def run(self, go_sources, exp_gos, **kws):
"""Create GoSubDag using specified GO sources."""
print("\nSRCS: {GOs}".format(GOs=go_sources))
gosubdag = GoSubDag(go_sources, self.go2obj_all, **kws)
gosubdag.prt_goids(gosubdag.go2nt)
assert set(gosubdag.go2nt) == exp_gos, "ACT({}) != EXP({})\n{} {}".format(
sorted(gosubdag.go2nt), sorted(exp_gos), go_sources, kws)
def test_nb():
"""Test notebook code"""
godag = get_godag("go-basic.obo", optional_attrs={'relationship'})
go_leafs = set(o.item_id for o in godag.values() if not o.children)
virion = 'GO:0019012'
gosubdag_r0 = GoSubDag(go_leafs, godag)
nt_virion = gosubdag_r0.go2nt[virion]
print(nt_virion)
print('r0 THE VALUE OF dcnt IS: {dcnt}'.format(dcnt=nt_virion.dcnt))
gosubdag_r1 = GoSubDag(go_leafs, godag, relationships=True)
nt_virion = gosubdag_r1.go2nt[virion]
print(nt_virion)
print('r1 THE VALUE OF dcnt IS: {dcnt}'.format(dcnt=nt_virion.dcnt))
gosubdag_partof = GoSubDag(go_leafs, godag, relationships={'part_of'})
nt_virion = gosubdag_partof.go2nt[virion]
print(nt_virion)
print('THE VALUE OF dcnt IS: {dcnt}'.format(dcnt=nt_virion.dcnt))
virion_descendants = gosubdag_partof.rcntobj.go2descendants[virion]
print('{N} descendants of virion were found'.format(
N=len(virion_descendants)))
# Limit plot of descendants to get a smaller plot
virion_capsid_fiber = {'GO:0098033', 'GO:0098032'}
gosubdag_partof.prt_goids(virion_capsid_fiber,
'{NS} {GO} dcnt({dcnt}) D-{depth:02} {GO_name}')
# Limit plot size by choosing just two virion descendants
# Get a subset containing only a couple virion descendants and their ancestors
pltdag = GoSubDag(virion_capsid_fiber, godag, relationships={'part_of'})
pltobj = GoSubDagPlot(pltdag)
pltobj.plt_dag('virion_capsid_fiber.png')
class Run(object):
"""Objects for running plotting test."""
def __init__(self, obo, gaf, prt):
self.prt = prt
self.cwd = os.getcwd()
# Gene Ontologies
self.go2obj_all = get_godag(os.path.join(REPO, "../goatools/", obo))
# Annotations
#_file_gaf = dnld_gaf(os.path.join(REPO, gaf))
_file_gaf = dnld_gaf(gaf)
print("GAF: {GAF}\n".format(GAF=_file_gaf))
self.gene2gos = read_gaf(_file_gaf)
self.tcntobj = TermCounts(self.go2obj_all, self.gene2gos)
# GoSubDag
self.gosubdag_all = GoSubDag(None, self.go2obj_all, tcntobj=self.tcntobj, prt=prt)
self.prtfmt = self.gosubdag_all.prt_attr['fmta']
def prt_goids_all(self, prt):
"""Print all GO IDs, including alternate GO IDs, in GODag."""
self.gosubdag_all.prt_goids(prtfmt=self.prtfmt, prt=prt)
def plt_goids(self, fout_img, go_sources):
"""Plot GO IDs."""
# % src/bin/go_plot.py GOs --obo=../goatools/data/i86.obo --outfile=t00.jpg --mark_alt_id
gosubdag = GoSubDag(go_sources, self.gosubdag_all.go2obj, prt=self.prt,
# rcntobj=False,
rcntobj=self.gosubdag_all.rcntobj,
go2nt=self.gosubdag_all.go2nt)
prtfmt = gosubdag.prt_attr['fmta']
goids_plt = GoSubDagPlot(gosubdag).get_goids_plt()
self.prt.write("\n{N} GO IDs\n".format(N=len(goids_plt)))
gosubdag.prt_goids(goids_plt, prtfmt=prtfmt, prt=self.prt)
objplt = GoSubDagPlot(gosubdag, mark_alt_id=True)
objplt.plt_dag(os.path.join(self.cwd, fout_img))
class Run(object):
"""Printing GO IDs and Plotting; GODag from obo using GoSubDag."""
def __init__(self, obo):
self.go2obj_all = get_godag(os.path.join(REPO, obo))
self.gosubdag_all = GoSubDag(None, self.go2obj_all)
self.prtfmt = self.gosubdag_all.prt_attr['fmta']
def prt_goids_all(self, prt):
"""Print all GO IDs, including alternate GO IDs, in GODag."""
self.gosubdag_all.prt_goids(prtfmt=self.prtfmt, prt=prt)
def plt_goids(self, fout_img, go_sources):
"""Plot GO IDs."""
# % src/bin/go_plot.py GOs --obo=../goatools/data/i86.obo --outfile=t00.jpg --mark_alt_id
gosubdag = GoSubDag(go_sources, self.go2obj_all)
objplt = GoSubDagPlot(gosubdag, mark_alt_id=True)
objplt.plt_dag(os.path.join(REPO, fout_img))
def run(self, go_sources, exp_gos, **kws):
"""Create GoSubDag using specified GO sources."""
print("\nSRCS: {GOs}".format(GOs=go_sources))
gosubdag = GoSubDag(go_sources, self.go2obj_all, **kws)
gosubdag.prt_goids(gosubdag.go2nt)
assert set(gosubdag.go2nt) == exp_gos, "ACT({}) != EXP({})\n{} {}".format(
sorted(gosubdag.go2nt), sorted(exp_gos), go_sources, kws)
def plt_goids(self, fout_img, go_sources):
"""Plot GO IDs."""
# % src/bin/go_plot.py GOs --obo=../goatools/data/i86.obo --outfile=t00.jpg --mark_alt_id
gosubdag = GoSubDag(go_sources, self.gosubdag_all.go2obj, prt=self.prt,
# rcntobj=False,
rcntobj=self.gosubdag_all.rcntobj,
go2nt=self.gosubdag_all.go2nt)
prtfmt = gosubdag.prt_attr['fmta']
goids_plt = GoSubDagPlot(gosubdag).get_goids_plt()
self.prt.write("\n{N} GO IDs\n".format(N=len(goids_plt)))
gosubdag.prt_goids(goids_plt, prtfmt=prtfmt, prt=self.prt)
objplt = GoSubDagPlot(gosubdag, mark_alt_id=True)
objplt.plt_dag(os.path.join(self.cwd, fout_img))
def plt_goids(self, fout_img, go_sources):
"""Plot GO IDs."""
# % src/bin/go_plot.py GOs --obo=../goatools/data/i86.obo --outfile=t00.jpg --mark_alt_id
gosubdag = GoSubDag(
go_sources,
self.gosubdag_all.go2obj,
prt=self.prt,
# rcntobj=False,
rcntobj=self.gosubdag_all.rcntobj,
go2nt=self.gosubdag_all.go2nt)
prtfmt = gosubdag.prt_attr['fmta']
goids_plt = GoSubDagPlot(gosubdag).get_goids_plt()
self.prt.write("\n{N} GO IDs\n".format(N=len(goids_plt)))
gosubdag.prt_goids(goids_plt, prtfmt=prtfmt, prt=self.prt)
objplt = GoSubDagPlot(gosubdag, mark_alt_id=True)
objplt.plt_dag(os.path.join(self.cwd, fout_img))
class Run(object):
"""Printing GO IDs and Plotting; GODag from obo using GoSubDag."""
def __init__(self, obo):
self.cwd = os.getcwd()
self.go2obj_all = get_godag(os.path.join(REPO, "../goatools/", obo))
self.gosubdag_all = GoSubDag(None, self.go2obj_all)
self.prtfmt = self.gosubdag_all.prt_attr['fmta']
def prt_goids_all(self, prt):
"""Print all GO IDs, including alternate GO IDs, in GODag."""
self.gosubdag_all.prt_goids(prtfmt=self.prtfmt, prt=prt)
def plt_goids(self, fout_img, go_sources):
"""Plot GO IDs."""
# % src/bin/go_plot.py GOs --obo=../goatools/data/i86.obo --outfile=t00.jpg --mark_alt_id
gosubdag = GoSubDag(go_sources, self.go2obj_all)
objplt = GoSubDagPlot(gosubdag, mark_alt_id=True)
objplt.plt_dag(os.path.join(self.cwd, fout_img))
def test_semantic_i88():
"""Computing basic semantic similarities between GO terms."""
godag = obo_parser.GODag("go-basic.obo")
goids = set(go for go, o in godag.items() if go == o.id)
goids = set(godag.keys())
# Get all the annotations from arabidopsis.
fin_gaf = os.path.join(REPO, "tair.gaf")
# dnld_assc includes read_gaf
associations = dnld_assc(fin_gaf, godag, prt=None)
# First get the counts and information content for each GO term.
termcounts = TermCounts(godag, associations)
gosubdag = GoSubDag(goids, godag, tcntobj=termcounts)
# Now we can calculate the semantic distance and semantic similarity, as so:
# "The semantic similarity between terms GO:0048364 and GO:0044707 is 0.25.
go_id3 = 'GO:0048364' # BP level-03 depth-04 root development
go_id4 = 'GO:0044707' # BP level-02 depth-02 single-multicellular organism process
go_root = deepest_common_ancestor([go_id3, go_id4], godag)
sim = semantic_similarity(go_id3, go_id4, godag)
print('\nThe semantic similarity between terms {GO1} and {GO2} is {VAL}.'.
format(GO1=go_id3, GO2=go_id4, VAL=sim))
gosubdag.prt_goids([go_root, go_id3, go_id4])
# Calculate the information content
go_id = "GO:0048364"
infocontent = get_info_content(go_id, termcounts)
print('\nInformation content ({GO}) = {INFO}\n'.format(GO=go_id,
INFO=infocontent))
# Resnik's similarity measure is defined as the information content of the most
# informative common ancestor. That is, the most specific common parent-term in
# the GO. Then we can calculate this as follows:
# "Resnik similarity score (GO:0048364, GO:0044707) = 4.0540784252
sim_r = resnik_sim(go_id3, go_id4, godag, termcounts)
print('Resnik similarity score ({GO1}, {GO2}) = {VAL}'.format(GO1=go_id3,
GO2=go_id4,
VAL=sim_r))
# Lin similarity score (GO:0048364, GO:0044707) = -0.607721957763
sim_l = lin_sim(go_id3, go_id4, godag, termcounts)
print('Lin similarity score ({GO1}, {GO2}) = {VAL}'.format(GO1=go_id3,
GO2=go_id4,
VAL=sim_l))
class Run(object):
"""Printing GO IDs and Plotting; GODag from obo using GoSubDag."""
def __init__(self, obo):
self.cwd = os.getcwd()
self.go2obj_all = get_godag(os.path.join(REPO, "../goatools/", obo))
self.gosubdag_all = GoSubDag(None, self.go2obj_all)
self.prtfmt = self.gosubdag_all.prt_attr['fmta']
def prt_goids_all(self, prt):
"""Print all GO IDs, including alternate GO IDs, in GODag."""
self.gosubdag_all.prt_goids(prtfmt=self.prtfmt, prt=prt)
def plt_goids(self, fout_img, go_sources):
"""Plot GO IDs."""
# % src/bin/go_plot.py GOs --obo=../goatools/data/i86.obo --outfile=t00.jpg --mark_alt_id
gosubdag = GoSubDag(go_sources, self.go2obj_all)
objplt = GoSubDagPlot(gosubdag, mark_alt_id=True)
objplt.plt_dag(os.path.join(self.cwd, fout_img))
def test_semantic_i88():
"""Computing basic semantic similarities between GO terms."""
godag = obo_parser.GODag("go-basic.obo")
goids = set(go for go, o in godag.items() if go == o.id)
goids = set(godag.keys())
# Get all the annotations from arabidopsis.
fin_gaf = os.path.join(REPO, "tair.gaf")
# dnld_assc includes read_gaf
associations = dnld_assc(fin_gaf, godag, prt=None)
# First get the counts and information content for each GO term.
termcounts = TermCounts(godag, associations)
gosubdag = GoSubDag(goids, godag, tcntobj=termcounts)
# Now we can calculate the semantic distance and semantic similarity, as so:
# "The semantic similarity between terms GO:0048364 and GO:0044707 is 0.25.
go_id3 = 'GO:0048364' # BP level-03 depth-04 root development
go_id4 = 'GO:0044707' # BP level-02 depth-02 single-multicellular organism process
go_root = deepest_common_ancestor([go_id3, go_id4], godag)
sim = semantic_similarity(go_id3, go_id4, godag)
print('\nThe semantic similarity between terms {GO1} and {GO2} is {VAL}.'.format(
GO1=go_id3, GO2=go_id4, VAL=sim))
gosubdag.prt_goids([go_root, go_id3, go_id4])
# Calculate the information content
go_id = "GO:0048364"
infocontent = get_info_content(go_id, termcounts)
print('\nInformation content ({GO}) = {INFO}\n'.format(GO=go_id, INFO=infocontent))
# Resnik's similarity measure is defined as the information content of the most
# informative common ancestor. That is, the most specific common parent-term in
# the GO. Then we can calculate this as follows:
# "Resnik similarity score (GO:0048364, GO:0044707) = 4.0540784252
sim_r = resnik_sim(go_id3, go_id4, godag, termcounts)
print('Resnik similarity score ({GO1}, {GO2}) = {VAL}'.format(
GO1=go_id3, GO2=go_id4, VAL=sim_r))
# Lin similarity score (GO:0048364, GO:0044707) = -0.607721957763
sim_l = lin_sim(go_id3, go_id4, godag, termcounts)
print('Lin similarity score ({GO1}, {GO2}) = {VAL}'.format(
GO1=go_id3, GO2=go_id4, VAL=sim_l))
class Run(object):
"""Objects for running plotting test."""
def __init__(self, obo, gaf, prt):
self.prt = prt
self.cwd = os.getcwd()
# Gene Ontologies
self.go2obj_all = get_godag(os.path.join(REPO, "../goatools/", obo))
# Annotations
#_file_gaf = dnld_gaf(os.path.join(REPO, gaf))
_file_gaf = dnld_gaf(gaf)
print("GAF: {GAF}\n".format(GAF=_file_gaf))
self.gene2gos = read_gaf(_file_gaf)
self.tcntobj = TermCounts(self.go2obj_all, self.gene2gos)
# GoSubDag
self.gosubdag_all = GoSubDag(None,
self.go2obj_all,
tcntobj=self.tcntobj,
prt=prt)
self.prtfmt = self.gosubdag_all.prt_attr['fmta']
def prt_goids_all(self, prt):
"""Print all GO IDs, including alternate GO IDs, in GODag."""
self.gosubdag_all.prt_goids(prtfmt=self.prtfmt, prt=prt)
def plt_goids(self, fout_img, go_sources):
"""Plot GO IDs."""
# % src/bin/go_plot.py GOs --obo=../goatools/data/i86.obo --outfile=t00.jpg --mark_alt_id
gosubdag = GoSubDag(
go_sources,
self.gosubdag_all.go2obj,
prt=self.prt,
# rcntobj=False,
rcntobj=self.gosubdag_all.rcntobj,
go2nt=self.gosubdag_all.go2nt)
prtfmt = gosubdag.prt_attr['fmta']
goids_plt = GoSubDagPlot(gosubdag).get_goids_plt()
self.prt.write("\n{N} GO IDs\n".format(N=len(goids_plt)))
gosubdag.prt_goids(goids_plt, prtfmt=prtfmt, prt=self.prt)
objplt = GoSubDagPlot(gosubdag, mark_alt_id=True)
objplt.plt_dag(os.path.join(self.cwd, fout_img))
def _wr_sub_obo(fout_obo, goid_chosen, godag_r1, fin_obo):
"""Sub plot used for visualizing this test file's elements"""
# Load GO-DAG: Load optional 'relationship'
godag = {go: o for go, o in godag_r1.items() if go == o.item_id}
_prt_rtel_ctr(godag)
rels_all = set([
'part_of', 'regulates', 'negatively_regulates', 'positively_regulates'
])
goids_leaf_all = set(o.id for o in godag.values() if not o.children)
gosubdag_r1 = GoSubDag(goids_leaf_all,
godag,
relationships=True,
prt=sys.stdout)
goids_src_r1_all = _get_leafs_w_relsinhier(rels_all, gosubdag_r1)
gosubdag_r1.prt_goids(goids_src_r1_all)
# Pick one of the GO IDs as a source for the subset DAG
gosubdag_viral = GoSubDag({goid_chosen},
godag,
relationships=True,
prt=sys.stdout)
goids_viral = set(gosubdag_viral.go2obj.keys())
with open(fout_obo, 'w') as prt:
WrSubObo.prt_goterms(fin_obo, goids_viral, prt)
print('{N} GO IDs WROTE: {OBO}'.format(N=len(goids_viral),
OBO=fout_obo))
# Plot obo subset
pat_r1 = '{REPO}/scripts/go_plot.py {GO} -o {PNG} -r'
pat_r0 = '{REPO}/scripts/go_plot.py {GO} -o {PNG}'
system(
pat_r1.format(REPO=REPO,
PNG=fout_obo.replace('.obo', '_r1.png'),
GO=goid_chosen))
system(
pat_r0.format(REPO=REPO,
PNG=fout_obo.replace('.obo', '_r0.png'),
GO=goid_chosen))
def plot_all(self, goids, name, prt=sys.stdout):
"""Create plots with various numbers of relationships."""
prt.write("\nCreate GoSubDag not loading any relationship")
gosubdag_orig = GoSubDag(goids, self.go2obj, relationships=False, prt=prt)
gosubdag_orig.prt_goids(gosubdag_orig.go2obj, prt=prt)
prt.write("{N} GO IDS".format(N=len(gosubdag_orig.go2obj)))
gopltdag = GoSubDagPlot(gosubdag_orig, mark_alt_id=True)
gopltdag.plt_dag(os.path.join(REPO, "a_relationship_{NAME}_r0.png".format(NAME=name)))
# goids.update(['GO:0007507'], ['GO:0072359'])
prt.write("\nCreate GoSubDag while loading only the 'part_of' relationship")
gosubdag = GoSubDag(goids, self.go2obj, relationships=['part_of'], prt=prt)
gosubdag.prt_goids(gosubdag.go2obj, prt=prt)
prt.write("{N} GO IDS".format(N=len(gosubdag.go2obj)))
gopltdag = GoSubDagPlot(gosubdag, mark_alt_id=True)
prt.write("GO SOURCES:")
gosubdag.prt_goids(gosubdag.go_sources, prt=prt)
gopltdag.plt_dag(os.path.join(REPO, "a_relationship_{NAME}_partof.png".format(NAME=name)))
prt.write("\nCreate GoSubDag while loading all relationships")
gosubdag = GoSubDag(goids, self.go2obj, relationships=True, prt=prt)
prt.write("ALL {N} GO IDS:".format(N=len(gosubdag.go2obj)))
gosubdag.prt_goids(gosubdag.go2obj, prt=prt)
prt.write("2 GO SOURCES:")
gosubdag.prt_goids(gosubdag.go_sources, prt=prt)
goids_new = set(gosubdag.go2obj).difference(set(gosubdag_orig.go2obj))
go2color = {go:'#d5ffff' for go in goids_new}
prt.write("{N} NEW GO IDS:".format(N=len(goids_new)))
gosubdag.prt_goids(goids_new, prt=prt)
prt.write("{N} GO IDS".format(N=len(gosubdag.go2obj)))
gopltdag = GoSubDagPlot(gosubdag, mark_alt_id=True, go2color=go2color)
gopltdag.plt_dag(os.path.join(REPO, "a_relationship_{NAME}_r1.png".format(NAME=name)))
def plot_all(self, goids, name, prt=sys.stdout):
"""Create plots with various numbers of relationships."""
prt.write("\nCreate GoSubDag not loading any relationship")
gosubdag_orig = GoSubDag(goids,
self.go2obj,
relationships=False,
prt=prt)
gosubdag_orig.prt_goids(gosubdag_orig.go2obj, prt=prt)
prt.write("{N} GO IDS".format(N=len(gosubdag_orig.go2obj)))
gopltdag = GoSubDagPlot(gosubdag_orig, mark_alt_id=True)
gopltdag.plt_dag(
os.path.join(REPO,
"a_relationship_{NAME}_r0.png".format(NAME=name)))
# goids.update(['GO:0007507'], ['GO:0072359'])
prt.write(
"\nCreate GoSubDag while loading only the 'part_of' relationship")
gosubdag = GoSubDag(goids,
self.go2obj,
relationships=['part_of'],
prt=prt)
gosubdag.prt_goids(gosubdag.go2obj, prt=prt)
prt.write("{N} GO IDS".format(N=len(gosubdag.go2obj)))
gopltdag = GoSubDagPlot(gosubdag, mark_alt_id=True)
prt.write("GO SOURCES:")
gosubdag.prt_goids(gosubdag.go_sources, prt=prt)
gopltdag.plt_dag(
os.path.join(REPO,
"a_relationship_{NAME}_partof.png".format(NAME=name)))
prt.write("\nCreate GoSubDag while loading all relationships")
gosubdag = GoSubDag(goids, self.go2obj, relationships=True, prt=prt)
prt.write("ALL {N} GO IDS:".format(N=len(gosubdag.go2obj)))
gosubdag.prt_goids(gosubdag.go2obj, prt=prt)
prt.write("2 GO SOURCES:")
gosubdag.prt_goids(gosubdag.go_sources, prt=prt)
goids_new = set(gosubdag.go2obj).difference(set(gosubdag_orig.go2obj))
go2color = {go: '#d5ffff' for go in goids_new}
prt.write("{N} NEW GO IDS:".format(N=len(goids_new)))
gosubdag.prt_goids(goids_new, prt=prt)
prt.write("{N} GO IDS".format(N=len(gosubdag.go2obj)))
gopltdag = GoSubDagPlot(gosubdag, mark_alt_id=True, go2color=go2color)
gopltdag.plt_dag(
os.path.join(REPO,
"a_relationship_{NAME}_r1.png".format(NAME=name)))
