Loading the Plink .tfam File is Broken

[ttbek]

In io_pedigree.py around line 60:

    data = np.genfromtxt(file_name, dtype=np.dtype(int), usecols=range(1, 6))
    print(data)
    nodes, missing = data[:, 0], MISSING
    num_samples, num_columns = data.shape
    if genotyped_ids is None:
        sample_id = nodes

The code seems to assume that this file will be all ints, this is not the case for .tfam in general. Names of individuals like '2_124' are perfectly acceptable in a .tfam file. Naively changing the type to 'str' gave somewhat better results (the data seems to be loading correctly) but the additional parsing may need further correction, here is the traceback:

  File "/media/Storage/NextCloud/Work/Saad/Imputation/Primal_Try_2/ober/code/impute/impute/preprocess/convert.py", line 99, in <module>
    __main(__parse_command_line_args())
  File "/media/Storage/NextCloud/Work/Saad/Imputation/Primal_Try_2/ober/code/impute/impute/preprocess/convert.py", line 79, in __main
    pedigree_genotyped=options.pedigree_genotyped)
  File "/media/Storage/NextCloud/Work/Saad/Imputation/Primal_Try_2/ober/code/impute/impute/data/io.py", line 212, in plink_to_npz
    verbose=verbose)
  File "/media/Storage/NextCloud/Work/Saad/Imputation/Primal_Try_2/ober/code/impute/impute/data/io.py", line 65, in read_plink
    p = io_pedigree.read(pedigree, genotyped_id_file=pedigree_genotyped)
  File "/media/Storage/NextCloud/Work/Saad/Imputation/Primal_Try_2/ober/code/impute/impute/data/io_pedigree.py", line 30, in read
    return __read_pedigree(file_name, genotyped_ids=genotyped_ids)
  File "/media/Storage/NextCloud/Work/Saad/Imputation/Primal_Try_2/ober/code/impute/impute/data/io_pedigree.py", line 111, in __read_pedigree
    graph.remove_node(missing)
  File "/media/Storage/NextCloud/Work/Saad/Imputation/Primal_Try_2/Apps/virtualenv/ober/local/lib/python2.7/site-packages/networkx/classes/digraph.py", line 461, in remove_node
    raise NetworkXError("The node %s is not in the digraph."%(n,))
networkx.exception.NetworkXError: The node -1 is not in the digraph.