def orfs(self, frame=0, revcomp=False):
        '''Returns a list of ORFs that the sequence has, starting on the given
           frame. Each returned ORF is an interval.Interval object.
           If revomp=True, then finds the ORFs of the reverse complement
           of the sequence.'''
        assert frame in [0,1,2]
        if revcomp:
            self.revcomp()

        aa_seq = self.translate(frame=frame).seq.rstrip('X')
        if revcomp:
            self.revcomp()

        orfs = _orfs_from_aa_seq(aa_seq)
        for i in range(len(orfs)):
            if revcomp:
                start = len(self) - (orfs[i].end * 3 + 3) - frame
                end = len(self) - (orfs[i].start * 3) - 1 - frame
            else:
                start = orfs[i].start * 3 + frame
                end = orfs[i].end * 3 + 2 + frame

            orfs[i] = intervals.Interval(start, end)

        return orfs
def orfs(self, frame=0, revcomp=False):
        '''Returns a list of ORFs that the sequence has, starting on the given
           frame. Each returned ORF is an interval.Interval object.
           If revomp=True, then finds the ORFs of the reverse complement
           of the sequence.'''
        assert frame in [0,1,2]
        if revcomp:
            self.revcomp()

        aa_seq = self.translate(frame=frame).seq.rstrip('X')
        if revcomp:
            self.revcomp()

        orfs = _orfs_from_aa_seq(aa_seq)
        for i in range(len(orfs)):
            if revcomp:
                start = len(self) - (orfs[i].end * 3 + 3) - frame
                end = len(self) - (orfs[i].start * 3) - 1 - frame
            else:
                start = orfs[i].start * 3 + frame
                end = orfs[i].end * 3 + 2 + frame

            orfs[i] = intervals.Interval(start, end)

        return orfs
def orfs ( self , frame = 0 , revcomp = False ) : assert frame in [ 0 , 1 , 2 ] if revcomp : self . revcomp ( ) aa_seq = self . translate ( frame = frame ) . seq . rstrip ( 'X' ) if revcomp : self . revcomp ( ) orfs = _orfs_from_aa_seq ( aa_seq ) for i in range ( len ( orfs ) ) : if revcomp : start = len ( self ) - ( orfs [ i ] . end * 3 + 3 ) - frame end = len ( self ) - ( orfs [ i ] . start * 3 ) - 1 - frame else : start = orfs [ i ] . start * 3 + frame end = orfs [ i ] . end * 3 + 2 + frame orfs [ i ] = intervals . Interval ( start , end ) return orfs
Returns a list of ORFs that the sequence has, starting on the given
           frame. Each returned ORF is an interval.Interval object.
           If revomp=True, then finds the ORFs of the reverse complement
           of the sequence.
Returns a list of ORFs that the sequence has starting on the given frame . Each returned ORF is an interval . Interval object . If revomp = True then finds the ORFs of the reverse complement of the sequence .