test_similarities.py 文件源码

def test_simmatrix_import_run():
    output_fn = tmpname()

    tsv = '''frag_id1   frag_id2    score
2mlm_2W7_frag1  2mlm_2W7_frag2  0.5877164873731594
2mlm_2W7_frag2  3wvm_STE_frag1  0.4633096818493935
'''
    inputfile = StringIO(tsv)

    try:
        script.simmatrix_import_run(inputfile=inputfile,
                                    inputformat='tsv',
                                    simmatrixfn=output_fn,
                                    fragmentsdb='data/fragments.sqlite',
                                    nrrows=2)

        simmatrix = SimilarityMatrix(output_fn)
        result = [r for r in simmatrix]
        simmatrix.close()
        expected = [('2mlm_2W7_frag1', '2mlm_2W7_frag2xx', 0.5877), ('2mlm_2W7_frag2', '3wvm_STE_frag1', 0.4633)]
        assert_array_almost_equal([r[2] for r in result], [r[2] for r in expected], 3)
        assert [(r[0], r[1],) for r in result] == [(r[0], r[1],) for r in result]
    finally:
        if os.path.exists(output_fn):
            os.remove(output_fn)