def _chk_sections(sections):
"""Check format of user-provided 'sections' variable"""
if sections:
assert len(sections[0]) == 2, \
"SECTIONS DATA MUST BE A 2-D LIST. FOUND: {S}".format(S=sections)
for _, hdrgos in sections:
chk_goids(hdrgos, "HdrgosSections::_chk_sections()")
def _chk_sections(sections):
"""Check format of user-provided 'sections' variable"""
if sections:
assert len(sections[0]) == 2, \
"SECTIONS DATA MUST BE A 2-D LIST. FOUND: {S}".format(S=sections)
for _, hdrgos in sections:
chk_goids(hdrgos, "HdrgosSections::_chk_sections()")
def internal_get_goids_or_sections(self):
"""Return GO IDs, Sections/GOs, or None."""
if self.goids_fin:
chk_goids(self.goids_fin, "read_goids")
return {'goids' : self.goids_fin}
else:
# Convert dict into 2D list retaining original section order
sections_2d = []
for section_name in self.sections_seen:
if section_name in self.section2goids:
goids = self.section2goids.get(section_name)
chk_goids(goids, "GO IDs IN SECTION({S})".format(S=section_name))
sections_2d.append((section_name, goids))
return {'sections' : sections_2d}
def internal_get_goids_or_sections(self):
"""Return GO IDs, Sections/GOs, or None."""
if self.goids_fin:
chk_goids(self.goids_fin, "read_goids")
return {'goids': self.goids_fin}
else:
# Convert dict into 2D list retaining original section order
sections_2d = []
for section_name in self.sections_seen:
if section_name in self.section2goids:
goids = self.section2goids.get(section_name)
chk_goids(goids,
"GO IDs IN SECTION({S})".format(S=section_name))
sections_2d.append((section_name, goids))
return {'sections': sections_2d}
def get_nts(self, goids=None, sortby=None):
"""Given GO IDs, get a list of namedtuples."""
nts = []
# User GO IDs
if goids is None:
goids = self.go_sources
else:
chk_goids(goids, "GoSubDag::get_nts")
if goids:
ntobj = cx.namedtuple("NtGo", " ".join(self.prt_attr['flds']))
go2nt = self.get_go2nt(goids)
for goid, ntgo in self._get_sorted_go2nt(go2nt, sortby):
assert ntgo is not None, "{GO} NOT IN go2nt".format(GO=goid)
if goid == ntgo.GO:
nts.append(ntgo)
else:
fld2vals = ntgo._asdict()
fld2vals['GO'] = goid
nts.append(ntobj(**fld2vals))
return nts
def _init_hdrgos(self, hdrgos_dflt, hdrgos_usr=None, add_dflt=True):
"""Initialize GO high"""
# Use default GO group header values
if (hdrgos_usr is None or hdrgos_usr is False) and not self.sections:
return set(hdrgos_dflt)
# Get GO group headers provided by user
hdrgos_init = set()
if hdrgos_usr:
chk_goids(hdrgos_usr, "User-provided GO group headers")
hdrgos_init |= set(hdrgos_usr)
if self.sections:
self._chk_sections(self.sections)
hdrgos_sec = set([hg for _, hdrgos in self.sections for hg in hdrgos])
chk_goids(hdrgos_sec, "User-provided GO group headers in sections")
hdrgos_init |= hdrgos_sec
# Add default depth-01 GOs to headers, if desired
if add_dflt:
return set(hdrgos_init).union(hdrgos_dflt)
# Return user-provided GO grouping headers
return hdrgos_init
def _init_hdrgos(self, hdrgos_dflt, hdrgos_usr=None, add_dflt=True):
"""Initialize GO high"""
# Use default GO group header values
if (hdrgos_usr is None or hdrgos_usr is False) and not self.sections:
return set(hdrgos_dflt)
# Get GO group headers provided by user
hdrgos_init = set()
if hdrgos_usr:
chk_goids(hdrgos_usr, "User-provided GO group headers")
hdrgos_init |= set(hdrgos_usr)
if self.sections:
self._chk_sections(self.sections)
hdrgos_sec = set(
[hg for _, hdrgos in self.sections for hg in hdrgos])
chk_goids(hdrgos_sec, "User-provided GO group headers in sections")
hdrgos_init |= hdrgos_sec
# Add default depth-01 GOs to headers, if desired
if add_dflt:
return set(hdrgos_init).union(hdrgos_dflt)
# Return user-provided GO grouping headers
return hdrgos_init