlappingSmallRef import CompareOverlappingSmallRef
+from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator
+from SMART.Java.Python.GetUpDownStream import GetUpDownStream
+
+REFERENCE = 0
+QUERY = 1
+
+class CountLoci(object):
+    
+    def __init__(self, verbosity = 1):
+        self.verbosity = verbosity
+        self.tmpFileNames = []
+
+    def __del__(self):
+        for fileName in self.tmpFileNames:
+            if os.path.exists(fileName):
+                os.remove(fileName)
+    
+    def setInputFile(self, fileName, format):
+        self.inputFileName = fileName
+        self.inputFormat = format
+        self.parser = TranscriptContainer(fileName, format, self.verbosity-1)
+        if self.verbosity > 0:
+            print "%d elements in input" % (self.parser.getNbTranscripts())
+
+    def setReference(self, fileName):
+        self.referenceFileName = fileName
+
+    def setDistance(self, distance):
+        self.distance = distance
+
+    def setOutputFileName(self, fileName):
+        self.outputFileName = fileName
+        self.writer         = Gff3Writer(fileName, self.verbosity-1)
+        self.outputBase     = "%s_%d_" % (os.path.splitext(fileName)[0], random.randint(0, 10000))
+
+    def _writeTmpRef(self, tags, outputFileName):
+        cleanGff = CleanGff(self.verbosity-1)
+        cleanGff.setInputFileName(self.referenceFileName)
+        cleanGff.setOutputFileName(outputFileName)
+        cleanGff.setAcceptedTypes(tags)
+        cleanGff.run()
+
+    def _getReferenceFiles(self):
+        self.referenceFiles = {"CDS":                       "%scds.gff3"      % (self.outputBase), \
+                               "five_prime_UTR":            "%sfive.gff3"     % (self.outputBase), \
+                               "three_prime_UTR":           "%sthree.gff3"    % (self.outputBase), \
+                               "mRNA":                      "%smrna.gff3"     % (self.outputBase), \
+                               "ncRNA":                     "%sncRNA.gff3"    % (self.outputBase), \
+                               "transposable_element_gene": "%sTE.gff3"       % (self.outputBase), \
+                               "vic":                       "%svicinity.gff3" % (self.outputBase)}
+        self.tmpFileNames.extend(self.referenceFiles.values())
+        for tag, fileName in self.referenceFiles.iteritems():
+            if tag == "ncRNA":
+                self._writeTmpRef(["miRNA", "ncRNA", "rRNA", "snoRNA", "snRNA", "tRNA"], fileName)
+            elif tag == "vic":
+                continue
+            else:
+                self._writeTmpRef([tag], fileName)
+
+    def _compare(self, queryFileName, queryFormat, referenceFileName, referenceFormat, outputFileName, exclusion = False):
+        co = CompareOverlappingSmallRef(self.verbosity-1)
+        co.setQueryFile(queryFileName, queryFormat)
+        co.setReferenceFile(referenceFileName, referenceFormat)
+        co.setOutputFile(outputFileName)
+        if exclusion:
+            co.setInvert(True)
+        co.run()
+        return co.nbWritten
+
+    def _copy(self, inputFile, tag):
+        parser = GffParser(inputFile, self.verbosity-1)
+        for transcript in parser.getIterator():
+            transcript.setTagValue("locus", tag)
+            self.writer.addTranscript(transcript)
+        
+    def _getCds(self):
+        outputFileName   = "%sin_cds.gff3" % (self.outputBase)
+        outputNoFileName = "%sin_nocds.gff3" % (self.outputBase)
+        self.tmpFileNames.extend([outputFileName, outputNoFileName])
+        nbOverlaps = self._compare(self.inputFileName, self.inputFormat, self.referenceFiles["CDS"], "gff3", outputFileName)
+        self._compare(self.inputFileName, self.inputFormat, self.referenceFiles["CDS"], "gff3", outputNoFileName, True)
+        self._copy(outputFileName, "CDS")
+        if self.verbosity > 0:
+            print "%d overlaps in CDS" % (nbOverlaps)
+        return outputNoFileName
+
+    def _getFivePrime(self, inputFileName):
+        outputFileName   = "%sin_five.gff3" % (self.outputBase)
+        outputNoFileName = "%sin_nofive.gff3" % (self.outputBase)
+        self.tmpFileNames.extend([outputFileName, outputNoFileName])
+        nbOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["five_prime_UTR"], "gff3", outputFileName)
+        self._compare(inputFileName, "gff3", self.referenceFiles["five_prime_UTR"], "gff3", outputNoFileName, True)
+        self._copy(outputFileName, "five_prime_UTR")
+        if self.verbosity > 0:
+            print "%d overlaps in 5' UTR" % (nbOverlaps)
+        return outputNoFileName
+    
+    def _getThreePrime(self, inputFileName):
+        outputFileName   = "%sin_three.gff3" % (self.outputBase)
+        outputNoFileName = "%sin_nothree.gff3" % (self.outputBase)
+        self.tmpFileNames.extend([outputFileName, outputNoFileName])
+        nbOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["three_prime_UTR"], "gff3", outputFileName)
+        self._compare(inputFileName, "gff3", self.referenceFiles["three_prime_UTR"], "gff3", outputNoFileName, True)
+        self._copy(outputFileName, "three_prime_UTR")
+        if self.verbosity > 0:
+            print "%d overlaps in 3' UTR" % (nbOverlaps)
+        return outputNoFileName
+    
+    def _getNcRna(self, inputFileName):
+        outputFileName   = "%sin_ncRna.gff3" % (self.outputBase)
+        outputNoFileName = "%sin_noNcRna.gff3" % (self.outputBase)
+        self.tmpFileNames.extend([outputFileName, outputNoFileName])
+        nbOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["ncRNA"], "gff3", outputFileName)
+        self._compare(inputFileName, "gff3", self.referenceFiles["ncRNA"], "gff3", outputNoFileName, True)
+        self._copy(outputFileName, "ncRNA")
+        if self.verbosity > 0:
+            print "%d overlaps in ncRNA" % (nbOverlaps)
+        return outputNoFileName
+    
+    def _getTe(self, inputFileName):
+        outputFileName   = "%sin_te.gff3" % (self.outputBase)
+        outputNoFileName = "%sin_noTe.gff3" % (self.outputBase)
+        self.tmpFileNames.extend([outputFileName, outputNoFileName])
+        nbOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["transposable_element_gene"], "gff3", outputFileName)
+        self._compare(inputFileName, "gff3", self.referenceFiles["transposable_element_gene"], "gff3", outputNoFileName, True)
+        self._copy(outputFileName, "TE")
+        if self.verbosity > 0:
+            print "%d overlaps in TE" % (nbOverlaps)
+        return outputNoFileName
+    
+    def _getIntron(self, inputFileName):
+        outputFileName   = "%sin_intron.gff3" % (self.outputBase)
+        outputNoFileName = "%sin_nointron.gff3" % (self.outputBase)
+        self.tmpFileNames.extend([outputFileName, outputNoFileName])
+        nbOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["mRNA"], "gff3", outputFileName)
+        self._compare(inputFileName, "gff3", self.referenceFiles["mRNA"], "gff3", outputNoFileName, True)
+        self._copy(outputFileName, "intron")
+        if self.verbosity > 0:
+            print "%d overlaps in introns" % (nbOverlaps)
+        return outputNoFileName
+    
+    def _getVicinity(self, inputFileName):
+        guds = GetUpDownStream(self.verbosity-1)
+        guds.setInputFile(self.referenceFiles["mRNA"], "gff3")
+        guds.setOutputFile(self.referenceFiles["vic"])
+        guds.setDistances(self.distance, self.distance)
+        guds.run()
+        outputFileName = "%sout_vicinity.gff3" % (self.outputBase)
+        outputNoFileName = "%sout_novicinity.gff3" % (self.outputBase)
+        self.tmpFileNames.extend([outputFileName, outputNoFileName])
+        nbOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["vic"], "gff3", outputFileName)
+        nbNoOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["vic"], "gff3", outputNoFileName, True)
+        self._copy(outputFileName, "vicinity")
+        self._copy(outputNoFileName, "intergenic")
+        if self.verbosity > 0:
+            print "%d overlaps in vicinity" % (nbOverlaps)
+            print "%d elsewhere" % (nbNoOverlaps)
+    
+    def run(self):
+        self._getReferenceFiles()
+        outputFileName = self._getCds()
+        outputFileName = self._getFivePrime(outputFileName)
+        outputFileName = self._getThreePrime(outputFileName)
+        outputFileName = self._getNcRna(outputFileName)
+        outputFileName = self._getTe(outputFileName)
+        outputFileName = self._getIntron(outputFileName)
+        self._getVicinity(outputFileName)
+
+
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Count Loci v1.0.0: Count input elements with respect to CDS, 5' UTR, 3' UTR, intron, downstream, upstream. [Category: Personal]"
+
+    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     [compulsory] [format: transcript file format]")
+    parser.add_option("-r", "--reference", dest="reference",      action="store",            type="string", help="reference file          [compulsory] [format: file in GFF 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("-d", "--distance",  dest="distance",       action="store",            type="int",    help="distance up/down stream [compulsory] [format: output file in GFF3 format]")
+    parser.add_option("-v", "--verbosity", dest="verbosity",      action="store", default=1, type="int",    help="trace level                          [format: int]")
+    (options, args) = parser.parse_args()
+
+    cl = CountLoci(options.verbosity)
+    cl.setInputFile(options.inputFileName, options.format)
+    cl.setDistance(options.distance)
+    cl.setReference(options.reference)
+    cl.setOutputFileName(options.outputFileName)
+    cl.run()