--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/FastqParser.py	Tue Apr 30 15:02:29 2013 -0400
@@ -0,0 +1,104 @@
+#
+# 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
+
+class FastqParser(SequenceListParser):
+    """A class that reads a list of sequences in FASTQ format"""
+
+    def __init__(self, fileName, verbosity = 0):
+        super(FastqParser, self).__init__(fileName, verbosity)
+
+
+    def getFileFormats():
+        return ["fastq", "mfq"]
+    getFileFormats = staticmethod(getFileFormats)
+
+
+    def getInfos(self):
+        """
+        Get some generic information about the sequences
+        """
+        self.nbSequences = 0
+        self.reset()
+        if self.verbosity >= 10:
+            print "Getting information on %s." % (self.fileName)
+
+        nbLines = 0
+        for line in self.handle:
+            line = line.strip()
+            if line == "":
+                continue
+            nbLines += 1
+            if self.verbosity >= 10 and nbLines % 400000 == 0:
+                sys.stdout.write("    %d sequences read\r" % (nbLines / 4))
+                sys.stdout.flush()
+        self.reset()
+        self.nbSequences = nbLines / 4
+        if self.verbosity >= 10:
+            print "    %d sequences read" % (self.nbSequences)
+            print "Done."
+
+
+    def parseOne(self):
+        """
+        Parse only one element in the file
+        """
+        string = ""
+        quality = ""
+        lineType = 0
+
+        for line in self.handle:
+            line = line.strip()
+            if lineType == 0:
+                if line[0] != "@":
+                    raise Exception("Line '%s' should start with '@'!" % (line))
+                name = line[1:]
+                inSequence = True
+                inQuality = False
+            elif lineType == 1:
+                string = line
+            elif lineType == 2:
+                if line[0] != "+":
+                    sys.exit("Line '%s' should start with '+'!" % (line))
+                if line[1:] != name and line != "+":
+                    sys.exit("Weird difference in sequence and quality names (%s and %s) while parsing FASTQ file %s." % (name, line[1:], self.fileName))
+                inQuality = True
+                inSequence = False
+            elif lineType == 3:
+                quality = line
+            lineType += 1
+            if lineType == 4:
+                sequence = Sequence(name, string)
+                sequence.setQuality(quality)
+                return sequence
+                
+        return None