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 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 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"
# kws = {k:v for k, v in self.kws.items() if k in self.kws_dct_wr}
# objwr.write_hier_all(prt=prt, **kws)
# max_indent=None, num_child=None, short_prt=False):
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 write_hier_up(gosubdag, out):
"""Print all paths, but mark GO Terms of interest. """
mark_dct = {'GO:0000001':'a', 'GO:0000003':'b', 'GO:0000006':'c', 'GO:0000008':'d'}
out.write('\nTEST MARK DICT: 01->03->06->08->09:\n')
objwr = WrHierGO(gosubdag, item_marks=mark_dct, sortby=lambda o: o.item_id)
gos_printed = objwr.prt_hier_up(["GO:0000005"], out)
assert gos_printed == ['GO:0000001', 'GO:0000002', 'GO:0000005', 'GO:0000003', 'GO:0000005']