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

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/SequenceListParser.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,228 @@
+#
+# 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 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