--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/getWigDistance.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,105 @@
+#! /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.
+#
+"""
+Cluster the data into regions (defined by size and overlap with next region) and keep only highest peaks.
+"""
+
+from optparse import OptionParser
+from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+from commons.core.parsing.WigParser import WigParser
+from SMART.Java.Python.misc.Progress import Progress
+from SMART.Java.Python.misc.RPlotter import RPlotter
+
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Get WIG Data v1.0.2: Compute the average data around some genomic coordinates using WIG files (thus covering a large proportion of the genome). [Category: WIG Tools]"
+
+    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", "--inputFormat", dest="inputFormat",    action="store",                     type="string", help="format of the input file [compulsory] [format: transcript file format]")
+    parser.add_option("-w", "--wig",         dest="wig",            action="store",                     type="string", help="wig file name [compulsory] [format: file in WIG format]")    
+    parser.add_option("-d", "--distance",    dest="distance",       action="store",      default=1000,  type="int",    help="distance around position [compulsory] [format: int] [default: 1000]")    
+    parser.add_option("-s", "--strands",     dest="strands",        action="store_true", default=False,                help="consider both strands separately [format: boolean] [default: False]")    
+    parser.add_option("-o", "--output",      dest="outputFileName", action="store",                     type="string", help="output file [compulsory] [format: output file in PNG format]")
+    parser.add_option("-a", "--default",     dest="defaultValue",   action="store",      default=0.0,   type="float",  help="default value (when value is NA) [default: 0.0] [format: float]")
+    parser.add_option("-l", "--log",         dest="log",            action="store_true", default=False,                help="use log scale for y-axis [format: boolean] [default: False]")
+    parser.add_option("-k", "--keep",        dest="keep",           action="store_true", default=False,                help="keep temporary files [format: boolean] [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()
+
+    # create parsers and writers
+    transcriptParser = TranscriptContainer(options.inputFileName, options.inputFormat, options.verbosity)
+    wigParser        = WigParser(options.wig)
+    wigParser.setStrands(options.strands)
+    wigParser.setDefaultValue(options.defaultValue)
+    
+    # allocate data
+    strands = (1, -1) if options.strands else (1, )
+    values    = {}
+    for strand in strands:
+        values[strand] = dict([(i, 0.0) for i in range(-options.distance, options.distance+1)])
+
+    # read transcripts
+    progress = Progress(transcriptParser.getNbTranscripts(), "Parsing %s" % (options.inputFileName), options.verbosity)
+    for transcript in transcriptParser.getIterator():
+        transcript.removeExons()
+        transcript.restrictStart(2)
+        transcript.extendStart(options.distance)
+        transcript.extendEnd(options.distance-1)
+        theseValues = transcript.extractWigData(wigParser)
+        if len(strands) == 1:
+            theseValues = {1: theseValues}
+        for strand in strands:
+            if len(theseValues[strand]) < 2 * options.distance + 1:
+                theseValues[strand] = [options.defaultValue] * (2 * options.distance + 1 - len(theseValues[strand])) + theseValues[strand]
+            if len(theseValues[strand]) != 2 * options.distance + 1:
+				raise Exception("Got something wrong with the size of the WIG data concerning %s: %d found instead of %d" % (transcript, len(theseValues[strand]), 2 * options.distance + 1))
+            for i in range(-options.distance, options.distance+1):
+                values[strand][i] += theseValues[strand][i + options.distance]
+        progress.inc()
+    progress.done()
+
+    for strand in strands:
+        for i in range(-options.distance, options.distance+1):
+            values[strand][i] /= transcriptParser.getNbTranscripts() * strand
+
+    # draw plot
+    plotter = RPlotter(options.outputFileName, options.verbosity, options.keep)
+    plotter.setXLabel("Distance")
+    plotter.setYLabel("WigValue")
+    for strand in strands:
+        plotter.addLine(values[strand])
+    if options.log:
+        plotter.setLog("y")
+    plotter.plot()
+