rlink_brady_batch7.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-

# Copyright (c) 2019-2021 CEA
#
# This software is governed by the CeCILL license under French law and
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import pandas
from rlink_barcode import LABELS

TIMEPOINTS = (
    'M00',  # before Li initiation
    'M03',  # 3 months after Li initiation
)

INPUT = 'R-LiNK_patients_batch7_2021-12-13.xlsx'
OUTPUT = 'R-LiNK_labels_batch7_2021-12-13.xlsx'


def main():
    converters = {
        'PSC1': str,
    }
    patients = pandas.read_excel(INPUT, converters=converters)

    labels = []
    for timepoint in TIMEPOINTS:
        for patient in patients['Patient']:
            barcode = patient + '-' + timepoint
            tmp = []
            for label in LABELS:
                tmp.append((barcode, label))
            if len(tmp) % 2:  # print complete rows of 2 labels
                tmp.append((barcode, ''))
            # the Brady BBP12 printer prints rows bottom to top
            # revert rows of 2 labels to print in "natural" order
            len_tmp = len(tmp)
            mid_tmp = len_tmp // 2
            lag_tmp = len_tmp -1
            for i in range(0, mid_tmp, 2):
                tmp[i], tmp[lag_tmp-i-1] = tmp[lag_tmp-i-1], tmp[i]
                tmp[i+1], tmp[lag_tmp-i] = tmp[lag_tmp-i], tmp[i+1]
            labels.extend(tmp)

    barcodes, types = zip(*labels)
    data = {
        'Barcode': barcodes,
        'Type': types,
    }
    df = pandas.DataFrame(data, columns=['Barcode', 'Type'])
    df.to_excel(OUTPUT, index=False)


if __name__ == '__main__':
    main()