def read_V1_data(data_file, learn_options, AML_file=cur_dir + "/data/V1_suppl_data.txt"):
    if data_file is None:
        data_file = cur_dir + "/data/V1_data.xlsx"
    human_data = pandas.read_excel(data_file, sheetname=0, index_col=[0, 1])
    mouse_data = pandas.read_excel(data_file, sheetname=1, index_col=[0, 1])
    Xdf, Y = combine_organisms(human_data, mouse_data)

    # get position within each gene, then join and re-order
    # note that 11 missing guides we were told to ignore
    annotations = pandas.read_csv(AML_file, delimiter='\t', index_col=[0, 4])
    annotations.index.names = Xdf.index.names
    gene_position = pandas.merge(Xdf, annotations, how="inner", left_index=True, right_index=True)
    gene_position = util.impute_gene_position(gene_position)
    gene_position = gene_position[['Amino Acid Cut position', 'Nucleotide cut position', 'Percent Peptide']]
    Y = Y.loc[gene_position.index]
    Xdf = Xdf.loc[gene_position.index]

    Y['test'] = 1  # for bookeeping to keep consistent with V2 which uses this for "extra pairs"

    target_genes = Y['Target gene'].unique()

    Y.index.names = ['Sequence', 'Target gene']

    assert Xdf.index.equals(Y.index), "The index of Xdf is different from the index of Y (this can cause inconsistencies/random performance later on)"

    if learn_options is not None and learn_options["flipV1target"]:
        print "************************************************************************"
        print "*****************MATCHING DOENCH CODE (DEBUG MODE)**********************"
        print "************************************************************************"
        # normally it is: Y['average threshold'] = Y['average rank'] > 0.8, where 1s are good guides, 0s are not
        Y['average threshold'] = Y['average rank'] < 0.2  # 1s are bad guides
        print "press c to continue"
        import ipdb
        ipdb.set_trace()

    return annotations, gene_position, target_genes, Xdf, Y
dataset/ETHPy150Open MicrosoftResearch/Azimuth/azimuth/load_data.py/read_V1_data/original