--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Python/cleanGff.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,195 @@
+#! /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.
+#
+"""
+Clean a GFF file (as given by NCBI or TAIR) and outputs a GFF3 file.
+"""
+
+import os
+import re
+from optparse import OptionParser
+from commons.core.parsing.GffParser import *
+from SMART.Java.Python.misc.RPlotter import *
+from SMART.Java.Python.misc.Progress import Progress
+from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
+
+count = {}
+
+class ParsedLine(object):
+    def __init__(self, line, cpt):
+        self.line = line
+        self.cpt  = cpt
+        self.parse()
+
+    def parse(self):
+        self.line = self.line.strip()
+        self.splittedLine = self.line.split(None, 8)
+        if len(self.splittedLine) < 9:
+            raise Exception("Line '%s' has less than 9 fields.  Exiting..." % (self.line))
+        self.type = self.splittedLine[2]
+        self.parseOptions()
+        self.getId()
+        self.getParents()
+
+    def parseOptions(self):
+        self.parsedOptions = {}
+        for option in self.splittedLine[8].split(";"):
+            option = option.strip()
+            if option == "": continue
+            posSpace = option.find(" ")
+            posEqual = option.find("=")
+            if posEqual != -1 and (posEqual < posSpace or posSpace == -1):
+                key, value = option.split("=", 1)
+            elif posSpace != -1:
+                key, value = option.split(None, 1)
+            else:
+                key   = "ID"
+                value = option
+            self.parsedOptions[key.strip()] = value.strip(" \"")
+
+    def getId(self):
+        for key in self.parsedOptions:
+            if key.lower() == "id":
+                self.id = self.parsedOptions[key]
+                return
+        if "Parent" in self.parsedOptions:
+            parent = self.parsedOptions["Parent"].split(",")[0]
+            if parent not in count:
+                count[parent] = {}
+            if self.type not in count[parent]:
+                count[parent][self.type] = 0
+            count[parent][self.type] += 1
+            self.id = "%s-%s-%d" % (parent, self.type, count[parent][self.type])
+        else:
+            self.id = "smart%d" % (self.cpt)
+        self.parsedOptions["ID"] = self.id
+
+    def getParents(self):
+        for key in self.parsedOptions:
+            if key.lower() in ("parent", "derives_from"):
+                self.parents = self.parsedOptions[key].split(",")
+                return
+        self.parents = None
+
+    def removeParent(self):
+        for key in self.parsedOptions.keys():
+            if key.lower() in ("parent", "derives_from"):
+                del self.parsedOptions[key]
+
+    def export(self):
+        self.splittedLine[8] = ";".join(["%s=%s" % (key, value) for key, value in self.parsedOptions.iteritems()])
+        return "%s\n" % ("\t".join(self.splittedLine))
+
+
+class CleanGff(object):
+
+    def __init__(self, verbosity = 1):
+        self.verbosity = verbosity
+        self.lines         = {}
+        self.acceptedTypes = []
+        self.parents       = []
+        self.children      = {}
+
+    def setInputFileName(self, name):
+        self.inputFile = open(name)
+        
+    def setOutputFileName(self, name):
+        self.outputFile = open(name, "w")
+
+    def setAcceptedTypes(self, types):
+        self.acceptedTypes = types
+
+    def parse(self):
+        progress = UnlimitedProgress(100000, "Reading input file", self.verbosity)
+        for cpt, line in enumerate(self.inputFile):
+            if not line or line[0] == "#": continue
+            if line[0] == ">": break
+            parsedLine = ParsedLine(line, cpt)
+            if parsedLine.type in self.acceptedTypes:
+                self.lines[parsedLine.id] = parsedLine
+            progress.inc()
+        progress.done()
+
+    def sort(self):
+        progress = Progress(len(self.lines.keys()), "Sorting file", self.verbosity)
+        for line in self.lines.values():
+            parentFound = False
+            if line.parents:
+                for parent in line.parents:
+                    if parent in self.lines:
+                        parentFound = True
+                        if parent in self.children:
+                            self.children[parent].append(line)
+                        else:
+                            self.children[parent] = [line]
+            if not parentFound:
+                line.removeParent()
+                self.parents.append(line)
+            progress.inc()
+        progress.done()
+
+    def write(self):
+        progress = Progress(len(self.parents), "Writing output file", self.verbosity)
+        for line in self.parents:
+            self.writeLine(line)
+            progress.inc()
+        self.outputFile.close()
+        progress.done()
+
+    def writeLine(self, line):
+        self.outputFile.write(line.export())
+        if line.id in self.children:
+            for child in self.children[line.id]:
+                self.writeLine(child)
+
+    def run(self):
+        self.parse()
+        self.sort()
+        self.write()
+
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Clean GFF v1.0.3: Clean a GFF file (as given by NCBI) and outputs a GFF3 file. [Category: Other]"
+
+    parser = OptionParser(description = description)
+    parser.add_option("-i", "--input",     dest="inputFileName",  action="store",                      type="string", help="input file name [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("-t", "--types",     dest="types",          action="store", default="mRNA,exon", type="string", help="list of comma-separated types that you want to keep [format: string] [default: mRNA,exon]")
+    parser.add_option("-v", "--verbosity", dest="verbosity",      action="store", default=1,           type="int",    help="trace level [format: int]")
+    (options, args) = parser.parse_args()
+
+    cleanGff = CleanGff(options.verbosity)
+    cleanGff.setInputFileName(options.inputFileName)
+    cleanGff.setOutputFileName(options.outputFileName)
+    cleanGff.setAcceptedTypes(options.types.split(","))
+    cleanGff.run()
+