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)
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