def update_association(assc_gene2gos,
go2obj,
relationships=None,
prt=sys.stdout):
"""Add the GO parents of a gene's associated GO IDs to the gene's association."""
if not assc_gene2gos:
print('**WARNING: {N} ASSOCATIONS. NO ACTION BY update_association'.
format(N=len(assc_gene2gos)))
return
if prt:
prt.write("Propagating term counts ")
# Replaces update_association in GODag
goids_avail = set(go2obj)
# Get all assc GO IDs that are current
assc_goid_sets = assc_gene2gos.values()
goids_assoc_all = set.union(*assc_goid_sets)
_chk_goids_notfound(goids_assoc_all, goids_avail)
# Get the subset of GO objects in the association
_goids_assoc_cur = goids_assoc_all.intersection(goids_avail)
_go2obj_assc = {go: go2obj[go] for go in _goids_assoc_cur}
go2ancestors = get_go2parents_go2obj(_go2obj_assc, relationships, prt)
# Update the GO sets in assc_gene2gos to include all GO ancestors
for assc_goids_cur in assc_goid_sets:
parents = set()
for goid in assc_goids_cur.intersection(goids_avail):
if goid in go2ancestors:
parents.update(go2ancestors[goid])
assc_goids_cur.update(parents)
def _get_go2ancestors(self, goids_assoc_usr, relationships, prt=sys.stdout):
"""Return go2ancestors (set of parent GO IDs) for all GO ID keys in go2obj."""
assert self.godag is not None
_godag = self.godag
# Get GO IDs in annotations that are in GO DAG
goids_avail = set(_godag)
self._rpt_goids_notfound(goids_assoc_usr, goids_avail)
goids_assoc_cur = goids_assoc_usr.intersection(goids_avail)
# Get GO Term for each current GO ID in the annotations
_go2obj_assc = {go:_godag[go] for go in goids_assoc_cur}
go2ancestors = get_go2parents_go2obj(_go2obj_assc, relationships, prt)
if prt:
prt.write('{N} GO IDs -> {M} go2ancestors\n'.format(
N=len(goids_avail), M=len(go2ancestors)))
return go2ancestors
def _plot_groups_hdrgos(self, hdrgos_usr, pltargs):
"""Plot GO DAGs for each group found under a specfied header GO."""
import datetime
import timeit
pngs = []
tic = timeit.default_timer()
# Loop through GO groups. Each group of GOs is formed under a single "header GO"
hdrgo2usrgos, go2obj = self._get_plt_data(hdrgos_usr)
for hdrgo, usrgos in hdrgo2usrgos.items():
pngs.extend(self._plot_go_group(
hdrgo, usrgos,
pltargs=pltargs,
go2parentids=get_go2parents_go2obj(go2obj)))
sys.stdout.write("\nElapsed HMS: {HMS} to write ".format(
HMS=str(datetime.timedelta(seconds=(timeit.default_timer()-tic)))))
sys.stdout.write("{P:5,} GO DAG plots for {H:>5,} GO grouping headers\n".format(
H=len(hdrgo2usrgos), P=len(pngs)))
return sorted(set(pngs))
def _get_pltdotstrs(self, hdrgos_usr, **kws):
"""Plot GO DAGs for each group found under a specfied header GO."""
import datetime
import timeit
dotstrs_all = []
tic = timeit.default_timer()
# Loop through GO groups. Each group of GOs is formed under a single "header GO"
hdrgo2usrgos, go2obj = self._get_plt_data(hdrgos_usr)
# get dot strings with _get_dotstrs_curs
for hdrgo, usrgos in hdrgo2usrgos.items():
dotstrs_cur = self._get_dotgraphs(
hdrgo, usrgos,
pltargs=PltGroupedGosArgs(self.grprobj, **kws),
go2parentids=get_go2parents_go2obj(go2obj))
dotstrs_all.extend(dotstrs_cur)
sys.stdout.write("\nElapsed HMS: {HMS} to write ".format(
HMS=str(datetime.timedelta(seconds=(timeit.default_timer()-tic)))))
sys.stdout.write("{P:5,} GO DAG plots for {H:>5,} GO grouping headers\n".format(
H=len(hdrgo2usrgos), P=len(dotstrs_all)))
return sorted(set(dotstrs_all))
def _plot_groups_hdrgos(self, hdrgos_usr, pltargs):
"""Plot GO DAGs for each group found under a specfied header GO."""
import datetime
import timeit
pngs = []
tic = timeit.default_timer()
# Loop through GO groups. Each group of GOs is formed under a single "header GO"
hdrgo2usrgos, go2obj = self._get_plt_data(hdrgos_usr)
for hdrgo, usrgos in hdrgo2usrgos.items():
pngs.extend(
self._plot_go_group(
hdrgo,
usrgos,
pltargs=pltargs,
go2parentids=get_go2parents_go2obj(go2obj)))
sys.stdout.write("\nElapsed HMS: {HMS} to write ".format(
HMS=str(datetime.timedelta(seconds=(timeit.default_timer() -
tic)))))
sys.stdout.write(
"{P:5,} GO DAG plots for {H:>5,} GO grouping headers\n".format(
H=len(hdrgo2usrgos), P=len(pngs)))
return sorted(set(pngs))
def _get_pltdotstrs(self, hdrgos_usr, **kws):
"""Plot GO DAGs for each group found under a specfied header GO."""
import datetime
import timeit
dotstrs_all = []
tic = timeit.default_timer()
# Loop through GO groups. Each group of GOs is formed under a single "header GO"
hdrgo2usrgos, go2obj = self._get_plt_data(hdrgos_usr)
# get dot strings with _get_dotstrs_curs
for hdrgo, usrgos in hdrgo2usrgos.items():
dotstrs_cur = self._get_dotgraphs(
hdrgo,
usrgos,
pltargs=PltGroupedGosArgs(self.grprobj, **kws),
go2parentids=get_go2parents_go2obj(go2obj))
dotstrs_all.extend(dotstrs_cur)
sys.stdout.write("\nElapsed HMS: {HMS} to write ".format(
HMS=str(datetime.timedelta(seconds=(timeit.default_timer() -
tic)))))
sys.stdout.write(
"{P:5,} GO DAG plots for {H:>5,} GO grouping headers\n".format(
H=len(hdrgo2usrgos), P=len(dotstrs_all)))
return sorted(set(dotstrs_all))