formatting

goatools/godag/go_tasks.py

@@ -1,15 +1,21 @@
 """item-DAG tasks."""
 
-__copyright__ = "Copyright (C) 2010-present, DV Klopfenstein, H Tang, All rights reserved."
+__copyright__ = (
+ "Copyright (C) 2010-present, DV Klopfenstein, H Tang, All rights reserved."
+)
 __author__ = "DV Klopfenstein"
 
-from goatools.godag.consts import RELATIONSHIP_SET
+from ..godag.consts import RELATIONSHIP_SET
 
 
 # ------------------------------------------------------------------------------------
 def get_go2parents(go2obj, relationships):
  """Get set of parents GO IDs, including parents through user-specfied relationships"""
- if go2obj and not hasattr(next(iter(go2obj.values())), 'relationship') or not relationships:
+ if (
+ go2obj
+ and not hasattr(next(iter(go2obj.values())), "relationship")
+ or not relationships
+ ):
  return get_go2parents_isa(go2obj)
  go2parents = {}
  for goid_main, goterm in go2obj.items():
@@ -21,10 +27,15 @@ def get_go2parents(go2obj, relationships):
  go2parents[goid_main] = parents_goids
  return go2parents
 
+
 # ------------------------------------------------------------------------------------
 def get_go2children(go2obj, relationships):
  """Get set of children GO IDs, including children through user-specfied relationships"""
- if go2obj and not hasattr(next(iter(go2obj.values())), 'relationship') or not relationships:
+ if (
+ go2obj
+ and not hasattr(next(iter(go2obj.values())), "relationship")
+ or not relationships
+ ):
  return get_go2children_isa(go2obj)
  go2children = {}
  for goid_main, goterm in go2obj.items():
@@ -36,6 +47,7 @@ def get_go2children(go2obj, relationships):
  go2children[goid_main] = children_goids
  return go2children
 
+
 # ------------------------------------------------------------------------------------
 def get_go2parents_isa(go2obj):
  """Get set of immediate parents GO IDs"""
@@ -46,6 +58,7 @@ def get_go2parents_isa(go2obj):
  go2parents[goid_main] = parents_goids
  return go2parents
 
+
 # ------------------------------------------------------------------------------------
 def get_go2children_isa(go2obj):
  """Get set of immediate children GO IDs"""
@@ -56,84 +69,95 @@ def get_go2children_isa(go2obj):
  go2children[goid_main] = children_goids
  return go2children
 
+
 # ------------------------------------------------------------------------------------
 def get_go2ancestors(terms, relationships, prt=None):
  """Get GO-to- ancestors (all parents)"""
  if not relationships:
  if prt is not None:
- prt.write('up: is_a\n')
+ prt.write("up: is_a\n")
  return get_id2parents(terms)
  if relationships == RELATIONSHIP_SET or relationships is True:
  if prt is not None:
- prt.write('up: is_a and {Rs}\n'.format(
- Rs=' '.join(sorted(RELATIONSHIP_SET))))
+ prt.write(
+ "up: is_a and {Rs}\n".format(Rs=" ".join(sorted(RELATIONSHIP_SET)))
+ )
  return get_id2upper(terms)
  if prt is not None:
- prt.write('up: is_a and {Rs}\n'.format(
- Rs=' '.join(sorted(relationships))))
+ prt.write("up: is_a and {Rs}\n".format(Rs=" ".join(sorted(relationships))))
  return get_id2upperselect(terms, relationships)
 
+
 def get_go2descendants(terms, relationships, prt=None):
  """Get GO-to- descendants"""
  if not relationships:
  if prt is not None:
- prt.write('down: is_a\n')
+ prt.write("down: is_a\n")
  return get_id2children(terms)
  if relationships == RELATIONSHIP_SET or relationships is True:
  if prt is not None:
- prt.write('down: is_a and {Rs}\n'.format(
- Rs=' '.join(sorted(RELATIONSHIP_SET))))
+ prt.write(
+ "down: is_a and {Rs}\n".format(Rs=" ".join(sorted(RELATIONSHIP_SET)))
+ )
  return get_id2lower(terms)
  if prt is not None:
- prt.write('down: is_a and {Rs}\n'.format(
- Rs=' '.join(sorted(relationships))))
+ prt.write("down: is_a and {Rs}\n".format(Rs=" ".join(sorted(relationships))))
  return get_id2lowerselect(terms, relationships)
 
+
 # ------------------------------------------------------------------------------------
 def get_go2depth(goobjs, relationships):
  """Get depth of each object"""
  if not relationships:
- return {o.item_id:o.depth for o in goobjs}
+ return {o.item_id: o.depth for o in goobjs}
  from goatools.godag.reldepth import get_go2reldepth
+
  return get_go2reldepth(goobjs, relationships)
 
+
 # ------------------------------------------------------------------------------------
 def get_id2parents(objs):
  """Get all parent IDs up the hierarchy"""
  id2parents = {}
  for obj in objs:
  _get_id2parents(id2parents, obj.item_id, obj)
- return {e:es for e, es in id2parents.items() if es}
+ return {e: es for e, es in id2parents.items() if es}
+
 
 def get_id2children(objs):
  """Get all child IDs down the hierarchy"""
  id2children = {}
  for obj in objs:
  _get_id2children(id2children, obj.item_id, obj)
- return {e:es for e, es in id2children.items() if es}
+ return {e: es for e, es in id2children.items() if es}
+
 
 def get_id2upper(objs):
  """Get all ancestor IDs, including all parents and IDs up all relationships"""
  id2upper = {}
  for obj in objs:
  _get_id2upper(id2upper, obj.item_id, obj)
- return {e:es for e, es in id2upper.items() if es}
+ return {e: es for e, es in id2upper.items() if es}
+
 
 def get_id2lower(objs):
  """Get all descendant IDs, including all children and IDs down all relationships"""
  id2lower = {}
  for obj in objs:
  _get_id2lower(id2lower, obj.item_id, obj)
- return {e:es for e, es in id2lower.items() if es}
+ return {e: es for e, es in id2lower.items() if es}
+
 
 def get_id2upperselect(objs, relationship_set):
  """Get all ancestor IDs, including all parents and IDs up selected relationships"""
  return IdToUpperSelect(objs, relationship_set).id2upperselect
 
+
 def get_id2lowerselect(objs, relationship_set):
  """Get all descendant IDs, including all children and IDs down selected relationships"""
  return IdToLowerSelect(objs, relationship_set).id2lowerselect
 
+
 def get_relationship_targets(item_ids, relationships, id2rec):
  """Get item ID set of item IDs in a relationship target set"""
  # Requirements to use this function:
@@ -148,6 +172,7 @@ def get_relationship_targets(item_ids, relationships, id2rec):
  reltgt_objs_all.update(reltgt_objs_cur)
  return reltgt_objs_all
 
+
 # ------------------------------------------------------------------------------------
 # pylint: disable=too-few-public-methods
 class IdToUpperSelect:
@@ -178,6 +203,7 @@ def _get_id2upperselect(self, item_id, item_obj):
  id2upperselect[item_id] = parent_ids
  return parent_ids
 
+
 class IdToLowerSelect:
  """Get all descendant IDs, including all children and IDs down selected relationships"""
 
@@ -206,8 +232,10 @@ def _get_id2lowerselect(self, item_id, item_obj):
  id2lowerselect[item_id] = child_ids
  return child_ids
 
+
 # ------------------------------------------------------------------------------------
 
+
 def _get_id2parents(id2parents, item_id, item_obj):
  """Add the parent item IDs for one item object and their parents."""
  if item_id in id2parents:
@@ -220,6 +248,7 @@ def _get_id2parents(id2parents, item_id, item_obj):
  id2parents[item_id] = parent_ids
  return parent_ids
 
+
 def _get_id2children(id2children, item_id, item_obj):
  """Add the child item IDs for one item object and their children."""
  if item_id in id2children:
@@ -232,6 +261,7 @@ def _get_id2children(id2children, item_id, item_obj):
  id2children[item_id] = child_ids
  return child_ids
 
+
 def _get_id2upper(id2upper, item_id, item_obj):
  """Add the parent item IDs for one item object and their upper."""
  if item_id in id2upper:
@@ -244,6 +274,7 @@ def _get_id2upper(id2upper, item_id, item_obj):
  id2upper[item_id] = upper_ids
  return upper_ids
 
+
 def _get_id2lower(id2lower, item_id, item_obj):
  """Add the lower item IDs for one item object and the objects below them."""
  if item_id in id2lower:
@@ -256,6 +287,7 @@ def _get_id2lower(id2lower, item_id, item_obj):
  id2lower[item_id] = lower_ids
  return lower_ids
 
+
 # ------------------------------------------------------------------------------------
 class CurNHigher:
  """Fill id2obj with item IDs in relationships."""