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read_plink returns 'nan' strings for sample_ids

Open jeromekelleher opened this issue 6 months ago • 0 comments

Here's my code:

        data_path = "tests/data/plink/"
        bed_path = data_path + "plink_sim_10s_100v_10pmiss.bed"
        fam_path = data_path + "plink_sim_10s_100v_10pmiss.fam"
        bim_path = data_path + "plink_sim_10s_100v_10pmiss.bim"
        # print(bed_path)
        # print(fam_path)
        sg_ds = sgkit.io.plink.read_plink(
            bed_path=bed_path, fam_path=fam_path, bim_path=bim_path
        )
        print("sample Id = ", sg_ds.sample_id.values)

giving

sample Id =  ['nan' 'nan' 'nan' 'nan' 'nan' 'nan' 'nan' 'nan' 'nan' 'nan']

I don't really know what's going on here, but the fact that no-one has spotted this suggests to me that the code isn't being used by anyone.

jeromekelleher avatar May 20 '25 15:05 jeromekelleher