--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/BedParser.py	Tue Apr 30 15:02:29 2013 -0400
@@ -0,0 +1,139 @@
+#
+# 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 re
+import sys
+from SMART.Java.Python.structure.Interval import Interval
+from commons.core.parsing.TranscriptListParser import TranscriptListParser
+from SMART.Java.Python.structure.Transcript import Transcript
+
+
+class BedParser(TranscriptListParser):
+    """A class that parses a BED file and create a transcript list"""
+
+
+    def __init__(self, fileName, verbosity = 0):
+        self.title = None
+        TranscriptListParser.__init__(self, fileName, verbosity)
+
+
+#    def __del__(self):
+#        super(BedParser, self).__del__()
+
+
+    def getFileFormats():
+        return ["bed"]
+    getFileFormats = staticmethod(getFileFormats)
+
+
+    def skipFirstLines(self):
+        mark = self.handle.tell()
+        line = self.handle.readline()
+        line = line.strip()
+        m = re.search(r"^\s*track\s+name\s*=\s*(\S+)\s+", line)
+        if m != None:
+            self.title = m.group(1)
+            self.currentLineNb += 1
+        else:
+            self.handle.seek(mark)
+        return
+            
+
+
+
+    def parseLine(self, line):
+        m = re.search(r"^\s*(\S+)\t+(\d+)\t+(\d+)\s*$", line)
+        if m != None:
+            transcript = Transcript()
+            transcript.setChromosome(m.group(1))
+            transcript.setStart(min(int(m.group(2)), int(m.group(3))-1))
+            transcript.setEnd(max(int(m.group(2)), int(m.group(3))-1))
+            transcript.setName("Unnamed")
+            transcript.setDirection(1)
+            return transcript
+
+        m = re.search(r"^\s*(\S+)\t+(\d+)\t+(\d+)\t+([^\t]+)\s*$", line)
+        if m != None:
+            transcript = Transcript()
+            transcript.setChromosome(m.group(1))
+            transcript.setStart(min(int(m.group(2)), int(m.group(3))-1))
+            transcript.setEnd(max(int(m.group(2)), int(m.group(3))-1))
+            transcript.setName(m.group(4))
+            transcript.setDirection(1)
+            return transcript
+
+        m = re.search(r"^\s*(\S+)\t+(\d+)\t+(\d+)\t+([^\t]+)\t+\d+\.?\d*\s*$", line)
+        if m != None:
+            transcript = Transcript()
+            transcript.setChromosome(m.group(1))
+            transcript.setStart(min(int(m.group(2)), int(m.group(3))-1))
+            transcript.setEnd(max(int(m.group(2)), int(m.group(3))-1))
+            transcript.setName(m.group(4))
+            transcript.setDirection(1)
+            return transcript
+
+        m = re.search(r"^\s*(\S+)\t+(\d+)\t+(\d+)\t+([^\t]+)\t+\d+\t+([+-])\t+\d+\t+\d+\t+0\t+(\d+)\t+(\S+)\t+(\S+)\s*$", line)
+        if m == None:
+            raise Exception("\nLine %d '%s' does not has a BED format." % (self.currentLineNb, line))
+        transcript = Transcript()
+        transcript.setChromosome(m.group(1))
+        transcript.setStart(min(int(m.group(2)), int(m.group(3))-1))
+        transcript.setEnd(max(int(m.group(2)), int(m.group(3))-1))
+        transcript.setName(m.group(4))
+        transcript.setDirection(m.group(5))
+        nbExons = int(m.group(6))
+        sizes = m.group(7).split(",")
+        starts = m.group(8).split(",")
+
+        # check for comment in name
+        m = re.search(r"^([^\(]*)\((\S+)\)$", transcript.getName())
+        if m != None:
+            transcript.setName(m.group(1))
+            transcript.setTagValues(m.group(2), ";", "=")
+        
+        # check for nb occurrences in name
+        m = re.search(r"(.*)-(\d+)$", transcript.getName())
+        if m != None:
+            transcript.setName(m.group(1))
+            transcript.setOccurrence(int(m.group(2)))
+
+        for i in range(nbExons):
+            exon = Interval(transcript)
+            exon.setStart(int(starts[i])+transcript.getStart())
+            exon.setEnd(transcript.getStart()+int(starts[i])+int(sizes[i])-1)
+            exon.setSize(int(sizes[i]))
+            transcript.addExon(exon)
+            
+        if transcript.exons[0].getStart() != transcript.getStart():
+            sys.exit("There is something wrong with the start of transcript line '%s': transcript starts at %d whereas first exon starts at %d" % (line.strip(), transcript.start, transcript.exons[0].start))
+        if transcript.exons[-1].getEnd() != transcript.getEnd():
+            sys.exit("There is something wrong with the end of transcript line '%s': transcript ends at %d whereas last exon ends at %d" % (line.strip(), transcript.end, transcript.exons[-1].end))
+
+        return transcript
+