annotate smart_toolShed/commons/core/coord/Path.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

# Copyright INRA (Institut National de la Recherche Agronomique)
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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