splicing_analyses/extract_SJs_from_sam.py
def fetch_splice_motif_code(chrom, start_pos, end_pos, strand, genome):
    """ Use Pyfasta to extract the splice motif sequence based on the start
        and end of the splice junction. Then, convert this sequence motif 
        to a numeric code. """

    start_motif = get_splice_seq(chrom, start_pos, 0, genome)
    end_motif = get_splice_seq(chrom, end_pos, 1, genome)

    motif_code = getSJMotifCode(start_motif, end_motif)
    return motif_code
 Use Pyfasta to extract the splice motif sequence based on the start
        and end of the splice junction. Then, convert this sequence motif 
        to a numeric code. 
Use Pyfasta to extract the splice motif sequence based on the start
and end of the splice junction. Then, convert this sequence motif
to a numeric code.
Use Pyfasta to extract the splice motif sequence based on the start and end of the splice junction . Then convert this sequence motif to a numeric code .
def fetch_splice_motif_code(chrom, start_pos, end_pos, strand, genome):
    start_motif = get_splice_seq(chrom, start_pos, 0, genome)
    end_motif = get_splice_seq(chrom, end_pos, 1, genome)
    motif_code = getSJMotifCode(start_motif, end_motif)
    return motif_code
def fetch_splice_motif_code ( chrom , start_pos , end_pos , strand , genome ) : start_motif = get_splice_seq ( chrom , start_pos , 0 , genome ) end_motif = get_splice_seq ( chrom , end_pos , 1 , genome ) motif_code = getSJMotifCode ( start_motif , end_motif ) return motif_code
Use Pyfasta to extract the splice motif sequence based on the start
and end of the splice junction.
Use Pyfasta to extract the splice motif sequence based on the start and end of the splice junction .
""" Use Pyfasta to extract the splice motif sequence based on the start
        and end of the splice junction. Then, convert this sequence motif 
        to a numeric code. """
chrom
start_pos
end_pos
strand
genome