__init__.py 文件源码

def write_umi_info(pickles, filename):
    """" Write an H5 with (bc, chain, read_count) tuples """
    filters = tables.Filters(complevel = cr_constants.H5_COMPRESSION_LEVEL)

    with tables.open_file(filename, 'w', filters=filters) as h5:
        umi_info = vdj_umi_info.create_arrays(h5)

        bc_to_int = {}
        chain_to_int = {}

        for pickle in pickles:
            bc_chain_umi_counts = cPickle.load(open(pickle))

            for bc, chain_umis in bc_chain_umi_counts.iteritems():
                for chain, umi_counts in chain_umis.iteritems():
                    n_umis = len(umi_counts)

                    if chain != cr_constants.MULTI_REFS_PREFIX and n_umis > 0:
                        if bc not in bc_to_int:
                            bc_to_int[bc] = len(bc_to_int)
                        if chain not in chain_to_int:
                            chain_to_int[chain] = len(chain_to_int)

                        umi_info['barcode_idx'].append(np.full(n_umis, bc_to_int[bc],
                                                               dtype=vdj_umi_info.get_dtype('barcode_idx')))
                        umi_info['chain_idx'].append(np.full(n_umis, chain_to_int[chain],
                                                             dtype=vdj_umi_info.get_dtype('chain_idx')))
                        umi_info['reads'].append(np.fromiter(umi_counts.itervalues(),
                                                             vdj_umi_info.get_dtype('reads'), count=n_umis))

        vdj_umi_info.set_ref_column(h5, 'barcodes', np.array(sorted(bc_to_int.keys(), key=bc_to_int.get)))
        vdj_umi_info.set_ref_column(h5, 'chains', np.array(sorted(chain_to_int.keys(), key=chain_to_int.get)))