--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/wigExploder.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,99 @@
+#! /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.
+#
+"""Explode wig files into several files, one for each chromosome"""
+
+import os, re, sys
+from optparse import OptionParser
+
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Wig Exploder v1.0.1: Explode a big WIG file into several smaller WIG files (one per chromosome). [Category: Personal]"
+
+    parser = OptionParser(description = description)
+    parser.add_option("-i", "--input",                        dest="inputFileName", action="store",                                         type="string", help="input file [compulsory] [format: file in WIG format]")
+    parser.add_option("-o", "--output",                     dest="output",                action="store",            default=None,    type="string", help="output directory [compulsory] [format: directory]")
+    parser.add_option("-s", "--strand",                     dest="strand",                action="store",            default=None,    type="string", help="strand of the input WIG file (if any) [format: choice (+, -)]")
+    parser.add_option("-v", "--verbosity",                dest="verbosity",         action="store",            default=1,         type="int",        help="trace level [format: int]")
+    (options, args) = parser.parse_args()
+
+    inputFile = open(options.inputFileName)
+
+    files         = {}
+    file            = None
+    trackLine = None
+    strand        = ""
+    if options.strand != None:
+        strand = options.strand
+
+    for line in inputFile:
+        line = line.strip()
+
+        if line.startswith("track"):
+            trackLine = line
+            continue
+
+        m1 = re.search(r"^\s*fixedStep\s+chrom=(\S+)\s+start=\d+\s+step=\d+\s*$", line)
+        m2 = re.search(r"^\s*fixedStep\s+chrom=(\S+)\s+start=\d+\s+step=\d+\s+span=\d+\s*$", line)
+        m3 = re.search(r"^\s*variableStep\s+chrom=(\S+)\s*$", line)
+        m4 = re.search(r"^\s*variableStep\s+chrom=(\S+)span=\d+\s*$", line)
+
+        m = None
+        if m1 != None:
+            m = m1
+        elif m2 != None:
+            m = m2
+        elif m3 != None:
+            m = m3
+        elif m4 != None:
+            m = m4
+
+        if m != None:
+            chromosome = m.group(1)
+
+            if chromosome in files:
+                file = files[chromosome]
+            else:
+                file = open("%s%s%s%s.wig" % (options.output, os.sep, chromosome, strand), "w")
+                files[chromosome] = file
+                if trackLine != None:
+                    file.write("%s\n" % (trackLine))
+
+        if file == None:
+            sys.exit("Header is missing (current first line is '%s')! Aborting..." % (line))
+
+        file.write("%s\n" % (line))
+
+    inputFile.close()
+
+    for chromosome in files:
+        files[chromosome].close()