--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/ElandParser.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,126 @@
+#
+# 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.MapperParser import MapperParser
+from SMART.Java.Python.structure import Mapping
+
+class ElandParser(MapperParser):
+    """A class that parses ELAND format"""
+
+    def __init__(self, fileName, verbosity = 0):
+        super(ElandParser, self).__init__(fileName, verbosity)
+
+
+    def __del__(self):
+        super(ElandParser, self).__del__()
+
+
+    def getFileFormats():
+        return ["eland"]
+    getFileFormats = staticmethod(getFileFormats)
+
+
+    def skipFirstLines(self):
+        pass
+
+
+    def getInfos(self):
+        super(ElandParser, self).getInfos()
+        
+
+    def parseLine(self, line):
+
+        line = line.strip()
+
+        fields = line.split("\t")
+        if len(fields) < 22:
+            sys.exit("Line %d '%s' does not look like a ELAND line (number of fields is %d instead of 22)" % (self.currentLineNb, line, len(fields)))
+
+        flowCell = fields[0]
+        run = fields[1]
+        lane = fields[2]
+        tile = fields[3]
+        xcoord = fields[4]
+        ycoord = fields[5]
+        index = fields[6]
+        number = fields[7]
+        read = fields[8]
+        quality = fields[9]
+        chromosome = fields[10]
+        contig = fields[11]
+        position = fields[12]
+        strand = fields[13]
+        description = fields[14]
+        singleScore = fields[15]
+        pairScore = fields[16]
+        partnerChromosome = fields[17]
+        partnerContig = fields[18]
+        partnerOffset = fields[19]
+        partnerStrand = fields[20]
+        filtering = fields[21]
+
+        if number != "1":
+            sys.exit("S-MART cannot handle pair-end reads yet!")
+
+        # nothing found
+        if position == "":
+            return None
+
+        name = "%s_%s:%s:%s:%s:%s#0/1" % (flowCell, run, lane, tile, xcoord, ycoord)
+        direction = 1 if strand == "F" else -1
+        nbMismatches = 0
+        for char in description:
+            if ord("A") <= ord(char) and ord(char) <= ord("Z"):
+                nbMismatches += 1
+
+        mapping = Mapping()
+        mapping.setTagValue("qualityString", quality)
+        
+        mapping.queryInterval.setName(name)
+        mapping.queryInterval.setDirection(direction)
+        mapping.queryInterval.setStart(1)
+        mapping.queryInterval.setEnd(len(read))
+
+        mapping.targetInterval.setChromosome(chromosome)
+        mapping.targetInterval.setStart(int(position))
+        mapping.targetInterval.setEnd(int(position) + len(read))
+        mapping.targetInterval.setDirection(1)
+
+        mapping.setSize(len(read))
+        mapping.setDirection(direction)
+
+        mapping.setNbGaps(0)
+        mapping.setNbMismatches(nbMismatches)
+        mapping.setTagValue("score", int(singleScore))
+
+        if filtering == "Y":
+            return mapping
+        # mapping filtered out
+        return None