annotate commons/core/parsing/SequenceListParser.py @ 6:769e306b7933

Change the repository level.

#
# 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.
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# 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 sys
from SMART.Java.Python.structure.SequenceList import SequenceList
from SMART.Java.Python.misc.Progress import Progress

class SequenceListParser(object):
	"""
	A virtual class that reads a list of sequences
	@ivar verbosity:	   verbosity
	@type verbosity:	   int
	@ivar fileName:		   name of the file to parse
	@type fileName:		   string
	@ivar handle:		   file to parse
	@type handle:		   file
	@ivar nbSequences:	   number of sequences in the file
	@type nbSequences:	   int
	@ivar nbReadSequences: number of sequences read
	@type nbReadSequences: int
	@ivar currentLine:	   line currently read
	@type currentLine:	   string
	@ivar size:			   total number of nucleotides in the sequences
	@type size:			   int
	@ivar sizes:		   number of nucleotides per sequences
	@type sizes:		   dict of string to int
	"""

	def __init__(self, fileName, verbosity = 0):
		"""
		Constructor
		@param verbosity:  verbosity
		@type	verbosity: int
		@param fileName:   name of the file to parse
		@type	fileName:  string
		"""
		self.verbosity = verbosity
		self.fileName = fileName
		self.nbSequences = None
		self.nbReadSequences = 0
		self.currentLine = None
		self.size = None
		self.sizes = None
		try:
			self.handle = open(self.fileName, "rb")
		except IOError:
			raise Exception("Error! Sequence file '%s' does not exist! Exiting..." % (self.fileName))


	def __del__(self):
		"""
		Destructor
		"""
		if not self.handle.closed:
			self.handle.close()
		

	def close(self):
		"""
		Close file handle
		"""
		self.handle.close()
		

	def reset(self):
		"""
		Prepare the file to be read again from start
		"""
		self.handle.seek(0)
		self.currentLine = None
		self.nbReadSequences = 0
				
		
	def getFileFormats(self):
		pass
	getFileFormats = staticmethod(getFileFormats)


	def parse(self):
		"""
		Parse the whole file in one shot
		@return: a list of sequence
		"""
		sequenceList = SequenceList()
		progress = Progress(self.getNbSequences(), "Reading %s" % (self.fileName), self.verbosity)
		for sequence in self.getIterator():
			sequenceList.addSequence(sequence)
			progress.inc()
		progress.done()
		return sequenceList


	def getIterator(self):
		"""
		Iterate on the file, sequence by sequence
		@return: an iterator to sequences
		"""
		self.reset()
		sequence = self.parseOne()
		while sequence != None:
			self.nbReadSequences += 1
			yield sequence
			sequence = self.parseOne()


	def getInfos(self):
		"""
		Get some generic information about the sequences
		"""
		self.nbSequences = 0
		self.size = 0
		self.reset()
		if self.verbosity >= 10:
			print "Getting information on %s." % (self.fileName)
		for sequence in self.getIterator():
			self.nbSequences += 1
			self.size += sequence.getSize()
			if self.verbosity >= 10 and self.nbSequences % 100000 == 0:
				sys.stdout.write("	%d sequences read\r" % (self.nbSequences))
				sys.stdout.flush()
		self.reset()
		if self.verbosity >= 10:
			print "	%d sequences read" % (self.nbSequences)
			print "Done."

	
	def getNbSequences(self):
		"""
		Get the number of sequences in the file
		@return: the number of sequences
		"""
		if self.nbSequences != None:
			return self.nbSequences
		self.getInfos()
		return self.nbSequences


	def getNbItems(self):
		"""
		Get the number of sequences in the file
		@return: the number of sequences
		"""
		return self.getNbSequences()


	def getSize(self):
		"""
		Get the size of all the sequences
		@return: the size
		"""
		if self.size != None:
			return self.size
		self.getInfos()
		return self.size
	

	def getRegions(self):
		"""
		Get the names of the sequences
		@return: the names
		"""
		if self.sizes != None:
			return self.sizes.keys()

		self.sizes = {}
		self.reset()
		if self.verbosity >= 10:
			print "Getting information on %s." % (self.fileName)
		self.nbSequences = 0
		for sequence in self.getIterator():
			self.sizes[sequence.name] = sequence.getSize()
			self.nbSequences += 1
			if self.verbosity >= 10 and self.nbSequences % 100000 == 0:
				sys.stdout.write("	%d sequences read\r" % (self.nbSequences))
				sys.stdout.flush()
		self.reset()
		if self.verbosity >= 10:
			print "	%d sequences read" % (self.nbSequences)
			print "Done."
		return self.sizes.keys()
			
			
	def getSizeOfRegion(self, region):
		"""
		Get the size of a sequence
		@param region: the name of the sequence
		@type	region: string
		@return: the size of the sequence
		"""
		if self.sizes != None:
			if region not in self.sizes:
				raise Exception("Region %s is not found" % region)
			return self.sizes[region]

		self.getRegions()
		if region not in self.sizes:
			raise Exception("Region %s is not found" % region)
			
	def __eq__(self, o):
		if o == None:
			return False
		return self.fileName == o.fileName and self.nbSequences == o.nbSequences