def test_fnc():
"""Test function, get_sections_2d, in the Grouper class."""
usrgo2nt = {getattr(nt, 'GO'):nt for nt in goea_results if getattr(nt, 'p_fdr_bh') < 0.05}
usrgos = usrgo2nt.keys()
grprdflt = _get_grprdflt()
hdrobj = HdrgosSections(grprdflt.gosubdag, grprdflt.hdrgos_dflt, sections=SECTIONS, hdrgos=None)
grprobj = Grouper("test", usrgos, hdrobj, grprdflt.gosubdag, go2nt=usrgo2nt)
assert set(usrgos) == grprobj.usrgos
sections_act = grprobj.get_sections_2d()
chk_results(sections_act, grprobj)
def get_sortobj(self, goea_results, **kws):
"""Return a Grouper object, given a list of GOEnrichmentRecord."""
nts_goea = MgrNtGOEAs(goea_results).get_goea_nts_prt(**kws)
goids = set(nt.GO for nt in nts_goea)
go2nt = {nt.GO:nt for nt in nts_goea}
grprobj = Grouper("GOEA", goids, self.hdrobj, self.grprdflt.gosubdag, go2nt=go2nt)
grprobj.prt_summary(sys.stdout)
# hdrgo_prt", "section_prt", "top_n", "use_sections"
sortobj = Sorter(grprobj, section_sortby=lambda nt: getattr(nt, self.pval_fld))
return sortobj
def get_sortobj(self, goea_results, **kws):
"""Return a Grouper object, given a list of GOEnrichmentRecord."""
nts_goea = MgrNtGOEAs(goea_results).get_goea_nts_prt(**kws)
goids = set(nt.GO for nt in nts_goea)
go2nt = {nt.GO:nt for nt in nts_goea}
grprobj = Grouper("GOEA", goids, self.hdrobj, self.grprdflt.gosubdag, go2nt=go2nt)
grprobj.prt_summary(sys.stdout)
# hdrgo_prt", "section_prt", "top_n", "use_sections"
sortobj = Sorter(grprobj, section_sortby=lambda nt: getattr(nt, self.pval_fld))
return sortobj
def test_wr_sections_all():
"""Test that all sections files generated by wr_sections have the same content."""
f_sec_rd = "data/gjoneska_pfenning/sections_in.txt"
f_sec_wr = "tmp_test_sections_out.txt"
# Travis-CI path is cwd
f_sec_py = "tmp_test_sections.py"
# f_sec_mod = "tmp_test_sections"
# Read user GO IDs. Setup to write sections text file and Python file
usrgos = [getattr(nt, 'GO') for nt in goea_results]
sec_rd = _read_sections(f_sec_rd)
# Do preliminaries
godag = get_godag("go-basic.obo", prt=None, loading_bar=False, optional_attrs=['relationship'])
gosubdag = GoSubDag(usrgos, godag, relationships=True, tcntobj=None)
grprdflt = GrouperDflts(gosubdag)
# Exclude ungrouped "Misc." section of sections var(sec_rd)
hdrobj = HdrgosSections(gosubdag, grprdflt.hdrgos_dflt, sec_rd[:-1])
assert sec_rd[-1][0] == hdrobj.secdflt, sec_rd[-1][0]
grprobj = Grouper("test", usrgos, hdrobj, gosubdag)
# Create text and Python sections files
objsecwr = WrSectionsTxt(grprobj)
objsecwr.wr_txt_section_hdrgos(os.path.join(REPO, f_sec_wr))
objsecpy = WrSectionsPy(grprobj)
objsecpy.wr_py_sections(os.path.join(REPO, f_sec_py), sec_rd, doc=godag.version)
# Read text and Python sections files
sec_wr = _read_sections(f_sec_wr)
sec_py = _read_sections(f_sec_py)
def cli(self, prt=sys.stdout):
"""Command-line interface for go_draw script."""
kws = self.objdoc.get_docargs(prt=None)
godag = get_godag(kws['obo'], prt=None, loading_bar=False, optional_attrs=['relationship'])
usrgos = GetGOs(godag, max_gos=200).get_usrgos(kws.get('GO_FILE'), prt)
tcntobj = self._get_tcntobj(usrgos, godag, **kws) # Gets TermCounts or None
self.gosubdag = GoSubDag(usrgos, godag, relationships=True, tcntobj=tcntobj, prt=None)
grprdflt = GrouperDflts(self.gosubdag, kws['slims'])
ver_list = [godag.version, grprdflt.ver_goslims]
prt.write("{VER}\n".format(VER="\n".join(ver_list)))
sections = self._read_sections(kws['ifile'])
# print("SECSECSEC", sections)
hdrobj = HdrgosSections(self.gosubdag, grprdflt.hdrgos_dflt, sections)
grprobj = Grouper("init", usrgos, hdrobj, self.gosubdag)
# Write sections
objsecwr = WrSectionsTxt(grprobj, ver_list)
if not os.path.exists(kws['ifile']):
objsecwr.wr_txt_section_hdrgos(kws['ifile'])
objsecwr.wr_txt_section_hdrgos(kws['ofile'])
objsecpy = WrSectionsPy(grprobj, ver_list)
if 'py' in kws:
objsecpy.wr_py_sections(kws['py'], sections, doc=godag.version)
# Write user GO IDs in sections
sortobj = Sorter(grprobj)
objgowr = WrXlsxSortedGos("init", sortobj, ver_list)
objgowr.wr_txt_gos(kws['txt'], sortby=objsecpy.fncsortnt)
#objwr.wr_txt_section_hdrgos(kws['ofile'], sortby=objwr.fncsortnt)
self._prt_cnt_usrgos(usrgos, sys.stdout)
def _get_grprobj():
"""Get object for grouping GO IDs."""
fin_obo = os.path.join(REPO, "go-basic.obo")
godag = get_godag(fin_obo, prt=None, loading_bar=False, optional_attrs=['relationship'])
gosubdag = GoSubDag(USER_GOS, godag, relationships=True, tcntobj=None)
grprdflt = GrouperDflts(gosubdag)
hdrobj = HdrgosSections(gosubdag, grprdflt.hdrgos_dflt, SECTIONS)
return Grouper("wrusrgos", USER_GOS, hdrobj, gosubdag)
def get_go2txt(grprobj_cur, grp_go2color, grp_go2bordercolor):
"""Adds section text in all GO terms if not Misc. Adds Misc in terms of interest."""
goids_main = set(o.id for o in grprobj_cur.gosubdag.go2obj.values())
hdrobj = grprobj_cur.hdrobj
grprobj_all = Grouper("all", grprobj_cur.usrgos.union(goids_main),
hdrobj, grprobj_cur.gosubdag)
# Adds section text to all GO terms in plot (misses middle GO terms)
_secdflt = hdrobj.secdflt
_hilight = set(grp_go2color.keys()).union(grp_go2bordercolor)
ret_go2txt = {}
# Keep sections text only if GO header, GO user, or not Misc.
if hdrobj.sections:
for goid, txt in grprobj_all.get_go2sectiontxt().items():
if txt == 'broad':
continue
if txt != _secdflt or goid in _hilight:
ret_go2txt[goid] = txt
return ret_go2txt
def _wr_sections_txt(fout_txt, usrgos, sections, grprdflt):
"""Given a list of usrgos and sections, write text file."""
try:
hdrobj = HdrgosSections(grprdflt.gosubdag, grprdflt.hdrgos_dflt, sections=sections)
grprobj = Grouper(fout_txt, usrgos, hdrobj, grprdflt.gosubdag, go2nt=None)
full_txt = os.path.join(REPO, fout_txt)
WrSectionsTxt(grprobj).wr_txt_section_hdrgos(full_txt, sortby=None, prt_section=True)
assert os.path.exists(full_txt)
except RuntimeError as inst:
sys.stdout.write("\n **FATAL: {MSG}\n\n".format(MSG=str(inst)))
def _get_grprobj():
"""Get object for grouping GO IDs."""
usrgos = _get_usrgos()
sections = _get_sections()
godag = get_godag("go-basic.obo",
prt=None,
loading_bar=False,
optional_attrs=['relationship'])
gosubdag = GoSubDag(usrgos, godag, relationships=True, tcntobj=None)
grprdflt = GrouperDflts(gosubdag)
hdrobj = HdrgosSections(gosubdag, grprdflt.hdrgos_dflt, sections)
return Grouper("wrusrgos", usrgos, hdrobj, gosubdag)
def __init__(self, name, goea_results, obj):
self.name = name
self.datobj = obj # AArtGeneProductSetsAll
_ini = _Init(obj)
self.go2nt = _ini.get_go2nt(goea_results)
_grprobj = Grouper("grp", self.go2nt, obj.hdrobj, obj.grprdflt.gosubdag, go2nt=self.go2nt)
self.sortobj = Sorter(_grprobj)
self.sec2gos = _ini.get_sec2gos(self.sortobj)
self.sec2chr = cx.OrderedDict([(s, obj.sec2chr[s]) for s in self.sec2gos.keys()])
self.go2chrs = _ini.get_go2chrs(self.sec2gos, self.sec2chr)
self.gene2gos = _ini.get_gene2gos(self.go2nt)
self.gene2section2gos = _ini.get_gene2section2gos(self.gene2gos, self.sec2gos)
self.gene2aart = _ini.get_gene2aart(self.gene2section2gos, self.sec2chr)
def test_alt_id():
"""Ensure that alternate GO IDs."""
obo_dag = get_godag("go-basic.obo")
# Create/Initialize GoSubDag
goids = _get_data0()
gosubdag = GoSubDag(obo_dag.keys(), obo_dag)
grprdflt = GrouperDflts(gosubdag)
# Create/Initialize Grouper
hdrobj = HdrgosSections(grprdflt.gosubdag, grprdflt.hdrgos_dflt, sections=None, hdrgos=None)
Grouper("test_altid_gosubdag", goids, hdrobj, grprdflt.gosubdag, go2nt=None)
alt_ids = _get_altids(obo_dag)
obo_goids = obo_dag.keys()
obo_goids_set = set(obo_goids)
assert len(alt_ids.intersection(obo_goids_set)) == len(alt_ids)
def __init__(self, gosubdag, godag_version, **kws):
_kws = {k: v for k, v in kws.items() if k in self.kws_dict}
self.grprdflt = GrouperDflts(gosubdag, _kws['slims'])
self.ver_list = [godag_version, self.grprdflt.ver_goslims]
self.sections = read_sections(self._get_secstr(**_kws),
exclude_ungrouped=False)
self.hdrobj = HdrgosSections(gosubdag, self.grprdflt.hdrgos_dflt,
self.sections)
_go2nt = _kws.get('go2nt')
self.grprobj = Grouper("all",
gosubdag.go_sources,
self.hdrobj,
gosubdag,
go2nt=_go2nt)
def test_grouper_d2(do_plot=False):
"""Group depth-02 GO terms under their most specific depth-01 GO parent(s)."""
# Get GOs to be grouped
# Since no "Grouping GOs" were provided, depth-01 GOs are used for grouping.
grprdflt = GrouperDflts()
hdrobj = HdrgosSections(grprdflt.gosubdag,
grprdflt.hdrgos_dflt,
sections=None,
hdrgos=None)
grprobj = Grouper("Transient Increase",
get_data0(),
hdrobj,
grprdflt.gosubdag,
go2nt=None)
objwr = WrSections(grprobj)
objwr.wr_txt_section_hdrgos("transient_increase_hdrgos.txt")
objwr.wr_txt_grouping_gos()
if do_plot:
# Don't run in Travis-CI because it does not contain 'dot'
from goatools.grouper.grprplt import GrouperPlot
GrouperPlot(grprobj).plot_groups_unplaced()
chk_hdrs(grprobj)
def _get_grprobj(self, goids, sections):
"""Get Grouper, given GO IDs and sections."""
grprdflt = GrouperDflts(self.gosubdag, "goslim_generic.obo")
hdrobj = HdrgosSections(self.gosubdag, grprdflt.hdrgos_dflt, sections)
return Grouper("sections", goids, hdrobj, self.gosubdag)
def test_dflthdrs(prt=sys.stdout, do_plt=False):
"""Group depth-02 GO terms under their most specific depth-01 GO parent(s)."""
# Initialize GoSubDag for grouping use once, since it takes a few seconds to initialize
grprdflt = _get_grprdflt()
# Get GOs to be grouped
data = get_data0()
# This may need to be updated if default hdrgos are changed
exp_hdrs0 = set([
"GO:0050789", # BP 11,095 L01 D01 B regulation of biological process
"GO:0044848", # BP 62 L01 D01 S biological phase
"GO:0050794", # BP 8,031 L02 D02 AB regulation of cellular process
"GO:0019222", # BP 3,227 L02 D02 AB regulation of metabolic process
"GO:0048583", # BP 2,377 L02 D02 AB regulation of response to stimulus
"GO:0050793", # BP 1,789 L02 D02 AB regulation of developmental process
"GO:0023051", # BP 1,364 L02 D02 AB regulation of signaling
"GO:0002682", # BP 1,183 L02 D02 AB regulation of immune system process
"GO:0007155", # BP 165 L02 D02 P cell adhesion
"GO:0080134", # BP 940 L03 D03 AB regulation of response to stress
"GO:0007165", # BP 717 L03 D03 AB signal transduction
"GO:0050877", # BP 96 L03 D03 K neurological system process
"GO:0007267"
]) # BP 99 L03 D04 CDR cell-cell signaling
# Since no "GO group headers" (None) were provided, depth-01 GOs are used for grouping.
hdrobj0 = HdrgosSections(grprdflt.gosubdag,
grprdflt.hdrgos_dflt,
sections=None,
hdrgos=None)
grprobj0 = Grouper("dflt", data, hdrobj0, grprdflt.gosubdag, go2nt=None)
_, _, nts0_go, act_hdrs0 = run(grprobj0, hdrobj0, exp_hdrs0)
# Grouping GOs are provided, these are added to the depth-01 defaults GOs are used for grouping.
hdrgos = set([
"GO:0099536", # BP 40 L04 D05 CDR regulation of response to stimulus
"GO:0051239", # BP 2,532 L02 D02 AB regulation of multicellular organismal process
"GO:0048519", # BP 3,293 L02 D02 AB negative regulation of biological process
"GO:0048518"
]) # BP 3,353 L02 D02 AB positive regulation of biological process
exp_hdrs1 = exp_hdrs0.union(hdrgos)
name = "usrhdrs4"
hdrobj1 = HdrgosSections(grprdflt.gosubdag,
grprdflt.hdrgos_dflt,
sections=None,
hdrgos=hdrgos)
grprobj1 = Grouper(name, data, hdrobj1, grprdflt.gosubdag, go2nt=None)
sortobj1, _, nts1_go, act_hdrs1 = run(grprobj1, hdrobj1, exp_hdrs1)
if do_plt:
from goatools.grouper.grprplt import GrouperPlot
prt.write("\nPLOT DAG\n")
GrouperPlot(grprobj1).plot_grouped_gos()
# GO:0099536 was a "middle" term (neither usrgo, not hdrgo) in run0, but is a hdrgo in run1
# print "THIS"
# grprdflt.gosubdag.prt_goids(nts1_go)
# print "MINUS"
# grprdflt.gosubdag.prt_goids(nts0_go)
# print "EQUALS"
# print nts1_go.difference(nts0_go)
assert nts1_go.difference(nts0_go) == set(["GO:0099536"])
assert act_hdrs1.difference(act_hdrs0) == set(hdrgos)
hdrgo_prt = False
sys.stdout.write("\n{NAME}: PRINT GOs hdrgo_prt({H}):\n".format(
H=hdrgo_prt, NAME=name))
sortobj1.prt_gos(hdrgo_prt=hdrgo_prt)
nts2 = sortobj1.get_nts_flat(hdrgo_prt)
nts2_go = set([nt.GO for nt in nts2])
assert len(nts1_go) > len(nts2_go)
assert nts1_go.intersection(data) == nts2_go
assert nts2_go == data