class WrHierCli(object):
"""Write hierarchy cli."""
kws_set_all = set(['relationship', 'up', 'f'])
kws_dct_all = set([
'GO', 'dag', 'i', 'o', 'max_indent', 'no_indent', 'concise', 'gaf',
'gene2go', 'dash_len', 'include_only'
])
kws_dct_wr = set(
['max_indent', 'no_indent', 'concise', 'relationship', 'dash_len'])
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 get_fouts(self):
"""Get output filename."""
fouts_txt = []
if 'o' in self.kws:
fouts_txt.append(self.kws['o'])
if 'f' in self.kws:
fouts_txt.append(self._get_fout_go())
return fouts_txt
def _get_fout_go(self):
"""Get the name of an output file based on the top GO term."""
assert self.goids, "NO VALID GO IDs WERE PROVIDED"
base = next(iter(self.goids)).replace(':', '')
upstr = '_up' if 'up' in self.kws else ''
return "hier_{BASE}{UP}.{EXT}".format(BASE=base, UP=upstr, EXT='txt')
def wrtxt_hier(self, fout_txt):
"""Write hierarchy below specfied GO IDs to an ASCII file."""
with open(fout_txt, 'wb') as prt:
self.prt_hier(prt)
print(" WROTE: {TXT}".format(TXT=fout_txt))
def prt_hier(self, prt=sys.stdout):
"""Write hierarchy below specfied GO IDs."""
objwr = WrHierGO(self.gosubdag, **self.kws)
assert self.goids, "NO VALID GO IDs WERE PROVIDED"
if 'up' not in objwr.usrset:
for goid in self.goids:
objwr.prt_hier_down(goid, prt)
else:
objwr.prt_hier_up(self.goids, prt)
class WrHierCli:
"""Write hierarchy cli."""
kws_set_all = set(['relationship', 'up', 'f'])
kws_dct_all = set([
'GO', 'dag', 'i', 'o', 'max_indent', 'no_indent', 'concise', 'gaf',
'gene2go', 'taxid', 'dash_len', 'include_only', 'item_marks'
])
kws_dct_wr = set(
['max_indent', 'no_indent', 'concise', 'relationship', 'dash_len'])
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.optional_exp.intersection(self.kws.keys())
godag = get_godag(self.kws['dag'], prt, optional_attrs=opt_attrs)
self.gene2gos = read_annotations(namespace='ALL', **self.kws)
self.tcntobj = TermCounts(godag,
self.gene2gos) if self.gene2gos else None
self.gosubdag = GoSubDag(godag.keys(),
godag,
relationships='relationship' in opt_attrs,
tcntobj=self.tcntobj,
children=True,
prt=prt)
self.goids = self.init_goids(self.kws.get('GO'), self.kws.get('i'),
self.gosubdag.go2nt)
self._adj_item_marks()
self._adj_include_only()
self._adj_for_assc()
@staticmethod
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
def get_fouts(self):
"""Get output filename."""
fouts_txt = []
if 'o' in self.kws:
fouts_txt.append(self.kws['o'])
if 'f' in self.kws:
fouts_txt.append(self._get_fout_go())
return fouts_txt
def _get_fout_go(self):
"""Get the name of an output file based on the top GO term."""
assert self.goids, "NO VALID GO IDs WERE PROVIDED AS STARTING POINTS FOR HIERARCHY REPORT"
base = next(iter(self.goids)).replace(':', '')
upstr = '_up' if 'up' in self.kws else ''
return "hier_{BASE}{UP}.{EXT}".format(BASE=base, UP=upstr, EXT='txt')
def wrtxt_hier(self, fout_txt):
"""Write hierarchy below specfied GO IDs to an ASCII file."""
with open(fout_txt, 'w') as prt:
self.prt_hier(prt)
print(" WROTE: {TXT}".format(TXT=fout_txt))
def prt_hier(self, prt=sys.stdout):
"""Write hierarchy below specfied GO IDs."""
objwr = WrHierGO(self.gosubdag, **self.kws)
assert self.goids, "NO VALID GO IDs WERE PROVIDED"
if 'up' not in objwr.usrset:
for goid in self.goids:
objwr.prt_hier_down(goid, prt)
else:
objwr.prt_hier_up(self.goids, prt)
def _adj_item_marks(self):
"""Adjust keywords, if needed."""
if 'item_marks' in self.kws:
# Process GO IDs specified in item_marks
goids = self._get_goids(self.kws['item_marks'])
# item_marks can take a list of GO IDs on cmdline or in a file.
# --item_marks=GO:0043473,GO:0009987
# --item_marks=item_marks.txt
if goids:
self.kws['item_marks'] = {go: '>' for go in goids}
else:
raise Exception("NO GO IDs FOUND IN item_marks")
def _adj_include_only(self):
"""Adjust keywords, if needed."""
if 'include_only' in self.kws:
# Process GO IDs specified in include_only
goids = self._get_goids(self.kws['include_only'])
# include_only can take a list of GO IDs on cmdline or in a file.
# --include_only=GO:0043473,GO:0009987
# --include_only=include_only.txt
if goids:
self.kws['include_only'] = goids
else:
raise Exception("NO GO IDs FOUND IN include_only")
def _adj_for_assc(self):
"""Print only GO IDs from associations and their ancestors."""
if self.gene2gos:
gos_assoc = set(get_b2aset(self.gene2gos).keys())
if 'item_marks' not in self.kws:
self.kws['item_marks'] = {go: '>' for go in gos_assoc}
if 'include_only' not in self.kws:
gosubdag = GoSubDag(gos_assoc, self.gosubdag.go2obj,
self.gosubdag.relationships)
self.kws['include_only'] = gosubdag.go2obj
@staticmethod
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(',')
if os.path.exists(gostr):
return GetGOs().get_goids(None, gostr, sys.stdout)
return None
