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

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/BowtieParser.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,91 @@
+#
+# Copyright INRA-URGI 2009-2011
+# 
+# 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 re
+import sys
+from commons.core.parsing.MapperParser import MapperParser
+from SMART.Java.Python.structure.Mapping import Mapping
+from SMART.Java.Python.structure.SubMapping import SubMapping
+from SMART.Java.Python.structure.Interval import Interval
+
+class BowtieParser(MapperParser):
+    """A class that parses BowTie format"""
+
+    def __init__(self, fileName, verbosity = 0):
+        super(BowtieParser, self).__init__(fileName, verbosity)
+
+
+    def __del__(self):
+        super(BowtieParser, self).__del__()
+
+
+    def getFileFormats():
+        return ["bowtie"]
+    getFileFormats = staticmethod(getFileFormats)
+
+
+    def skipFirstLines(self):
+        pass
+
+
+    def parseLine(self, line):
+        line   = line.strip()
+        fields = line.split("\t")
+        if len(fields) not in (7, 8):
+            raise Exception("Line %d '%s' does not look like a BowTie line (number of fields is %d instead of 7 or 8)" % (self.currentLineNb, line, len(fields)))
+        name         = fields[0]
+        direction    = 1 if fields[1] == "+" else -1
+        chromosome   = fields[2]
+        genomeStart  = int(fields[3]) + 1
+        sequence     = fields[4]
+        quality      = fields[5]
+        number       = int(fields[6])
+        nbMismatches = 0
+        if len(fields) == 8:
+            tags         = fields[7]
+            nbMismatches = len(tags.split(","))
+
+        mapping = Mapping()
+        queryInterval = Interval()
+        queryInterval.setName(name)
+        queryInterval.setStart(1)
+        queryInterval.setEnd(len(sequence) + 1)
+        targetInterval = Interval()
+        targetInterval.setChromosome(chromosome)
+        targetInterval.setStart(genomeStart)
+        targetInterval.setEnd(genomeStart + len(sequence) - 1)
+        subMapping = SubMapping()
+        subMapping.setQueryInterval(queryInterval)
+        subMapping.setTargetInterval(targetInterval)
+        mapping.addSubMapping(subMapping)
+        mapping.setSize(len(sequence))
+        mapping.setNbMismatches(nbMismatches)
+        mapping.setDirection(direction)
+        return mapping
+