Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/ShrimpParser.py @ 42:2abc37c27164
Deleted selected files
author | m-zytnicki |
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date | Wed, 18 Sep 2013 07:45:59 -0400 |
parents | 769e306b7933 |
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# # 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.Mapping import Mapping from commons.core.parsing.MapperParser import MapperParser class ShrimpParser(MapperParser): """A class that parses the output of Shrimp""" def __init__(self, fileName, verbosity = 0): super(ShrimpParser, self).__init__(fileName, verbosity) def __del__(self): super(ShrimpParser, self).__del__() def getFileFormats(): return ["shrimp"] getFileFormats = staticmethod(getFileFormats) def skipFirstLines(self): self.handle.readline() self.currentLineNb += 1 def parseLine(self, line): m = re.search(r"^\s*>([^\t]+)\t+(\S+)\s+([+-])\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s*$", line) if m == None: sys.exit("\nLine %d '%s' does not have a Shrimp format" % (self.currentLineNb, line)) mapping = Mapping() mapping.queryInterval.setName(m.group(1)) mapping.queryInterval.setStart(min(int(m.group(6)), int(m.group(7)))) mapping.queryInterval.setEnd(max(int(m.group(6)), int(m.group(7)))) mapping.targetInterval.setChromosome(m.group(2)) mapping.targetInterval.setStart(min(int(m.group(4)), int(m.group(5)))) mapping.targetInterval.setEnd(max(int(m.group(4)), int(m.group(5)))) mapping.setSize(int(m.group(8))) mapping.setDirection(m.group(3)) editString = m.group(10) nbMismatches = 0 nbGaps = 0 while editString != "": m = re.search(r"^(\d+)(\D.*)$", editString) if m != None: editString = m.group(2) else: m = re.search(r"^(\d+)$", editString) if m != None: editString = "" else: m = re.search(r"^([A-Z])(.*)$", editString) if m != None: nbMismatches += 1 editString = m.group(2) else: m = re.search(r"^\((\w+)\)(.*)$", editString) if m != None: nbGaps += len(m.group(1)) editString = m.group(2) else: m = re.search(r"^-(.*)$", editString) if m != None: nbGaps += 1 editString = m.group(1) else: sys.exit("Cannot understand edit string %s from line %s" % (editString, line)) mapping.setNbMismatches(nbMismatches) mapping.setNbGaps(nbGaps) return mapping