--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/cleaning/GtfCleaner.py	Tue Apr 30 15:02:29 2013 -0400
@@ -0,0 +1,121 @@
+#! /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 GTF file
+"""
+
+import shlex
+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()
+
+	def parseOptions(self):
+		self.parsedOptions = {}
+		key   = None
+		value = ""
+		for option in shlex.split(self.splittedLine[8]):
+			option = option.strip()
+			if option == "": continue
+			if key == None:
+				key = option
+			else:
+				endValue = False
+				if option[-1] == ";":
+					endValue = True
+					option.rstrip(";")
+				value = "%s \"%s\"" % (value, option)
+				if endValue:
+					self.parsedOptions[key] = value
+					if key == "transcript_id":
+						self.transcriptId = value
+					key   = None
+					value = ""
+
+	def export(self):
+		return "%s\n" % (self.line)
+
+
+class GtfCleaner(TranscriptListCleaner):
+
+	def __init__(self, verbosity = 1):
+		super(GtfCleaner, self).__init__(verbosity)
+		self.acceptedTypes = ["exon"]
+		self.parents	   = {}
+
+	def getFileFormats():
+		return ["gtf"]
+	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
+			parsedLine = ParsedLine(line, cpt)
+			if self.acceptedTypes == None or parsedLine.type in self.acceptedTypes:
+				transcriptId = parsedLine.transcriptId
+				if transcriptId not in self.parents:
+					self.parents[parsedLine.transcriptId] = [parsedLine]
+				else:
+					self.parents[parsedLine.transcriptId].append(parsedLine)
+			progress.inc()
+		progress.done()
+
+	def write(self):
+		progress = Progress(len(self.parents.keys()), "Writing output file", self.verbosity)
+		for parent in sorted(self.parents.keys()):
+			for line in self.parents[parent]:
+				self.outputHandle.write(line.export())
+			progress.inc()
+		progress.done()
+
+	def _clean(self):
+		self.parse()
+		self.write()
+