diff TEisotools-1.1.a/commons/core/parsing/GtfParser.py @ 16:836ce3d9d47a draft default tip

Uploaded

--- a/TEisotools-1.1.a/commons/core/parsing/GtfParser.py	Thu Jul 21 07:36:44 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,167 +0,0 @@
-#
-# 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 GtfParser(TranscriptListParser):
-    """A class that parses a GTF file and create a transcript list"""
-
-
-    def __init__(self, fileName, verbosity = 0, assemblyTools=False):
-        super(GtfParser, self).__init__(fileName, verbosity)
-        self._assemblyTools=assemblyTools
-
-
-    def __del__(self):
-        super(GtfParser, self).__del__()
-
-
-    def getFileFormats():
-        return ["gtf", "gtf2"]
-    getFileFormats = staticmethod(getFileFormats)
-
-
-    def skipFirstLines(self):
-        pass
-
-
-    def parseLine(self, line):
-        if line[0] == "#":
-            return None
-        m = re.search(r"^\s*(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\S+)\s+([+-.])\s+(\S+)\s+(\S.*)$", line)
-        if m == None:
-            raise Exception("\nLine %d '%s' does not have a GTF format\n" % (self.currentLineNb, line))
-        if(self._assemblyTools==False):
-            interval = Interval()
-            interval.setChromosome(m.group(1))
-            interval.setName("unnamed transcript")
-            interval.setStart(min(int(m.group(4)), int(m.group(5))))
-            interval.setEnd(max(int(m.group(4)), int(m.group(5))))
-            if m.group(7) == ".":
-                interval.setDirection("+")
-            else:
-                interval.setDirection(m.group(7))
-            if m.group(6).isdigit():
-                interval.setTagValue("score", m.group(6))
-            type = m.group(3)
-    
-            if type not in ("transcript", "exon"):
-                return None
-    
-            remainings = m.group(9).split(";")
-            for remaining in remainings:
-                remaining = remaining.strip()
-                if remaining == "":
-                    continue
-                parts = remaining.split(" ", 1)
-                field = parts[0].strip()
-                value = " ".join(parts[1:]).strip(" \"")
-                if field == "transcript_id":
-                    interval.setTagValue("ID", value)
-                elif field == "gene_name":
-                    interval.setName(value)
-                elif field == "transcript_name":
-                    interval.setName(value)
-                elif field == "exon_number":
-                    continue
-                else:
-                    try:
-                        intValue = int(value)
-                        interval.setTagValue(field, intValue)
-                    except ValueError:
-                        interval.setTagValue(field, value)
-    
-            self.currentTranscriptAddress = self.previousTranscriptAddress
-            if self.currentTranscript == None or interval.getTagValue("ID") != self.currentTranscript.getTagValue("ID"):
-                transcript = self.currentTranscript
-                self.currentTranscript = Transcript()
-                self.currentTranscript.copy(interval)
-                self.currentTranscript.setTagValue("feature", "transcript")
-                self.previousTranscriptAddress = self.currentAddress
-                return transcript
-            if type == "exon":
-                self.currentTranscript.addExon(interval)
-            return None
-        else:
-            if m.group(7) != ".":
-                interval = Interval()
-                interval.setChromosome(m.group(1))
-                interval.setName("unnamed transcript")
-                interval.setStart(min(int(m.group(4)), int(m.group(5))))
-                interval.setEnd(max(int(m.group(4)), int(m.group(5))))
-                if m.group(7) == ".":
-                    interval.setDirection("+")
-                else:
-                    interval.setDirection(m.group(7))
-                if m.group(6).isdigit():
-                    interval.setTagValue("score", m.group(6))
-                type = m.group(3)
-        
-                if type not in ("transcript", "exon"):
-                    return None
-        
-                remainings = m.group(9).split(";")
-                for remaining in remainings:
-                    remaining = remaining.strip()
-                    if remaining == "":
-                        continue
-                    parts = remaining.split(" ", 1)
-                    field = parts[0].strip()
-                    value = " ".join(parts[1:]).strip(" \"")
-                    if field == "transcript_id":
-                        interval.setTagValue("ID", value)
-                    elif field == "gene_name":
-                        interval.setName(value)
-                    elif field == "transcript_name":
-                        interval.setName(value)
-                    elif field == "exon_number":
-                        continue
-                    else:
-                        try:
-                            intValue = int(value)
-                            interval.setTagValue(field, intValue)
-                        except ValueError:
-                            interval.setTagValue(field, value)
-        
-                self.currentTranscriptAddress = self.previousTranscriptAddress
-                if self.currentTranscript == None or interval.getTagValue("ID") != self.currentTranscript.getTagValue("ID"):
-                    transcript = self.currentTranscript
-                    self.currentTranscript = Transcript()
-                    self.currentTranscript.copy(interval)
-                    self.currentTranscript.setTagValue("feature", "transcript")
-                    self.previousTranscriptAddress = self.currentAddress
-                    return transcript
-                if type == "exon":
-                    self.currentTranscript.addExon(interval)
-                return None