diff SMART/Java/Python/mergeTranscriptLists.py @ 6:769e306b7933

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/mergeTranscriptLists.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,174 @@
+#! /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.
+#
+"""Merge elements of two transcript lists with some condition"""
+
+import os, random, shutil, glob
+from optparse import OptionParser
+from commons.core.parsing.SequenceListParser import SequenceListParser
+from commons.core.parsing.BedParser import BedParser
+from commons.core.parsing.GffParser import GffParser
+from commons.core.writer.TranscriptWriter import TranscriptWriter
+from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator
+from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+from SMART.Java.Python.misc.RPlotter import RPlotter
+from SMART.Java.Python.misc.Progress import Progress
+
+
+
+class MergeLists(object):
+
+    def __init__(self, verbosity):
+        self.verbosity     = verbosity
+        self.seed          = random.randint(0, 100000)
+        self.aggregation   = False
+        self.normalization = False
+        self.distance      = False
+        self.antisense     = False
+        self.colinear      = False
+        self.fileNames     = {}
+        self.formats       = {}
+        self.tmpFileNames  = []
+        self.logHandle     = None
+
+#    def __del__(self):
+#        for fileNameRoot in self.tmpFileNames:
+#            for fileName in glob.glob("%s*" % (fileNameRoot)):
+#                os.remove(fileName)
+#        if self.logHandle != None:
+#            self.logHandle.close()
+#            self.logHandle = None
+
+    def setLogFileName(self, fileName):
+        self.logHandle = open(fileName, "w")
+
+    def setInputFileName(self, fileName, format, id):
+        self.fileNames[id] = fileName
+        self.formats[id]   = format
+
+    def setOutputFileName(self, fileName):
+        self.outputFileName = fileName
+
+    def setAggregate(self, aggregation):
+        self.aggregation = aggregation
+
+    def setNormalization(self, normalization):
+        self.normalization = normalization
+
+    def setDistance(self, distance):
+        self.distance = distance
+
+    def setAntisense(self, antisense):
+        self.antisense = antisense
+
+    def setColinear(self, colinear):
+        self.colinear = colinear
+
+    def createTmpFileName(self, root):
+        fileName = "tmp_%s_%d.gff3" % (root, self.seed)
+        self.tmpFileNames.append(fileName)
+        return fileName
+
+    def selfMerge(self, fileName, format, outputFileName):
+        transcriptListComparator = TranscriptListsComparator(self.logHandle, self.verbosity)
+        transcriptListComparator.getColinearOnly(True)
+        transcriptListComparator.setNormalization(self.normalization)
+        transcriptContainer = TranscriptContainer(fileName, format, self.verbosity)
+        writer              = TranscriptWriter(outputFileName, "gff3", self.verbosity)
+        transcriptListComparator.setInputTranscriptContainer(transcriptListComparator.QUERY, transcriptContainer)
+        transcriptListComparator.setOutputWriter(writer)
+        transcriptListComparator.compareTranscriptListSelfMerge()
+
+    def keepOverlapping(self, fileNames, formats, outputFileName):
+        transcriptListComparator = TranscriptListsComparator(self.logHandle, self.verbosity)
+        transcriptListComparator.getAntisenseOnly(self.antisense)
+        transcriptListComparator.getColinearOnly(self.colinear)
+        for i in (0, 1):
+            transcriptContainer = TranscriptContainer(fileNames[i], formats[i], self.verbosity)
+            transcriptListComparator.setInputTranscriptContainer(i, transcriptContainer)
+        transcriptListComparator.aggregate(self.aggregation)
+        transcriptListComparator.setNormalization(self.normalization)
+        transcriptListComparator.setMaxDistance(self.distance)
+        writer = TranscriptWriter(outputFileName, "gff3", self.verbosity)
+        transcriptListComparator.setOutputWriter(writer)
+        transcriptListComparator.compareTranscriptList()
+
+    def mergeFiles(self, fileName1, fileName2, outputFileName):
+        outputFile = open(outputFileName, "w")
+        shutil.copyfileobj(open(fileName1, "r"), outputFile)
+        shutil.copyfileobj(open(fileName2, "r"), outputFile)
+        outputFile.close()
+
+    def run(self):
+        selectedFileQuery = self.createTmpFileName("query")
+        self.keepOverlapping({0: self.fileNames[0], 1: self.fileNames[0]}, {0: "gff3", 1: "gff3"}, selectedFileQuery)
+        mergeFileTarget = self.createTmpFileName("target")
+        self.selfMerge(self.fileNames[1], self.formats[1], mergeFileTarget)
+        if not self.aggregation:
+            overlapFile = self.createTmpFileName("overlap")
+            self.keepOverlapping({0: mergeFileTarget, 1: selectedFileQuery}, {0: "gff3", 1: "gff3"}, overlapFile)
+            mergeFileTarget = overlapFile
+        mergeFileMerged = self.createTmpFileName("merged")
+        self.mergeFiles(mergeFileTarget, selectedFileQuery, mergeFileMerged)
+        self.selfMerge(mergeFileMerged, "gff3", self.outputFileName)
+
+
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Merge Lists v1.0.3: Merge the elements of two lists of genomic coordinates. [Category: Merge]"
+
+    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",      default=None,    type="string", help="input file 2 [compulsory] [format: file in transcript format given by -g]")
+    parser.add_option("-g", "--format2",   dest="format2",        action="store",      default=None,    type="string", help="format of file 2 [compulsory] [format: file in transcript format]")
+    parser.add_option("-o", "--output",    dest="outputFileName", action="store",      default=None,    type="string", help="output file [compulsory] [format: output file in GFF3 format]")
+    parser.add_option("-k", "--all",       dest="all",            action="store_true", default=False,                  help="print all the transcripts, not only those overlapping [format: bool] [default: false]")
+    parser.add_option("-d", "--distance",  dest="distance",       action="store",      default=0,       type="int",    help="max. distance between two transcripts [format: int] [default: 0]")
+    parser.add_option("-a", "--antisense", dest="antisense",      action="store_true", default=False,                  help="antisense only [format: bool] [default: false]")
+    parser.add_option("-c", "--colinear",  dest="colinear",       action="store_true", default=False,                  help="colinear only [format: bool] [default: false]")
+    parser.add_option("-n", "--normalize", dest="normalize",      action="store_true", default=False,                  help="normalize the number of reads per cluster by the number of mappings per read [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()
+
+#    ml = MergeLists(logHandle, options.verbosity)
+    
+    ml = MergeLists(0)
+    ml.setInputFileName(options.inputFileName1, options.format1, 0)
+    ml.setInputFileName(options.inputFileName2, options.format2, 1)
+    ml.setOutputFileName(options.outputFileName)
+    ml.setAntisense(options.antisense)
+    ml.setColinear(options.colinear)
+    ml.setAggregate(options.all)
+    ml.setNormalization(options.normalize)
+    ml.setDistance(options.distance)
+    ml.run()