Mercurial > repos > urgi-team > teiso
diff TEisotools-1.1.a/commons/core/coord/Path.py @ 16:836ce3d9d47a draft default tip
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| author | urgi-team |
|---|---|
| date | Thu, 21 Jul 2016 07:42:47 -0400 |
| parents | 255c852351c5 |
| children |
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--- a/TEisotools-1.1.a/commons/core/coord/Path.py Thu Jul 21 07:36:44 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,161 +0,0 @@ -# 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.Set import Set -from commons.core.coord.Align import Align -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 ): - - __slots__ = ("id") - - ## 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 type(o) is not type(self) or self.id != o.id: - return False - return Align.__eq__(self, o) - - ## Not equal operator - # - def __ne__(self, o): - return not self.__eq__(o) - - ## repr - # - def __repr__(self): - return self.toString() - - ## 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