Mercurial > repos > yufei-luo > s_mart
diff commons/core/parsing/BlastParser.py @ 36:44d5973c188c
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 15:02:29 -0400 |
parents | 769e306b7933 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/core/parsing/BlastParser.py Tue Apr 30 15:02:29 2013 -0400 @@ -0,0 +1,88 @@ +# +# 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 commons.core.parsing.MapperParser import MapperParser +from SMART.Java.Python.structure.Interval import Interval +from SMART.Java.Python.structure.SubMapping import SubMapping +from SMART.Java.Python.structure.Mapping import Mapping + + +class BlastParser(MapperParser): + """A class that parses the output of Blast (-m 8 format)""" + + def __init__(self, fileName, verbosity = 0): + super(BlastParser, self).__init__(fileName, verbosity) + + + def __del__(self): + super(BlastParser, self).__del__() + + + def getFileFormats(): + return ["blast"] + getFileFormats = staticmethod(getFileFormats) + + + def skipFirstLines(self): + pass + + + def parseLine(self, line): + m = re.search(r"^(\S+)\s+(\S+)\s+(\d+\.?\d*)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+([-+]?\d+\.?\d*[eE]?[-+]?\d*)\s+(\d+\.?\d*)\s*$", line) + if m == None: + sys.exit("\nLine %d '%s' does not have an Blast format" % (self.currentLineNb, line)) + + mapping = Mapping() + + queryInterval = Interval() + queryInterval.setName(m.group(1)) + queryInterval.setStart(min(int(m.group(7)), int(m.group(8)))) + queryInterval.setEnd(max(int(m.group(7)), int(m.group(8)))) + + targetInterval = Interval() + targetInterval.setChromosome(m.group(2)) + targetInterval.setStart(min(int(m.group(9)), int(m.group(10)))) + targetInterval.setEnd(max(int(m.group(9)), int(m.group(10)))) + + subMapping = SubMapping() + subMapping.setQueryInterval(queryInterval) + subMapping.setTargetInterval(targetInterval) + + mapping.addSubMapping(subMapping) + + mapping.setIdentity(round(float(m.group(3)))) + mapping.setSize(int(m.group(4))) + mapping.setNbMismatches(int(m.group(5))) + mapping.setNbGaps(int(m.group(6))) + mapping.setDirection((int(m.group(8)) - int(m.group(7))) * (int(m.group(10)) - int(m.group(9)))) + mapping.setEvalue(float(m.group(11))) + + return mapping