--- a/TEisotools-1.1.a/commons/core/parsing/GffParser.py	Thu Jul 21 07:36:44 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,149 +0,0 @@
-#
-# 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.
-#
-import re
-import sys
-from SMART.Java.Python.structure.Interval import Interval
-from SMART.Java.Python.structure.Transcript import Transcript
-from commons.core.parsing.TranscriptListParser import TranscriptListParser
-
-
-class GffParser(TranscriptListParser):
-	"""A class that parses a GFF file and create a transcript list"""
-
-
-	def __init__(self, fileName, verbosity = 0):
-		super(GffParser, self).__init__(fileName, verbosity)
-
-
-	def __del__(self):
-		super(GffParser, self).__del__()
-
-
-	def getFileFormats():
-		return ["gff", "gff2", "gff3"]
-	getFileFormats = staticmethod(getFileFormats)
-
-
-	def skipFirstLines(self):
-		pass
-
-
-	def getInfos(self):
-		self.chromosomes = set()
-		self.nbTranscripts = 0
-		self.size = 0
-		self.reset()
-		if self.verbosity >= 10:
-			print "Getting information on %s." % (self.fileName)
-		self.reset()
-		for line in self.handle:
-			line = line.strip()
-			if line == "" or line[0] == "#":
-				continue
-			parts = line.split("\t")
-			if len(parts) != 9:
-				raise Exception("Error! Line '%s' has %d tab-separated fields instead of 9!" % (line, len(parts)))
-			self.chromosomes.add(parts[0])
-			if parts[8].find("Parent") == -1:
-				self.nbTranscripts += 1
-			else:
-				self.size += max(int(parts[3]), int(parts[4])) - min(int(parts[3]), int(parts[4])) + 1
-			if self.verbosity >= 10 and self.nbTranscripts % 100000 == 0:
-				sys.stdout.write("	%d transcripts read\r" % (self.nbTranscripts))
-				sys.stdout.flush()
-		self.reset()
-		if self.verbosity >= 10:
-			print "	%d transcripts read" % (self.nbTranscripts)
-			print "Done."
-
-
-	def parseLine(self, line):
-		if not line or line[0] == "#":
-			return None
-		m = re.search(r"^\s*(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\S+)\s+([+-.])\s+(\S+)\s+(\S.*)$", line)
-		if m == None:
-			raise Exception("\nLine %d '%s' does not have a GFF format\n" % (self.currentLineNb, line))
-		interval = Interval()
-		interval.setChromosome(m.group(1))
-		interval.setName("unnamed transcript")
-		interval.setStart(min(int(m.group(4)), int(m.group(5))))
-		interval.setEnd(max(int(m.group(4)), int(m.group(5))))
-		if m.group(7) == ".":
-			interval.setDirection("+")
-		else:
-			interval.setDirection(m.group(7))
-		interval.setTagValue("feature", m.group(3))
-		if m.group(6).isdigit():
-			interval.setTagValue("score", m.group(6))
-
-		remainings = m.group(9).split(";")
-		for remaining in remainings:
-			remaining = remaining.strip()
-			if remaining == "":
-				continue
-			posSpace = remaining.find(" ")
-			posEqual = remaining.find("=")
-			if posEqual != -1 and (posEqual < posSpace or posSpace == -1):
-				parts = remaining.split("=")
-			else:
-				parts = remaining.split()
-			field = parts[0].strip()
-			value = " ".join(parts[1:]).strip(" \"")
-			if field in ("Name", "name", "Sequence", "TE", "SAT"):
-				interval.setName(value)
-			else:
-				try:
-					intValue = int(value)
-					interval.setTagValue(field, intValue)
-				except ValueError:
-					interval.setTagValue(field, value)
-
-		self.currentTranscriptAddress = self.previousTranscriptAddress
-		if "Parent" in interval.getTagNames():
-			if self.currentTranscript == None:
-				raise Exception("GFF file does not start with a transcript! First line is '%s'." % (line.strip()))
-			if interval.getTagValue("Parent") != self.currentTranscript.getTagValue("ID"):
-				raise Exception("Exon '%s' is not right after its transcript in GFF file!" % (interval))
-			self.currentTranscript.addExon(interval)
-			if interval.name == None:
-				interval.name = self.currentTranscript.name
-			return None
-		
-		if interval is not None and interval.name.startswith("unnamed"):
-			if "ID" in interval.getTagNames():
-				interval.name = interval.getTagValue("ID")
-			else:
-				interval.name = "unnamed transcript %s" % (self.currentLineNb)
-
-		transcript = self.currentTranscript
-		self.currentTranscript = Transcript()
-		self.currentTranscript.copy(interval)
-		self.previousTranscriptAddress = self.currentAddress
-		return transcript