--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/FastaParser.py	Tue Apr 30 15:02:29 2013 -0400
@@ -0,0 +1,173 @@
+#
+# 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 commons.core.parsing.SequenceListParser import SequenceListParser
+from SMART.Java.Python.structure.Sequence import Sequence
+from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
+
+class FastaParser(SequenceListParser):
+	"""A class that reads a list of sequences in FASTA"""
+
+	def __init__(self, fileName, verbosity = 0):
+		super(FastaParser, self).__init__(fileName, verbosity)
+		self.tags = {}
+		
+		
+	def getTags(self):
+		return self.tags
+
+
+	def getFileFormats():
+		return ["fasta", "mfa", "fas"]
+	getFileFormats = staticmethod(getFileFormats)
+
+
+	def getInfos(self):
+		"""
+		Get some generic information about the sequences
+		"""
+		self.nbSequences = 0
+		self.size		= 0
+		self.reset()
+		progress = UnlimitedProgress(100000, "Reading input file", self.verbosity - 9)
+		for line in self.handle:
+			line = line.strip()
+			if line == "":
+				continue
+			if line[0] == ">":
+				self.nbSequences += 1
+			else:
+				self.size += len(line)
+			progress.inc()
+		progress.done()
+		self.reset()
+
+
+	def parseOne(self):
+		"""
+		Parse only one element in the file
+		"""
+		name	 = None
+		string = ""
+
+		if self.currentLine != None:
+			if self.currentLine[0] != ">":
+				raise Exception("First line is weird: %s" % (self.currentLine))
+			name = self.currentLine[1:].split()[0].replace("|", "_").replace(".", "_")
+			self.currentLine = None
+
+		for line in self.handle:
+			line = line.strip()
+			if line == "":
+				pass
+			elif line[0] == ">":
+				if name == None:
+					name = line[1:].split()[0].replace("|", "_").replace(".", "_")
+				else:
+					self.currentLine = line
+					return Sequence(name, string)
+			else:
+				string += line
+
+		if name == None:
+			return None
+		return Sequence(name, string)
+	
+	
+	def setTags(self):
+		mark	= self.handle.tell()
+		thisTag = mark
+		
+		line = self.handle.readline()
+		while line != "":
+			if line[0] == ">":
+				line = line.strip()
+				self.tags[line[1:].split()[0]] = thisTag
+			thisTag = self.handle.tell()
+			line = self.handle.readline()
+			
+		self.handle.seek(mark)
+		
+
+	def getSubSequence(self, chromosome, start, end, direction, name = None):
+		if not self.tags:
+			self.setTags()
+
+		if chromosome not in self.tags:
+			raise Exception("Cannot find " + chromosome)
+			
+		if name == None:
+			name = "%s:%d-%d (%d)" % (chromosome, start, end, direction)
+		sequence = Sequence(name)
+
+		# switch from 0-based to 1-based coordinates
+		start -= 1
+		end   -= 1
+		
+		self.handle.seek(self.tags[chromosome])
+		line = self.handle.readline().strip()
+		if line != ">" + chromosome:
+			raise Exception("Arrived in a wrong place (got %s)" % (line))
+			
+		position1 = self.handle.tell()
+		line	  = self.handle.readline().strip()
+		position2 = self.handle.tell()
+		size	  = len(line)
+		address   = position1 + ((start - (start % size)) / size) * (position2 - position1);
+
+		count	 = max(0, start - (start % size));
+		self.handle.seek(address)
+
+		newSequence = ""
+		for line in self.handle:
+			line = line.strip()
+
+			if line[0] == ">":
+				break
+			
+			subStart = start - count
+			if subStart < 0:
+				subStart = 0
+			subEnd  = end - count
+			subSize = subEnd - subStart + 1
+			if subSize + subStart > len(line):
+				subSize = len(line) - subStart
+			if subEnd < 0:
+				break
+			if subStart <= len(line):
+				newSequence += line[subStart:subStart+subSize]
+			count += len(line)
+
+		if newSequence == "":
+			raise Exception("Error, sequence %s is empty" % (name))
+		sequence.sequence = newSequence
+		if direction == -1:
+			sequence.reverseComplement()
+		return sequence