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#!/usr/bin/env python |
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"""Test get_all_children vs """ |
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from __future__ import print_function |
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__copyright__ = "Copyright (C) 2010-2018, H Tang et al. All rights reserved." |
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import os |
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import sys |
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import timeit |
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from goatools.base import get_godag |
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from goatools.godag.go_tasks import get_go2children |
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from goatools.test_data.godag_timed import prt_hms |
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from goatools.test_data.checks import _chk_a2bset |
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View Code Duplication |
def test_get_children(prt=sys.stdout): |
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"""Semantic Similarity test for Issue #86.""" |
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# Load GO-DAG |
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fin_obo = "go-basic.obo" |
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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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go2obj = {go:o for go, o in godag.items() if go == o.id} |
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# Get all children for all GO IDs using get_all_children in GOTerm class |
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tic = timeit.default_timer() |
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go2children_orig = {} |
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for goobj in go2obj.values(): |
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go2children_orig[goobj.id] = goobj.get_all_children() |
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tic = prt_hms(tic, "Get all goobj's children using GOTerm.get_all_children()", prt) |
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# Get all children for all GO IDs using GOTerm get_all_children |
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go2children_fast = get_go2children(go2obj.values()) |
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prt_hms(tic, "Get all goobj's children using go_tasks::get_go3children", prt) |
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# Compare children lists |
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_chk_a2bset(go2children_orig, go2children_fast) |
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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_get_children(PRT) |
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# Copyright (C) 2010-2018, H Tang et al. All rights reserved. |
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tanghaibao /
goatools
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