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Solve the following problem using Python, implementing the functions described below, one line at a time
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Description:
 def _read_miraligner(fn):
 """Read ouput of miraligner and create compatible output."""

    reads = defaultdict(realign)
    with open(fn) as in_handle:
        in_handle.next()
        for line in in_handle:
            cols = line.strip().split("\t")
            iso = isomir()
            query_name, seq = cols[1], cols[0]
            chrom, reference_start = cols[-2], cols[3]
            iso.mirna = cols[3]
            subs, add, iso.t5, iso.t3 = cols[6:10]
            if query_name not in reads:
                reads[query_name].sequence = seq
            iso.align = line
            iso.start = reference_start
            iso.subs, iso.add = _parse_mut(subs), add
            logger.debug("%s %s %s %s %s" % (query_name, reference_start, chrom, iso.subs, iso.add))
            reads[query_name].set_precursor(chrom, iso)
    return reads