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Show forward and backward probability matrices from tskit and BEAGLE
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python/tests/test_imputation.py

+13-6
Original file line numberDiff line numberDiff line change
@@ -286,9 +286,16 @@ def test_toy_example():
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print(list(ref_ts.haplotypes()))
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print(ref_ts)
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print(query)
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fw, bw = get_tskit_forward_backward_matrices(ref_ts, query[0])
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print(fw)
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print(bw)
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df_beagle = parse_matrix(beagle_fwd_matrix_text_1)
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# compare beagle results with tskit
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print(df_beagle["val"])
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tskit_fwd, tskit_bwd = get_tskit_forward_backward_matrices(ref_ts, query[0])
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beagle_fwd = parse_matrix(beagle_fwd_matrix_text_1)
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beagle_bwd = parse_matrix(beagle_bwd_matrix_text_1)
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print("Forward probability matrix")
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print("tskit")
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print(tskit_fwd)
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print("beagle")
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print(beagle_fwd["val"].reshape((4, 6)))
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print("Backward probability matrix")
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print("tskit")
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print(tskit_bwd)
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print("beagle")
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print(beagle_bwd["val"].reshape((4, 6)))

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