Closed otienoanyango closed 4 months ago
bgsu-rna-pipeline
commented
4 months ago Many thanks for the bug report!
This error came from line 2731 of NA_pairwise_interactions.py, and not line 273 as it says in the traceback.
Cause was an unusual case trying to use a variable that had not been defined. That is fixed now.
Testing on the latest representative set release, will update again if any more problems are found.
clzirbel
commented
4 months ago Fixed and closed. Thank you for the bug report!
From: Otieno Anyango @.> Sent: Friday, June 14, 2024 9:44 AM To: BGSU-RNA/fr3d-python @.> Cc: Subscribed @.***> Subject: [EXTERNAL] [BGSU-RNA/fr3d-python] UnboundLocalError: local variable 'LW_bond_rank' referenced before assignment (Issue #40)
https://www.ebi.ac.uk/pdbe/entry-files/download/8r3v.cif
Some CIF files fail with the above error:
Sample traceback for the 8r3v entry:
Traceback (most recent call last):
File "/venv/lib/python3.10/site-packages/orc/base/batchable.py", line 351, in process_remote
self.__process_entry(entry)File "/venv/lib/python3.10/site-packages/orc/base/batchable.py", line 376, in __process_entry
self.process_entry(entry_id)File "/venv/lib/python3.10/site-packages/orc/rna/pairwise_interactions.py", line 112, in process>
generatePairwiseAnnotation(File "/venv/lib/python3.10/site-packages/fr3d/classifiers/NA_pairwise_interactions.py", line 323>
interaction_to_list_of_tuples, category_to_interactions, timerData, pair_to_data = annotate_nt_nt_in_structure(structure,categories,focused_bas>File "/venv/lib/python3.10/site-packages/fr3d/classifiers/NA_pairwise_interactions.py", line 123>
interaction_to_list_of_tuples, category_to_interactions, timerData, pair_to_data = annotate_nt_nt_interactions(bases, nt_nt_screen_distance, ba>File "/venv/lib/python3.10/site-packages/fr3d/classifiers/NA_pairwise_interactions.py", line 916>
interaction21, subcategory21, quality21, datapoint21 = check_basepair_cutoffs(nt2,nt1,pair_data,cutoffs,hydrogen_bonds,datapoint21)File "/venv/lib/python3.10/site-packages/fr3d/classifiers/NA_pairwise_interactions.py", line 273>
for LW,bond_counter,checked_counter,max_badness in LW_bond_rank:UnboundLocalError: local variable 'LW_bond_rank' referenced before assignment
Reading file /tmp/tmp3sy7_4d2/8r3v, which is number 1 out of 1
Duplicate annotation in second direction: ntWW and ntWWa for 8R3V|1|X2|C|49 and 8R3V|1|X2|C|16
http://rna.bgsu.edu/rna3dhub/display3D/unitid/8R3V|1|X2|C|16,8R3V|1|X2|C|49http://rna.bgsu.edu/rna3dhub/display3D/unitid/8R3V%7C1%7CX2%7CC%7C16,8R3V%7C1%7CX2%7CC%7C49
Using ntWW
http://rna.bgsu.edu/rna3dhub/display3D/unitid/8R3V|1|X2|A|20,8R3V|1|X2|C|57http://rna.bgsu.edu/rna3dhub/display3D/unitid/8R3V%7C1%7CX2%7CA%7C20,8R3V%7C1%7CX2%7CC%7C57
Multiple annotations meet all cutoffs, {'cWS', 'cWW'}
- Reply to this email directly, view it on GitHubhttps://github.com/BGSU-RNA/fr3d-python/issues/40, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAHQ7E7MEJ6RINICEL3E2A3ZHLXSVAVCNFSM6AAAAABJKMPWDGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGM2TGNBRHE4DSNQ. You are receiving this because you are subscribed to this thread.Message ID: @.**@.>>
https://www.ebi.ac.uk/pdbe/entry-files/download/8r3v.cif
Some CIF files fail with the above error:
Sample traceback for the 8r3v entry: