def get_go_color(self, **kws):
"""Return source GO IDs and GO color, if provided."""
ret = {'GOs': set(), 'go2color': {}}
if 'go_color_file' in kws:
_, go2color = ClassGetGOs.rdtxt_gos_color(kws['go_color_file'])
self._update_ret(ret, None, go2color)
if 'GO' in kws:
# goids, go2color = self._goargs(ret, kws['GO'])
goids, go2color = ClassGetGOs.get_goargs(kws['GO'], prt=sys.stdout)
self._update_ret(ret, goids, go2color)
if 'go_file' in kws:
goids, go2color = ClassGetGOs.rdtxt_gos_color(kws['go_file'])
self._update_ret(ret, goids, go2color)
if 'draw-children' in kws:
ret['GOs'].update(get_leaf_children(ret['GOs'], self.go2obj))
# If there have been no GO IDs explicitly specified by the user
if not ret['GOs']:
# If the GO-DAG is sufficiently small, print all GO IDs
if len(self.go2obj) < self.max_gos:
main_gos = set(o.id for go, o in self.go2obj.items()
if go != o.id)
go_leafs = set(go for go, o in self.go2obj.items()
if not o.children)
ret['GOs'] = go_leafs.difference(main_gos)
go2obj = {go: self.go2obj[go] for go in ret['GOs']}
ret['GOs'] = set(get_go2obj_unique(go2obj))
return [ret['GOs'], ret['go2color']]
def _init_go_sets(self, go_fins):
"""Get lists of GO IDs."""
go_sets = []
assert go_fins, "EXPECTED FILES CONTAINING GO IDs"
assert len(go_fins) >= 2, "EXPECTED 2+ GO LISTS. FOUND: {L}".format(
L=' '.join(go_fins))
obj = GetGOs(self.godag)
for fin in go_fins:
assert os.path.exists(fin), "GO FILE({F}) DOES NOT EXIST".format(F=fin)
go_sets.append(obj.get_usrgos(fin, sys.stdout))
return go_sets
def _init_go_sets(self, go_fins):
"""Get lists of GO IDs."""
go_sets = []
assert go_fins, "EXPECTED FILES CONTAINING GO IDs"
assert len(go_fins) >= 2, "EXPECTED 2+ GO LISTS. FOUND: {L}".format(
L=' '.join(go_fins))
obj = GetGOs(self.godag)
for fin in go_fins:
assert os.path.exists(fin), "GO FILE({F}) DOES NOT EXIST".format(F=fin)
go_sets.append(obj.get_usrgos(fin, sys.stdout))
return go_sets
def _get_goids(gostr):
"""Return GO IDs from a GO str (e.g., GO:0043473,GO:0009987) or a file."""
if 'GO:' in gostr:
return gostr.split(',')
elif os.path.exists(gostr):
return GetGOs().get_goids(None, gostr, sys.stdout)
return None
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_remove_goids(self):
"""Get arguments to get a list of broad GO IDs to remove"""
# None: (Default) Remove a small number (~14) of broad GO IDs from the association
if self.args.remove_goids is None:
return self.args.remove_goids
# True: Remove a slightly larger number of broad GO IDs (~100)
if self.args.remove_goids.lower() == 'true':
return True
# False: Do not remove any broad GO IDs
if self.args.remove_goids.lower() == 'false':
return False
if os.path.exists(self.args.remove_goids):
GetGOs.rdtxt_gos(self.args.remove_goids, sys.stdout)
if isinstance(self.args.remove_goids,
str) and 'GO' in self.args.remove_goids:
return self.args.remove_goids.split(',')
return None
def cli(self, prt=sys.stdout):
"""Command-line interface to print specified GO Terms from the DAG source ."""
kws = self.objdoc.get_docargs(prt=None)
print("KWS", kws)
goids = GetGOs().get_goids(kws.get('GO'), kws.get('GO_FILE'),
sys.stdout)
if not goids and 'name' in kws:
goids = self.objsub.get_goids(kws['obo'], kws['name'])
self.objsub.prt_goterms(kws['obo'], goids, prt, b_prt=False)
print("Printing {N:6} GO IDs: {GOs}".format(N=len(goids), GOs=goids))
def __init__(self, args=None, prt=sys.stdout):
self.kws = DocOptParse(__doc__, self.kws_dct_all,
self.kws_set_all).get_docargs(
args,
intvals=set(['max_indent', 'dash_len']))
opt_attrs = OboOptionalAttrs.attributes.intersection(self.kws.keys())
godag = get_godag(self.kws['dag'], prt, optional_attrs=opt_attrs)
self.gosubdag = GoSubDag(godag.keys(),
godag,
relationships='relationship' in opt_attrs,
tcntobj=get_tcntobj(godag, **self.kws),
children=True,
prt=prt)
self.goids = GetGOs().get_goids(self.kws.get('GO'), self.kws.get('i'),
sys.stdout)
def _init_goids(self):
goids_ret = []
if 'GO' in self.kws:
for goid in self.kws['GO']:
if goid[:3] == "GO:":
assert len(goid) == 10, "BAD GO ID({GO})".format(GO=goid)
goids_ret.append(goid)
elif goid in NS2GO:
goids_ret.append(NS2GO[goid])
if 'i' in self.kws:
goids_fin = GetGOs().rdtxt_gos(self.kws['i'], sys.stdout)
if goids_fin:
goids_ret.extend(list(goids_fin))
if goids_ret:
return goids_ret
# If GO DAG is small, print hierarchy for the entire DAG
if len(self.gosubdag.go2nt) < 100:
return set(self.gosubdag.go2nt.keys())
return None
def init_goids(goids_args, infile, go2nt):
"""Extract GO IDs in the report from arguments"""
goids_ret = []
if goids_args is not None:
for goid in goids_args:
if goid[:3] == "GO:":
assert len(goid) == 10, "BAD GO ID({GO})".format(GO=goid)
goids_ret.append(goid)
elif goid in NS2GO:
goids_ret.append(NS2GO[goid])
if infile is not None:
goids_fin = GetGOs().rdtxt_gos(infile, sys.stdout)
if goids_fin:
goids_ret.extend(list(goids_fin))
if goids_ret:
return goids_ret
# If GO DAG is small, print hierarchy for the entire DAG
if len(go2nt) < 100:
return set(go2nt.keys())
return None
