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#!/usr/bin/env python |
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"""Plot both the standard 'is_a' field and the optional 'part_of' relationship.""" |
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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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import os |
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import sys |
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from goatools.test_data.wr_subobo import WrSubObo |
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from goatools.base import download_go_basic_obo |
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from goatools.obo_parser import 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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NAME2GOIDS = { |
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'smell': set([ |
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"GO:0007608", # sensory perception of smell |
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"GO:0050911"]), # detection of chemical stimulus involved in sensory perception of smell |
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'secretory':set([ |
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"GO:0030141", # CC 20 L06 D07 AC P... p... secretory granule |
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"GO:0034774"]), # CC 8 L05 D06 ABD P... .... secretory granule lumen |
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# MISSING Edge source(GO:0007507); target(GO:0072359) |
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# MISSING: GO:0061371 # BP 0 L06 D06 B P p determination of heart left/right asymmetry |
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# ERROR: GO:0007507 |
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'heartjogging':set([ |
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"GO:0003304", # BP 0 L06 D06 A P . myocardial epithelial involution in heart jogging |
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"GO:0003146"]) # BP 0 L05 D07 A P p heart jogging |
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} |
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def test_plot_part_of(): |
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"""Plot both the standard 'is_a' field and the 'part_of' relationship.""" |
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fout_log = "plot_relationship_part_of.log" |
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obj = _Run() |
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names = NAME2GOIDS |
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# names = ["heartjogging"] |
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with open(fout_log, 'w') as prt: |
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for name in names: |
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goids = NAME2GOIDS[name] |
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obj.plot_all(goids, name, prt) |
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print(" WROTE: {LOG}\n".format(LOG=fout_log)) |
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# pylint: disable=too-few-public-methods |
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class _Run(object): |
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"""Holds data and steps for this test.""" |
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obopat = "../goatools/data/{NAME}.obo" |
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def __init__(self): |
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_fin_obo = os.path.join(REPO, "go-basic.obo") |
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self.go2obj = GODag(_fin_obo, optional_attrs=['relationship']) |
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def plot_all(self, goids, name, prt=sys.stdout): |
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"""Create plots with various numbers of relationships.""" |
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prt.write("\nCreate GoSubDag not loading any relationship") |
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gosubdag_orig = GoSubDag(goids, self.go2obj, relationships=False, prt=prt) |
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gosubdag_orig.prt_goids(gosubdag_orig.go2obj, prt=prt) |
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prt.write("{N} GO IDS".format(N=len(gosubdag_orig.go2obj))) |
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gopltdag = GoSubDagPlot(gosubdag_orig, mark_alt_id=True) |
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gopltdag.plt_dag(os.path.join(REPO, "a_relationship_{NAME}_r0.png".format(NAME=name))) |
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# goids.update(['GO:0007507'], ['GO:0072359']) |
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prt.write("\nCreate GoSubDag while loading only the 'part_of' relationship") |
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gosubdag = GoSubDag(goids, self.go2obj, relationships=['part_of'], prt=prt) |
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gosubdag.prt_goids(gosubdag.go2obj, prt=prt) |
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prt.write("{N} GO IDS".format(N=len(gosubdag.go2obj))) |
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gopltdag = GoSubDagPlot(gosubdag, mark_alt_id=True) |
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prt.write("GO SOURCES:") |
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gosubdag.prt_goids(gosubdag.go_sources, prt=prt) |
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gopltdag.plt_dag(os.path.join(REPO, "a_relationship_{NAME}_partof.png".format(NAME=name))) |
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prt.write("\nCreate GoSubDag while loading all relationships") |
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gosubdag = GoSubDag(goids, self.go2obj, relationships=True, prt=prt) |
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prt.write("ALL {N} GO IDS:".format(N=len(gosubdag.go2obj))) |
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gosubdag.prt_goids(gosubdag.go2obj, prt=prt) |
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prt.write("2 GO SOURCES:") |
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gosubdag.prt_goids(gosubdag.go_sources, prt=prt) |
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goids_new = set(gosubdag.go2obj).difference(set(gosubdag_orig.go2obj)) |
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go2color = {go:'#d5ffff' for go in goids_new} |
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prt.write("{N} NEW GO IDS:".format(N=len(goids_new))) |
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gosubdag.prt_goids(goids_new, prt=prt) |
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prt.write("{N} GO IDS".format(N=len(gosubdag.go2obj))) |
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gopltdag = GoSubDagPlot(gosubdag, mark_alt_id=True, go2color=go2color) |
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gopltdag.plt_dag(os.path.join(REPO, "a_relationship_{NAME}_r1.png".format(NAME=name))) |
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def wr_subobo(self): |
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"""Write a subset obo to be used for testing.""" |
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# Load GO-DAG: Load optional 'relationship' |
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for name, goids in NAME2GOIDS.items(): |
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fout_obo = self.get_obo_name(name) |
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fin_obo = os.path.join(REPO, "go-basic.obo") |
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download_go_basic_obo(fin_obo, prt=sys.stdout, loading_bar=None) |
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obj = WrSubObo(fin_obo, optional_attrs=['relationship']) |
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# obj = WrSubObo(fin_obo) |
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obj.wrobo(fout_obo, goids) |
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def get_obo_name(self, name): |
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"""Get the name of the obo for a small subset.""" |
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return os.path.join(REPO, self.obopat.format(NAME=name)) |
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if __name__ == '__main__': |
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#_Run().wr_subobo() |
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test_plot_part_of() |
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# Copyright (C) 2016-2018, DV Klopfenstein, H Tang, All rights reserved. |
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tanghaibao /
goatools
