INNER CODE UNIT · Python

_add_read_tags

timoast/sinto · sinto/addtags.py:11

def _add_read_tags(intervals, bam, sam, output, cb, trim_suffix, mode):
    inputBam = pysam.AlignmentFile(bam, "rb")
    header = inputBam.header.to_dict()
    validKeys = [x for x in ["HD", "SQ", "RG"] if x in header.keys()]
    newhead = dict((k, header[k]) for k in validKeys)
    ident = "".join(
        random.choice(string.ascii_uppercase + string.digits) for _ in range(6)
    )
    outfmt = 'w' if sam else 'wb'
    outputBam = pysam.AlignmentFile(output + ident, outfmt, header=newhead)
    for i in intervals:
        for r in inputBam.fetch(i[0], i[1], i[2]):
            if mode == "tag":
                cell_barcode, _ = utils.scan_tags(r.tags)
            elif mode == "readname":
                cell_barcode = r.qname.split(":")[0]
            else:
                raise Exception("Unknown mode. Use either tag or readname")

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