diff commons/core/parsing/GbParser.py @ 38:2c0c0a89fad7

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/GbParser.py	Thu May 02 09:56:47 2013 -0400
@@ -0,0 +1,111 @@
+#
+# 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 SMART.Java.Python.structure.Transcript import Transcript
+from commons.core.parsing.TranscriptListParser import TranscriptListParser
+
+
+class GbParser(TranscriptListParser):
+    """A class that parses a GBrowse file and create a transcript list"""
+
+
+    def __init__(self, fileName, verbosity = 0):
+        self.reference = None
+        self.color         = None
+        super(GbParser, self).__init__(fileName, verbosity)
+
+
+    def __del__(self):
+        super(GbParser, self).__del__()
+
+
+    def getFileFormats():
+        return ["gb", "gbrowse"]
+    getFileFormats = staticmethod(getFileFormats)
+
+
+    def skipFirstLines(self):
+        for line in self.handle:
+            self.currentLineNb += 1
+            line = line.strip()
+            m = re.search(r"^\s*bgcolor\s*=\s*(\S+)\s*$", line)
+            if m != None:
+                self.color = m.group(1)
+            if line == "":
+                return
+
+
+    def parseLine(self, line):
+        transcript = Transcript()
+        # first line (reference)
+        m = re.search(r"^\s*reference\s*=\s*(\S+)\s*$", line)
+        if m != None:
+            self.reference = m.group(1)
+            for line in self.handle:
+                line = line.strip()
+                self.currentLineNb += 1
+                break
+        # second line (genomic coordinates)
+        m = re.search(r"^\s*READS\s+(\S+)\s+(\S+)\s+\"([^\"]*)\"\s*$", line)
+        if m == None:
+            sys.exit("\nLine %d '%s' does not have a GBrowse format" % (self.currentLineNb, line))
+        if self.reference == None:
+            sys.exit("Cannot get reference of GBrowse line %d '%s'" % (self.currentLineNb, line))
+        transcript.setChromosome(self.reference)
+        transcript.setName(m.group(1))
+        transcript.setComment(m.group(3))
+        # exons
+        exons = m.group(2).split(",")
+        transcriptStart = 1000000000
+        transcriptEnd = 0
+        direction = 0
+        for exon in exons:
+            m = re.search(r"^(\d+)-(\d+)$", exon)
+            if m == None:
+                sys.exit("\nCannot read GBrowse exon line %d '%s'" % (self.currentLineNb, exon))
+            interval = Interval()
+            interval.setChromosome(transcript.chromosome)
+            direction += int(m.group(2)) - int(m.group(1))
+            start = min(int(m.group(1)), int(m.group(2)))
+            end     = max(int(m.group(1)), int(m.group(2)))
+            interval.setStart(start)
+            interval.setEnd(end)
+            transcriptStart = min(transcriptStart, start)
+            transcriptEnd     = max(transcriptEnd, end)
+            transcript.addExon(interval)
+        transcript.setStart(transcriptStart)
+        transcript.setEnd(transcriptEnd)
+        transcript.setDirection(direction)
+        for exon in transcript.getExons():
+            exon.setDirection(direction)
+        return transcript
+