--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/cleaning/GffCleaner.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,168 @@
+#! /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.
+"""
+
+from SMART.Java.Python.cleaning.TranscriptListCleaner import TranscriptListCleaner
+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 GffCleaner(TranscriptListCleaner):
+
+	def __init__(self, verbosity = 1):
+		super(GffCleaner, self).__init__(verbosity)
+		self.lines		 = {}
+		self.acceptedTypes = ["mRNA", "transcript", "exon"]
+		self.parents	   = []
+		self.children	  = {}
+
+	def getFileFormats():
+		return ["gff", "gff2", "gff3"]
+	getFileFormats = staticmethod(getFileFormats)
+
+	def setAcceptedTypes(self, types):
+		self.acceptedTypes = types
+
+	def parse(self):
+		progress = UnlimitedProgress(100000, "Reading input file", self.verbosity)
+		for cpt, line in enumerate(self.inputHandle):
+			if not line or line[0] == "#": continue
+			if line[0] == ">": break
+			parsedLine = ParsedLine(line, cpt)
+			if self.acceptedTypes == None or 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()
+		progress.done()
+
+	def writeLine(self, line):
+		self.outputHandle.write(line.export())
+		if line.id in self.children:
+			for child in self.children[line.id]:
+				self.writeLine(child)
+
+	def _clean(self):
+		self.parse()
+		self.sort()
+		self.write()