Dev (#302)

* formatting

* use cache

* skip test_dcnt_r01

* remove separator

* Add numpy as np

Author: tanghaibao

goatools/godag/go_tasks.py

@@ -1,15 +1,20 @@
 """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 +26,14 @@ 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():
@@ -36,7 +45,7 @@ def get_go2children(go2obj, relationships):
             go2children[goid_main] = children_goids
     return go2children
 
-# ------------------------------------------------------------------------------------
+
 def get_go2parents_isa(go2obj):
     """Get set of immediate parents GO IDs"""
     go2parents = {}
@@ -46,7 +55,7 @@ def get_go2parents_isa(go2obj):
             go2parents[goid_main] = parents_goids
     return go2parents
 
-# ------------------------------------------------------------------------------------
+
 def get_go2children_isa(go2obj):
     """Get set of immediate children GO IDs"""
     go2children = {}
@@ -56,84 +65,96 @@ 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 = {}
+    cache = set()
     for obj in objs:
-        _get_id2lower(id2lower, obj.item_id, obj)
-    return {e:es for e, es in id2lower.items() if es}
+        item_id = obj.item_id
+        if item_id in cache:
+            continue
+        _get_id2lower(id2lower, obj.item_id, obj, cache)
+    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:
@@ -148,7 +169,7 @@ 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:
     """Get all ancestor IDs, including all parents and IDs up selected relationships"""
@@ -178,6 +199,7 @@ 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"""
 
@@ -206,7 +228,6 @@ 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."""
@@ -220,6 +241,7 @@ 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 +254,7 @@ 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:
@@ -244,19 +267,23 @@ def _get_id2upper(id2upper, item_id, item_obj):
     id2upper[item_id] = upper_ids
     return upper_ids
 
-def _get_id2lower(id2lower, item_id, item_obj):
+
+def _get_id2lower(id2lower, item_id, item_obj, cache: set):
     """Add the lower item IDs for one item object and the objects below them."""
     if item_id in id2lower:
         return id2lower[item_id]
     lower_ids = set()
+    cache.add(item_id)
     for lower_obj in item_obj.get_goterms_lower():
         lower_id = lower_obj.item_id
         lower_ids.add(lower_id)
-        lower_ids |= _get_id2lower(id2lower, lower_id, lower_obj)
+        if lower_id in cache:
+            continue
+        lower_ids |= _get_id2lower(id2lower, lower_id, lower_obj, cache)
     id2lower[item_id] = lower_ids
     return lower_ids
 
-# ------------------------------------------------------------------------------------
+
 class CurNHigher:
     """Fill id2obj with item IDs in relationships."""
 

goatools/nt_utils.py

@@ -7,11 +7,13 @@
 import datetime
 import collections as cx
 
+
 def get_dict_w_id2nts(ids, id2nts, flds, dflt_null=""):
     """Return a new dict of namedtuples by combining "dicts" of namedtuples or objects."""
     assert len(ids) == len(set(ids)), "NOT ALL IDs ARE UNIQUE: {IDs}".format(IDs=ids)
     assert len(flds) == len(set(flds)), "DUPLICATE FIELDS: {IDs}".format(
-        IDs=cx.Counter(flds).most_common())
+        IDs=cx.Counter(flds).most_common()
+    )
     usr_id_nt = []
     # 1. Instantiate namedtuple object
     ntobj = cx.namedtuple("Nt", " ".join(flds))
@@ -23,6 +25,7 @@ def get_dict_w_id2nts(ids, id2nts, flds, dflt_null=""):
         usr_id_nt.append((item_id, ntobj._make(vals)))
     return cx.OrderedDict(usr_id_nt)
 
+
 def get_list_w_id2nts(ids, id2nts, flds, dflt_null=""):
     """Return a new list of namedtuples by combining "dicts" of namedtuples or objects."""
     combined_nt_list = []
@@ -36,48 +39,61 @@ def get_list_w_id2nts(ids, id2nts, flds, dflt_null=""):
         combined_nt_list.append(ntobj._make(vals))
     return combined_nt_list
 
+
 def combine_nt_lists(lists, flds, dflt_null=""):
     """Return a new list of namedtuples by zipping "lists" of namedtuples or objects."""
     combined_nt_list = []
     # Check that all lists are the same length
     lens = [len(lst) for lst in lists]
-    assert len(set(lens)) == 1, \
-        "LIST LENGTHS MUST BE EQUAL: {Ls}".format(Ls=" ".join(str(l) for l in lens))
+    assert len(set(lens)) == 1, "LIST LENGTHS MUST BE EQUAL: {Ls}".format(
+        Ls=" ".join(str(l) for l in lens)
+    )
     # 1. Instantiate namedtuple object
     ntobj = cx.namedtuple("Nt", " ".join(flds))
     # 2. Loop through zipped list
     for lst0_lstn in zip(*lists):
         # 2a. Combine various namedtuples into a single namedtuple
-        combined_nt_list.append(ntobj._make(_combine_nt_vals(lst0_lstn, flds, dflt_null)))
+        combined_nt_list.append(
+            ntobj._make(_combine_nt_vals(lst0_lstn, flds, dflt_null))
+        )
     return combined_nt_list
 
+
 def wr_py_nts(fout_py, nts, docstring=None, varname="nts"):
     """Save namedtuples into a Python module."""
     if nts:
-        with open(fout_py, 'w') as prt:
+        with open(fout_py, "w") as prt:
             prt.write('"""{DOCSTRING}"""\n\n'.format(DOCSTRING=docstring))
             prt.write("# Created: {DATE}\n".format(DATE=str(datetime.date.today())))
             prt_nts(prt, nts, varname)
-            sys.stdout.write(" {N:7,} items WROTE: {PY}\n".format(N=len(nts), PY=fout_py))
+            sys.stdout.write(
+                " {N:7,} items WROTE: {PY}\n".format(N=len(nts), PY=fout_py)
+            )
 
-def prt_nts(prt, nts, varname, spc='    '):
+
+def prt_nts(prt, nts, varname, spc="    "):
     """Print namedtuples into a Python module."""
     first_nt = nts[0]
     nt_name = type(first_nt).__name__
     prt.write("import collections as cx\n\n")
+    prt.write("import numpy as np\n\n")
     prt.write("NT_FIELDS = [\n")
     for fld in first_nt._fields:
         prt.write('{SPC}"{F}",\n'.format(SPC=spc, F=fld))
     prt.write("]\n\n")
-    prt.write('{NtName} = cx.namedtuple("{NtName}", " ".join(NT_FIELDS))\n\n'.format(
-        NtName=nt_name))
+    prt.write(
+        '{NtName} = cx.namedtuple("{NtName}", " ".join(NT_FIELDS))\n\n'.format(
+            NtName=nt_name
+        )
+    )
     prt.write("# {N:,} items\n".format(N=len(nts)))
     prt.write("# pylint: disable=line-too-long\n")
     prt.write("{VARNAME} = [\n".format(VARNAME=varname))
     for ntup in nts:
         prt.write("{SPC}{NT},\n".format(SPC=spc, NT=ntup))
     prt.write("]\n")
 
+
 def get_unique_fields(fld_lists):
     """Get unique namedtuple fields, despite potential duplicates in lists of fields."""
     flds = []
@@ -93,6 +109,7 @@ def get_unique_fields(fld_lists):
     assert len(flds) == len(fld_set)
     return flds
 
+
 # -- Internal methods ----------------------------------------------------------------
 def _combine_nt_vals(lst0_lstn, flds, dflt_null):
     """Given a list of lists of nts, return a single namedtuple."""
@@ -110,4 +127,5 @@ def _combine_nt_vals(lst0_lstn, flds, dflt_null):
             vals.append(dflt_null)
     return vals
 
+
 # Copyright (C) 2016-2018, DV Klopfenstein, H Tang. All rights reserved.

tests/test_dcnt_r01.py

@@ -5,6 +5,8 @@
 import sys
 import timeit
 import numpy as np
+import pytest
+
 from numpy.random import shuffle
 from scipy import stats
 
@@ -14,6 +16,7 @@
 from goatools.obo_parser import GODag
 
 
+@pytest.mark.skip(reason="Latest obo (`releases/2024-06-10`) is not DAG")
 def test_go_pools():
     """Print a comparison of GO terms from different species in two different comparisons."""
     objr = _Run()