Mercurial > repos > yufei-luo > s_mart
view commons/core/coord/Map.py @ 46:169d364ddd91
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author | m-zytnicki |
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date | Mon, 30 Sep 2013 03:19:26 -0400 |
parents | 769e306b7933 |
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# Copyright INRA (Institut National de la Recherche Agronomique) # http://www.inra.fr # http://urgi.versailles.inra.fr # # 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. from commons.core.coord.Range import Range ## Record a named region on a given sequence # class Map( Range ): ## Constructor # # @param name the name of the region # @param seqname the name of the sequence # @param start the start coordinate # @param end the end coordinate # def __init__(self, name="", seqname="", start=-1, end=-1): self.name = name Range.__init__( self, seqname, start, end ) ## Equal operator # # @param o a Map instance # def __eq__(self, o): if self.name == o.name: return Range.__eq__(self, o) return False ## Return name # def getName( self ): return self.name ## Set attributes from tuple # # @param tuple: a tuple with (name,seqname,start,end) # def setFromTuple(self, tuple): self.name = tuple[0] Range.setFromTuple(self, tuple[1:]) ## Set attributes from string # # @param string a string formatted like name<sep>seqname<sep>start<sep>end # @param sep field separator # def setFromString(self, string, sep="\t"): if string[-1] == "\n": string = string[:-1] self.setFromTuple( string.split(sep) ) ## Reset # def reset(self): self.setFromTuple( [ "", "", -1, -1 ] ) ## Read attributes from a Map file # # @param fileHandler: file handler of the file being read # @return: 1 on success, 0 at the end of the file # def read(self, fileHandler): self.reset() line = fileHandler.readline() if line == "": return 0 tokens = line.split("\t") if len(tokens) < len(self.__dict__.keys()): return 0 self.setFromTuple(tokens) return 1 ## Return the attributes as a formatted string # def toString(self): string = "%s" % (self.name) string += "\t%s" % (Range.toString(self)) return string ## Write attributes into a Map file # # @param fileHandler: file handler of the file being filled # def write(self, fileHandler): fileHandler.write("%s\n" % (self.toString())) ## Save attributes into a Map file # # @param file: name of the file being filled # def save(self, file): fileHandler = open( file, "a" ) self.write( fileHandler ) fileHandler.close() ## Return a Range instance with the attributes # def getRange(self): return Range( self.seqname, self.start, self.end) ## Remove in the instance the region overlapping with another Map instance # # @param o a Map instance # def diff(self, o): iRange = Range.diff(self, o.getRange()) new = Map() if not iRange.isEmpty(): new.name = self.name new.seqname = self.seqname new.start = iRange.start new.end = iRange.end return new ## Write attributes in a Path file, the name being the subject and the rest the Range query # # @param fileHandler: file handler of a Path file # def writeAsQueryOfPath(self, fileHandler): string = "0" string += "\t%s" % ( self.seqname ) string += "\t%i" % ( self.getMin() ) string += "\t%i" % ( self.getMax() ) string += "\t%s" % ( self.name ) string += "\t0" string += "\t0" string += "\t0.0" string += "\t0" string += "\t0" fileHandler.write( "%s\n" % ( string ) )