intronBound.py

# This file contains the IntronBound class for TranscriptClean


class IntronBound:
    """ An instance of this class represents the left or right side
        of a splice junction.  """

    def __init__(self, transcriptID, jnNumber, ibNumber, chrom, pos, strand):

        # An ibNumber of 0 signifies that this is the left hand intron boundary
        # of the splice junction (wrt reference genome)
        # An ibNumber of 1 indicates the right hand side.
        self.ID = "__".join([transcriptID, str(jnNumber), str(ibNumber)])
        self.transcriptID = transcriptID
        self.jnNumber = int(jnNumber)
        self.bound = int(ibNumber)
        self.chrom = chrom
        self.pos = int(pos)
        self.strand = strand

    def getBED(self):
        """ Format the intron boundary with 0-based start and end. 
         If mode == "start", we return a bed for the start position."""

        bedstr = "\t".join([self.chrom, str(self.pos - 1), str(self.pos),
                            self.ID, "0", self.strand])
        return bedstr

    def getSpliceMotif(self, genome):
        """ The splice motif consists of the first two or last two bases of the
            intron (first two if bound == 0 and last two if bound == 1) """

        if self.bound == 0:
            motif = genome.sequence(
                {'chr': self.chrom, 'start': self.pos, 'stop': self.pos + 1}, one_based=True)
        else:
            motif = genome.sequence(
                {'chr': self.chrom, 'start': self.pos - 1, 'stop': self.pos}, one_based=True)
        return motif