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"""Semantic Similarity test for Issue #86. |
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https://github.com/tanghaibao/goatools/issues/86 |
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semantic_similarity & resnik_sim works for few entities but it's giving an error: |
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return max(common_parent_go_ids(terms, go), key=lambda t: go[t].depth) |
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ValueError: max() arg is an empty sequence |
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It issues this error when these is no common parent in both provided |
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entities/genes. Here is one example producing this error |
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semantic_similarity(GO:0003676, GO:0007516, godag) |
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""" |
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import os |
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import sys |
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from goatools.base import get_godag |
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from goatools.associations import dnld_assc |
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from goatools.semantic import semantic_distance, semantic_similarity, TermCounts |
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from goatools.semantic import resnik_sim, lin_sim |
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def test_top_parent(prt=sys.stdout): |
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"""Semantic Similarity test for Issue #86.""" |
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fin_obo = "data/i86.obo" |
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branch_dist = 5 |
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repo = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..") |
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godag = get_godag(os.path.join(repo, fin_obo)) |
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# Get all the annotations from arabidopsis. |
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# Calculate the semantic distance and semantic similarity: |
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_test_path_same(godag, prt) |
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_test_path_parallel(godag, prt) |
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_test_path_bp_mf(branch_dist, godag, prt) |
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sys.stdout.write("TESTS PASSed: similarity_top_parent\n") |
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def _test_path_bp_mf(branch_dist, godag, prt): |
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"""Test distances between BP branch and MF branch.""" |
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go_mf = 'GO:0003676' # level-03 depth-03 nucleic acid binding [molecular_function] |
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go_bp = 'GO:0007516' # level-04 depth-05 hemocyte development [biological_process] |
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dst_none = semantic_distance(go_mf, go_bp, godag) |
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sim_none = semantic_similarity(go_mf, go_bp, godag) |
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assc = dnld_assc("gene_association.tair", godag) |
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termcounts = TermCounts(godag, assc) |
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fmt = '({GO1}, {GO2}) {TYPE:6} score = {VAL}\n' |
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sim_r = resnik_sim(go_mf, go_bp, godag, termcounts) |
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sim_l = lin_sim(go_mf, go_bp, godag, termcounts) |
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if prt is not None: |
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prt.write(fmt.format(TYPE='semantic distance', GO1=go_mf, GO2=go_bp, VAL=dst_none)) |
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prt.write(fmt.format(TYPE='semantic similarity', GO1=go_mf, GO2=go_bp, VAL=sim_none)) |
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prt.write(fmt.format(TYPE='Resnik similarity', GO1=go_mf, GO2=go_bp, VAL=sim_r)) |
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prt.write(fmt.format(TYPE='Lin similarity', GO1=go_mf, GO2=go_bp, VAL=sim_l)) |
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assert dst_none is None |
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assert sim_none is None |
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assert sim_r is None |
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assert sim_l is None |
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sim_d = semantic_distance(go_mf, go_bp, godag, branch_dist) |
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if prt is not None: |
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prt.write(fmt.format(TYPE='semantic distance', GO1=go_mf, GO2=go_bp, VAL=sim_d)) |
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assert sim_d == godag[go_mf].depth + godag[go_bp].depth + branch_dist |
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def _test_path_parallel(godag, prt): |
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"""Test distances between GO IDs on parallel branches.""" |
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goid_bottom = 'GO:0007516' # BP level-04 depth-05 hemocyte development |
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# Test distances up a parallel branch |
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goids = [ |
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'GO:0044763', # BP level-02 depth-02 single-organism cellular process |
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'GO:0008219', # BP level-03 depth-03 cell death |
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'GO:0070997', # BP level-04 depth-04 neuron death |
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'GO:0036475', # BP level-05 depth-05 neuron death in response to oxidative stress |
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'GO:0036476'] # BP level-06 depth-06 neuron death in response to hydrogen peroxide |
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fmt = '{DST} semantic_distance between {GO1} and {GO2} on parallel branches\n' |
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for dst_exp, goid in enumerate(goids, 3): |
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dst_act = semantic_distance(goid_bottom, goid, godag) |
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if prt is not None: |
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prt.write(fmt.format(DST=dst_act, GO1=goid_bottom, GO2=goid)) |
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assert dst_act == dst_exp |
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def _test_path_same(godag, prt): |
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"""Test distances btween GO IDs on the same path.""" |
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goid_bottom = 'GO:0007516' # level-04 depth-05 hemocyte development [biological_process] |
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# Test distances up the same branch |
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goids_bp = [ |
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'GO:0008150', # level-00 depth-00 biological_process [biological_process] |
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'GO:0009987', # level-01 depth-01 cellular process [biological_process] |
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'GO:0044763', # level-02 depth-02 single-organism cellular process [biological_process] |
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'GO:0048869', # level-03 depth-03 cellular developmental process [biological_process] |
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'GO:0048468'] # level-03 depth-04 cell development [biological_process] |
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fmt = '{DST} semantic_distance for {GO1} and {GO2} on the same branch\n' |
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for dst_exp, goid in enumerate(reversed(goids_bp), 1): |
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dst_act = semantic_distance(goid_bottom, goid, godag) |
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if prt is not None: |
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prt.write(fmt.format(DST=dst_act, GO1=goid_bottom, GO2=goid)) |
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assert dst_act == dst_exp |
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if __name__ == '__main__': |
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PRT = None if len(sys.argv) != 1 else sys.stdout |
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test_top_parent(PRT) |
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tanghaibao /
goatools
