Python recursion error

[karolina-precisionlife]

Hey, when I try to run your code I run into python recursion errors (even with the example gene lists). This is not an issue when using any other method than GOntoSlim.

from goatools.obo_parser import GODag
from goatools.base import get_godag
import pandas as pd
import requests, sys

from GOntoSim import Similarity_of_Two_GOTerms, Similarity_of_Set_of_GOTerms, Semantic_Value

go = get_godag("go-basic.obo", optional_attrs={'relationship'})

gene1 = ['GO:0004022','GO:0004024', 'GO:0004174', 'GO:0046872','GO:0008270','GO:0004023', 'GO:0016491']
gene2 = ['GO:0009055','GO:0005515','GO:0046872','GO:0008270','GO:0020037']

unique_goterms = list(set().union(gene1, gene2))
S_values = [(x,Semantic_Value(x, go, 'Baseline_LCA_avg')) for x in unique_goterms ]
S_values = dict(S_values)
Similarity_of_Set_of_GOTerms(gene1, gene2, 'GOntoSim', S_values)

Traceback:

RecursionError                            Traceback (most recent call last)

File [~/Code/cross-study-vis/GOntoSim.py:796](https://vscode-remote+wsl-002bubuntu-002d18-002e04.vscode-resource.vscode-cdn.net/home/karolina/Code/cross-study-vis/~/Code/cross-study-vis/GOntoSim.py:796), in Similarity_of_Set_of_GOTerms(set1, set2, method, S_values)
    793     Sim1.append([])
    794     for goid in set2:
    795         #print (goterm , goid)
--> 796         Sim1[idx].append((goterm, goid,(Similarity_of_Two_GOTerms(goterm, goid, go, method, S_values))))
    797 #print(Sim1)
    798 #print([y[0][0] for y in Sim1])
    799 #print([[y[1] for y in  x] for x in Sim1])
    800 #print([y[1] for y in Sim1[0]])
    801 
    802 #print(pd.DataFrame(data = [[y[2] for y in  x] for x in Sim1], index = [y[0][0] for y in Sim1], columns = [y[1] for y in Sim1[0]]))
    804 for idx, goterm in enumerate(set2):

File [~/Code/cross-study-vis/GOntoSim.py:669](https://vscode-remote+wsl-002bubuntu-002d18-002e04.vscode-resource.vscode-cdn.net/home/karolina/Code/cross-study-vis/~/Code/cross-study-vis/GOntoSim.py:669), in Similarity_of_Two_GOTerms(go_id1, go_id2, go, method, S_values)
    667 else:   
    668     if go_id1 != 'GO:0003674' and go_id1 !='GO:0005575' and go_id1 != 'GO:0008150' and  go_id2 != 'GO:0003674' and go_id2 !='GO:0005575' and go_id2 != 'GO:0008150':
--> 669         hcd = highest_common_descendant((go_id1, go_id2), go)
    670         if hcd != 0:
    671             hcd_depth = go[hcd].depth

File [~/Code/cross-study-vis/GOntoSim.py:464](https://vscode-remote+wsl-002bubuntu-002d18-002e04.vscode-resource.vscode-cdn.net/home/karolina/Code/cross-study-vis/~/Code/cross-study-vis/GOntoSim.py:464), in highest_common_descendant(goterms, godag)
    458 '''
    459     This function gets the nearest common descendant
    460     using the above function.
    461     Only returns single most specific - assumes unique exists.
    462 '''
    463 # Take the element at minimum depth.
--> 464 common_children = common_children_go_ids(goterms, godag)
    465 if len(common_children) != 0:
    466     return min(common_children, key=lambda t: godag[t].depth)

File [~/Code/cross-study-vis/GOntoSim.py:446](https://vscode-remote+wsl-002bubuntu-002d18-002e04.vscode-resource.vscode-cdn.net/home/karolina/Code/cross-study-vis/~/Code/cross-study-vis/GOntoSim.py:446), in common_children_go_ids(goids, godag)
    444 rec = godag[goids[0]]
    445 #candidates = rec.get_all_children()
--> 446 candidates = rec.get_all_lower()
    447 candidates.update({goids[0]})
    448 # Find intersection with second to nth goid

File [~/Code/cross-study-vis/cross-study-vis-venv/lib/python3.9/site-packages/goatools/obo_parser.py:255](https://vscode-remote+wsl-002bubuntu-002d18-002e04.vscode-resource.vscode-cdn.net/home/karolina/Code/cross-study-vis/~/Code/cross-study-vis/cross-study-vis-venv/lib/python3.9/site-packages/goatools/obo_parser.py:255), in GOTerm.get_all_lower(self)
    253 for lower in self.get_goterms_lower():
    254     all_lower.add(lower.item_id)
--> 255     all_lower |= lower.get_all_lower()
    256 return all_lower

File [~/Code/cross-study-vis/cross-study-vis-venv/lib/python3.9/site-packages/goatools/obo_parser.py:255](https://vscode-remote+wsl-002bubuntu-002d18-002e04.vscode-resource.vscode-cdn.net/home/karolina/Code/cross-study-vis/~/Code/cross-study-vis/cross-study-vis-venv/lib/python3.9/site-packages/goatools/obo_parser.py:255), in GOTerm.get_all_lower(self)
    253 for lower in self.get_goterms_lower():
    254     all_lower.add(lower.item_id)
--> 255     all_lower |= lower.get_all_lower()
    256 return all_lower

    [... skipping similar frames: GOTerm.get_all_lower at line 255 (2964 times)]

File [~/Code/cross-study-vis/cross-study-vis-venv/lib/python3.9/site-packages/goatools/obo_parser.py:255](https://vscode-remote+wsl-002bubuntu-002d18-002e04.vscode-resource.vscode-cdn.net/home/karolina/Code/cross-study-vis/~/Code/cross-study-vis/cross-study-vis-venv/lib/python3.9/site-packages/goatools/obo_parser.py:255), in GOTerm.get_all_lower(self)
    253 for lower in self.get_goterms_lower():
    254     all_lower.add(lower.item_id)
--> 255     all_lower |= lower.get_all_lower()
    256 return all_lower

File [~/Code/cross-study-vis/cross-study-vis-venv/lib/python3.9/site-packages/goatools/obo_parser.py:253](https://vscode-remote+wsl-002bubuntu-002d18-002e04.vscode-resource.vscode-cdn.net/home/karolina/Code/cross-study-vis/~/Code/cross-study-vis/cross-study-vis-venv/lib/python3.9/site-packages/goatools/obo_parser.py:253), in GOTerm.get_all_lower(self)
    251 """Return all parent GO IDs through both reverse 'is_a' and all relationships."""
    252 all_lower = set()
--> 253 for lower in self.get_goterms_lower():
    254     all_lower.add(lower.item_id)
    255     all_lower |= lower.get_all_lower()

File [~/Code/cross-study-vis/cross-study-vis-venv/lib/python3.9/site-packages/goatools/obo_parser.py:295](https://vscode-remote+wsl-002bubuntu-002d18-002e04.vscode-resource.vscode-cdn.net/home/karolina/Code/cross-study-vis/~/Code/cross-study-vis/cross-study-vis-venv/lib/python3.9/site-packages/goatools/obo_parser.py:295), in GOTerm.get_goterms_lower(self)
    292 """Returns a set containing children and all reverse-relationship GO Terms."""
    293 # Requires GODag is created with 'relationship' in optional_attrs argument
    294 # pylint: disable=no-member
--> 295 return set.union(self.children, *self.relationship_rev.values())

RecursionError: maximum recursion depth exceeded while calling a Python object

As you see I am using the GOntoSim.py , is that the correct one to use? the SImilarity.py looks quite similar but doesn't need the semantic similarity to be calculated prior?

I am super happy smb wrote smth for the GO similarity in python as most of it is in R :/

Thanks a lot

[A-Kamran]

Hi,

I've attempted to replicate the issue you reported but couldn't do so successfully. The GOntoSim method is running fine for me (even on a completely new machine). Even running the exact same code you have provided in this issue gives a similarity value as can be seen in the attached screenshot. It's possible the issue is environment-specific.

Please ensure you're using the latest version and provide more specific details if the problem persists.

Your feedback is valuable, and we're here to assist further if needed.

[karolina-precisionlife]

Hey thanks a lot.

I have attempted to rerun it in a new venv but still getting the same issue. I am also getting a slighly different print output for some reason (additional GOID printed?):

python3 gontsim_test.py
  EXISTS: go-basic.obo
go-basic.obo: fmt(1.2) rel(2022-09-19) 46,823 Terms; optional_attrs(relationship)
  EXISTS: go-basic.obo
go-basic.obo: fmt(1.2) rel(2022-09-19) 46,823 Terms; optional_attrs(relationship)
GO:0003674
GO:0022900
GO:0005488
Traceback (most recent call last):
  File "/home/karolina/Code/cross-study-vis/gontsim_test.py", line 17, in <module>
    print(Similarity_of_Set_of_GOTerms(gene1, gene2, 'GOntoSim', S_values))
  File "/home/karolina/Code/cross-study-vis/GOntoSim.py", line 796, in Similarity_of_Set_of_GOTerms
    Sim1[idx].append((goterm, goid,(Similarity_of_Two_GOTerms(goterm, goid, go, method, S_values))))
  File "/home/karolina/Code/cross-study-vis/GOntoSim.py", line 669, in Similarity_of_Two_GOTerms
    hcd = highest_common_descendant((go_id1, go_id2), go)
  File "/home/karolina/Code/cross-study-vis/GOntoSim.py", line 464, in highest_common_descendant
    common_children = common_children_go_ids(goterms, godag)
  File "/home/karolina/Code/cross-study-vis/GOntoSim.py", line 446, in common_children_go_ids
    candidates = rec.get_all_lower()
  File "/home/karolina/Code/cross-study-vis/.venv/lib/python3.9/site-packages/goatools/obo_parser.py", line 251, in get_all_lower
    all_lower |= lower.get_all_lower()
  File "/home/karolina/Code/cross-study-vis/.venv/lib/python3.9/site-packages/goatools/obo_parser.py", line 251, in get_all_lower
    all_lower |= lower.get_all_lower()
  File "/home/karolina/Code/cross-study-vis/.venv/lib/python3.9/site-packages/goatools/obo_parser.py", line 251, in get_all_lower
    all_lower |= lower.get_all_lower()
  [Previous line repeated 990 more times]
  File "/home/karolina/Code/cross-study-vis/.venv/lib/python3.9/site-packages/goatools/obo_parser.py", line 249, in get_all_lower
    for lower in self.get_goterms_lower():
  File "/home/karolina/Code/cross-study-vis/.venv/lib/python3.9/site-packages/goatools/obo_parser.py", line 291, in get_goterms_lower
    return set.union(self.children, *self.relationship_rev.values())
RecursionError: maximum recursion depth exceeded while calling a Python object

My pip freeze:

asttokens==2.4.0
backcall==0.2.0
certifi==2023.7.22
charset-normalizer==3.3.1
comm==0.1.4
debugpy==1.8.0
decorator==5.1.1
docopt==0.6.2
et-xmlfile==1.1.0
exceptiongroup==1.1.3
executing==2.0.0
goatools==1.3.9
idna==3.4
importlib-metadata==6.8.0
ipykernel==6.25.2
ipython==8.16.1
jedi==0.19.1
joblib==1.3.2
jupyter_client==8.4.0
jupyter_core==5.4.0
matplotlib-inline==0.1.6
nest-asyncio==1.5.8
numpy==1.26.1
openpyxl==3.1.2
packaging==23.2
pandas==2.1.1
parso==0.8.3
patsy==0.5.3
pexpect==4.8.0
pickleshare==0.7.5
platformdirs==3.11.0
prompt-toolkit==3.0.39
psutil==5.9.6
ptyprocess==0.7.0
pure-eval==0.2.2
pydot==1.4.2
Pygments==2.16.1
pyparsing==3.1.1
python-dateutil==2.8.2
pytz==2023.3.post1
pyzmq==25.1.1
requests==2.31.0
scikit-learn==1.3.1
scipy==1.11.3
six==1.16.0
stack-data==0.6.3
statsmodels==0.14.0
threadpoolctl==3.2.0
tornado==6.3.3
traitlets==5.11.2
typing_extensions==4.8.0
tzdata==2023.3
urllib3==2.0.7
wcwidth==0.2.8
XlsxWriter==3.1.9
zipp==3.17.0

[A-Kamran]

Can you please share the gene ontology file you are using? Also, let me know your Python version.