Mercurial > repos > yufei-luo > s_mart
view commons/core/coord/Path.py @ 14:c79b9ae3f65f
Deleted selected files
author | m-zytnicki |
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date | Fri, 19 Apr 2013 10:13:11 -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.Align import Align from commons.core.coord.Set import Set from commons.core.coord.Range import Range ## Handle a match between two sequences, query and subject (pair of coordinates with E-value, score and identity) with an identifier # class Path( Align ): ## Constructor # # @param id identifier # @param range_q: a Range instance for the query # @param range_s: a Range instance for the subject # @param e_value: E-value of the match # @param score: score of the match # @param identity: identity percentage of the match # def __init__( self, id=-1, range_q=Range(), range_s=Range(), e_value=0, score=0, identity=0 ): self.id = int( id ) Align.__init__( self, range_q, range_s, e_value, score, identity ) ## Equal operator # def __eq__(self, o): if o == None or self.id != o.id: return False return Align.__eq__(self, o) ## Set attributes from tuple # # @param tuple a tuple with (id,queryName,queryStart,queryEnd,subjectName,subjectStar,subjectEnd,E-value,score,identity) # @note data are loaded such that the query is always on the direct strand # def setFromTuple(self, tuple): self.id = int(tuple[0]) Align.setFromTuple(self, tuple[1:]) ## Reset # def reset(self): self.id = -1 Align.reset(self) ## Return the attributes as a formatted string # def toString(self): string = "%i" % ( self.id ) string += "\t%s" % (Align.toString(self)) return string ## Return the identifier of the Path instance # def getIdentifier( self ): return self.id ## Return a Set instance with the subject mapped on the query # def getSubjectAsSetOfQuery(self): iSet = Set() iSet.id = self.id iSet.name = self.range_subject.seqname iSet.seqname = self.range_query.seqname if self.range_subject.isOnDirectStrand(): iSet.start = self.range_query.start iSet.end = self.range_query.end else: iSet.start = self.range_query.end iSet.end = self.range_query.start return iSet #TODO: add tests !!!! #WARNING: subject always in direct strand !!! ## Return a Set instance with the subject mapped on the query # def getQuerySetOfSubject(self): iSet = Set() iSet.id = self.id iSet.name = self.range_query.seqname iSet.seqname = self.range_subject.seqname if self.range_subject.isOnDirectStrand(): iSet.start = self.range_subject.start iSet.end = self.range_subject.end else: iSet.start = self.range_subject.end iSet.end = self.range_subject.start return iSet ## Return True if the instance can be merged with another Path instance, False otherwise # # @param o a Path instance # def canMerge(self, o): return o.id != self.id \ and o.range_query.seqname == self.range_query.seqname \ and o.range_subject.seqname == self.range_subject.seqname \ and o.range_query.isOnDirectStrand() == self.range_query.isOnDirectStrand() \ and o.range_subject.isOnDirectStrand() == self.range_subject.isOnDirectStrand() \ and o.range_query.isOverlapping(self.range_query) \ and o.range_subject.isOverlapping(self.range_subject) ## Return an Align instance with the same attributes, except the identifier # def getAlignInstance(self): iAlign = Align() lAttributes = [] lAttributes.append( self.range_query.seqname ) lAttributes.append( self.range_query.start ) lAttributes.append( self.range_query.end ) lAttributes.append( self.range_subject.seqname ) lAttributes.append( self.range_subject.start ) lAttributes.append( self.range_subject.end ) lAttributes.append( self.e_value ) lAttributes.append( self.score ) lAttributes.append( self.identity ) iAlign.setFromTuple( lAttributes ) return iAlign