diff smart_toolShed/SMART/Java/Python/ncList/FindOverlapsWithSeveralIntervalsIndex.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Python/ncList/FindOverlapsWithSeveralIntervalsIndex.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,137 @@
+#! /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 random, os, time, MySQLdb
+from optparse import OptionParser
+from commons.core.parsing.ParserChooser import ParserChooser
+from commons.core.writer.TranscriptWriter import TranscriptWriter
+from SMART.Java.Python.structure.Transcript import Transcript
+from SMART.Java.Python.misc.Progress import Progress
+from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
+
+
+class FindOverlapsWithSeveralIntervalsIndex(object):
+
+    def __init__(self, verbosity):
+        self.verbosity = verbosity
+        randomNumber   = random.randint(0, 10000)
+        self.dbName    = "smartdb"
+        if "SMARTTMPPATH" in os.environ:
+            self.dbName = os.join(os.environ["SMARTTMPPATH"], self.dbName)
+        self.db         = MySQLdb.connect(db = self.dbName)
+        self.tableName  = "table_%s" % (randomNumber)
+        self.nbQueries  = 0
+        self.nbRefs     = 0
+        self.nbOverlaps = 0
+
+    def __del__(self):
+        cursor = self.db.cursor()
+        cursor.execute("DROP TABLE IF EXISTS %s" % (self.tableName))
+        
+
+    def setReferenceFile(self, fileName, format):
+        cursor = self.db.cursor()
+        cursor.execute("CREATE TABLE %s (start INT, end INT)" % (self.tableName))
+        cursor.execute("CREATE INDEX index_%s ON %s (start, end)" % (self.tableName, self.tableName))
+        chooser = ParserChooser(self.verbosity)
+        chooser.findFormat(format)
+        parser = chooser.getParser(fileName)
+        progress = UnlimitedProgress(1000, "Reading references", self.verbosity)
+        for transcript in parser.getIterator():
+            start      = transcript.getStart()
+            end        = transcript.getEnd()
+            cursor     = self.db.cursor()
+            cursor.execute("INSERT INTO %s (start, end) VALUES (%d, %d)" % (self.tableName, start, end))
+            self.nbRefs += 1
+            progress.inc()
+        self.db.commit()
+        progress.done()
+
+    def setQueryFile(self, fileName, format):
+        chooser = ParserChooser(self.verbosity)
+        chooser.findFormat(format)
+        self.queryParser = chooser.getParser(fileName)
+        self.nbQueries = self.queryParser.getNbTranscripts()
+
+    def setOutputFile(self, fileName):
+        self.writer = TranscriptWriter(fileName, "gff3", self.verbosity)
+
+    def compare(self):
+        progress = Progress(self.nbQueries, "Reading queries", self.verbosity)
+        startTime = time.time()
+        for queryTranscript in self.queryParser.getIterator():
+            queryStart = queryTranscript.getStart()
+            queryEnd   = queryTranscript.getEnd()
+            command    = "SELECT 1 FROM %s WHERE start <= %d and end >= %d" % (self.tableName, queryEnd, queryStart)
+            cursor     = self.db.cursor()
+            cursor.execute(command)
+            overlap = False
+            line = cursor.fetchone()
+            while line:
+                overlap = True
+                line    = cursor.fetchone()
+            if overlap:
+                self.writer.addTranscript(queryTranscript)
+                self.nbOverlaps += 1
+            progress.inc()
+        progress.done()
+        endTime = time.time()
+        self.timeSpent = endTime - startTime
+
+    def displayResults(self):
+        print "# queries:  %d" % (self.nbQueries)
+        print "# refs:     %d" % (self.nbRefs)
+        print "# overlaps: %d" % (self.nbOverlaps)
+        print "time:       %.2gs" % (self.timeSpent)
+
+    def run(self):
+        self.compare()
+        self.displayResults()
+
+if __name__ == "__main__":
+    
+    description = "Find Overlaps With Several Intervals Using Indices v1.0.1: Use MySQL to compare intervals. [Category: Personal]"
+
+    parser = OptionParser(description = description)
+    parser.add_option("-i", "--input1",      dest="inputFileName1", action="store",            type="string", help="query input file [compulsory] [format: file in transcript format given by -f]")
+    parser.add_option("-f", "--format1",     dest="format1",        action="store",            type="string", help="format of previous file [compulsory] [format: transcript file format]")
+    parser.add_option("-j", "--input2",      dest="inputFileName2", action="store",            type="string", help="reference input file [compulsory] [format: file in transcript format given by -g]")
+    parser.add_option("-g", "--format2",     dest="format2",        action="store",            type="string", help="format of previous file [compulsory] [format: transcript file format]")
+    parser.add_option("-o", "--output",      dest="outputFileName", action="store",            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 [format: int]")
+    (options, args) = parser.parse_args()
+
+    fowsii = FindOverlapsWithSeveralIntervalsIndex(options.verbosity)
+    fowsii.setQueryFile(options.inputFileName1, options.format1)
+    fowsii.setReferenceFile(options.inputFileName2, options.format2)
+    fowsii.setOutputFile(options.outputFileName)
+    fowsii.run()
+
+