def _fetch_seq(self):
        """Fetches gene sequence from PySAM fasta object.

        Returns
        -------
        exons : list of str
            list of exon nucleotide sequences
        five_prime_ss : list of str
            list of 5' splice site sequences
        three_prime_ss : list of str
            list of 3' splice site sequences
        """
        exons = []
        three_prime_ss = []
        five_prime_ss = []
        num_exons = self.bed.get_num_exons()
        for i in range(num_exons):
            # add exon sequence
            tmp_id = '{0};exon{1}'.format(self.bed.gene_name, i)
            tmp_exon = self.fasta.fetch(reference=tmp_id)
            exons.append(tmp_exon)

            # add splice site sequence
            tmp_id_3ss = '{0};3SS'.format(tmp_id)
            tmp_id_5ss = '{0};5SS'.format(tmp_id)
            if num_exons == 1:
                pass
            elif i == 0:
                tmp_5ss = self.fasta.fetch(tmp_id_5ss)
                five_prime_ss.append(tmp_5ss)
            elif i == (num_exons - 1):
                tmp_3ss = self.fasta.fetch(tmp_id_3ss)
                three_prime_ss.append(tmp_3ss)
            else:
                tmp_3ss = self.fasta.fetch(tmp_id_3ss)
                tmp_5ss = self.fasta.fetch(tmp_id_5ss)
                three_prime_ss.append(tmp_3ss)
                five_prime_ss.append(tmp_5ss)
        return exons, five_prime_ss, three_prime_ss
def _fetch_seq ( self ) : exons = [ ] three_prime_ss = [ ] five_prime_ss = [ ] num_exons = self . bed . get_num_exons ( ) for i in range ( num_exons ) : tmp_id = '{0};exon{1}' . format ( self . bed . gene_name , i ) tmp_exon = self . fasta . fetch ( reference = tmp_id ) exons . append ( tmp_exon ) tmp_id_3ss = '{0};3SS' . format ( tmp_id ) tmp_id_5ss = '{0};5SS' . format ( tmp_id ) if num_exons == 1 : pass elif i == 0 : tmp_5ss = self . fasta . fetch ( tmp_id_5ss ) five_prime_ss . append ( tmp_5ss ) elif i == ( num_exons - 1 ) : tmp_3ss = self . fasta . fetch ( tmp_id_3ss ) three_prime_ss . append ( tmp_3ss ) else : tmp_3ss = self . fasta . fetch ( tmp_id_3ss ) tmp_5ss = self . fasta . fetch ( tmp_id_5ss ) three_prime_ss . append ( tmp_3ss ) five_prime_ss . append ( tmp_5ss ) return exons , five_prime_ss , three_prime_ss
Fetches gene sequence from PySAM fasta object.

        Returns
        -------
        exons : list of str
            list of exon nucleotide sequences
        five_prime_ss : list of str
            list of 5' splice site sequences
        three_prime_ss : list of str
            list of 3' splice site sequences