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#!/usr/bin/env python |
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"""Test creation of GoSubDag's rcntobj data member.""" |
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from __future__ import print_function |
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__copyright__ = "Copyright (C) 2016-2018, DV Klopfenstein, H Tang. All rights reserved." |
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__author__ = "DV Klopfenstein" |
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import os |
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from goatools.base import get_godag |
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from goatools.gosubdag.gosubdag import GoSubDag |
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from goatools.gosubdag.plot.gosubdag_plot import GoSubDagPlot |
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REPO = os.path.join(os.path.dirname(os.path.abspath(__file__)), "../") |
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def test_plotgosubdag(): |
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"""Test creation of GoSubDag's rcntobj data member.""" |
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objrun = Run("../goatools/tests/data/mini_obo.obo") |
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#objrun.prt_goids_all(prt) |
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in_exp = [ |
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(["GO:0000002"], set(["GO:0000001", "GO:0000002"]), {}), |
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(["GO:0000002"], set(["GO:0000001", "GO:0000002", |
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"GO:0000003", "GO:0000005", |
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"GO:0000006", "GO:0000008", |
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"GO:0000010", ]), {'children':True}), |
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(["GO:0000002"], set(["GO:0000001", "GO:0000002"]), {'children':0}), |
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(["GO:0000002"], set(["GO:0000001", "GO:0000002", |
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"GO:0000003", "GO:0000005", |
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"GO:0000006", "GO:0000008", |
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"GO:0000010", ]), {'children':1}), |
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(["GO:0000008"], set(["GO:0000001", "GO:0000003", |
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"GO:0000006", "GO:0000008"]), {}), |
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(["GO:0000008"], set(["GO:0000001", "GO:0000003", |
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"GO:0000006", "GO:0000008"]), {'children':False}), |
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(["GO:0000008"], set(["GO:0000001", "GO:0000003", |
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"GO:0000006", "GO:0000008"]), {'children':None}), |
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(["GO:0000008"], set(["GO:0000001", "GO:0000003", |
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"GO:0000006", "GO:0000008", |
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"GO:0000002", "GO:0000005", |
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"GO:0000004", "GO:0000007", |
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"GO:0000009", "GO:0000010"]), {'children':True}), |
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] |
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for in_goids, exp_goids, kws in in_exp: |
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objrun.run(in_goids, exp_goids, **kws) |
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# objrun.plt_goids("mini_obo.png", None) |
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class Run(object): |
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"""Printing GO IDs and Plotting; GODag from obo using GoSubDag.""" |
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def __init__(self, obo): |
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self.go2obj_all = get_godag(os.path.join(REPO, obo)) |
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self.gosubdag_all = GoSubDag(None, self.go2obj_all) |
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self.prtfmt = self.gosubdag_all.prt_attr['fmta'] |
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def prt_goids_all(self, prt): |
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"""Print all GO IDs, including alternate GO IDs, in GODag.""" |
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self.gosubdag_all.prt_goids(prtfmt=self.prtfmt, prt=prt) |
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def plt_goids(self, fout_img, go_sources): |
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"""Plot GO IDs.""" |
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# % src/bin/go_plot.py GOs --obo=../goatools/data/i86.obo --outfile=t00.jpg --mark_alt_id |
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gosubdag = GoSubDag(go_sources, self.go2obj_all) |
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objplt = GoSubDagPlot(gosubdag, mark_alt_id=True) |
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objplt.plt_dag(os.path.join(REPO, fout_img)) |
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def run(self, go_sources, exp_gos, **kws): |
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"""Create GoSubDag using specified GO sources.""" |
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print("\nSRCS: {GOs}".format(GOs=go_sources)) |
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gosubdag = GoSubDag(go_sources, self.go2obj_all, **kws) |
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gosubdag.prt_goids(gosubdag.go2nt) |
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assert set(gosubdag.go2nt) == exp_gos, "ACT({}) != EXP({})\n{} {}".format( |
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sorted(gosubdag.go2nt), sorted(exp_gos), go_sources, kws) |
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if __name__ == '__main__': |
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test_plotgosubdag() |
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# Copyright (C) 2016-2018, DV Klopfenstein, H Tang. All rights reserved. |
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tanghaibao /
goatools
