#! /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
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# software by the user in light of its specific status of free software,
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from optparse import OptionParser
from commons.core.parsing.ParserChooser import ParserChooser
from commons.core.writer.TranscriptWriter import TranscriptWriter
from SMART.Java.Python.structure.Transcript import Transcript
from SMART.Java.Python.misc.Progress import Progress

class RemoveExons(object):

	def __init__(self, verbosity):
		self.verbosity = verbosity
		self.selection = False

	def setInputFile(self, fileName, format):
		chooser = ParserChooser(self.verbosity)
		chooser.findFormat(format)
		self.parser = chooser.getParser(fileName)

	def setOutputFile(self, fileName):
		self.writer = TranscriptWriter(fileName, "gff3", self.verbosity)
		
	def run(self):
		progress = Progress(self.parser.getNbTranscripts(), "Reading input file", self.verbosity)
		for transcript in self.parser.getIterator():
			transcript.removeExons()
			self.writer.addTranscript(transcript)
			progress.inc()
		self.writer.write()
		self.writer.close()
		progress.done()

if __name__ == "__main__":
	
	description = "Remove Exons v1.0.1: Excluse the exons of a set of transcripts. [Category: Data Modification]"

	parser = OptionParser(description = description)
	parser.add_option("-i", "--input",     dest="inputFileName",  action="store",            type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
	parser.add_option("-f", "--format",    dest="format",         action="store",            type="string", help="format of file [compulsory] [format: transcript file format]")
	parser.add_option("-o", "--output",    dest="outputFileName", action="store",            type="string", help="output file [format: output file in GFF3 format]")
	parser.add_option("-v", "--verbosity", dest="verbosity",      action="store", default=1, type="int",	help="trace level [format: int]")
	(options, args) = parser.parse_args()

	re = RemoveExons(options.verbosity)
	re.setInputFile(options.inputFileName, options.format)
	re.setOutputFile(options.outputFileName)
	re.run()