Goreverselookup

MacOS absolut filepath duplication error in FileUtil check_path function. Resulted in duplicate base paths, such as:


2024-10-15 07:34:18,373 [DEBUG] check_path: path=Users/simonzetko/goreverselookup/research_models/10oct_allsteps_ortho/IEAda/2IEA+indann8/results/data.json, is_file=True, auto_create=False
2024-10-15 07:34:18,373 [DEBUG] check_path: path converted to absolute path: /Users/simonzetko/Users/simonzetko/goreverselookup/research_models/10oct_allsteps_ortho/IEAda/2IEA+indann8/results/data.json
2024-10-15 07:34:18,373 [DEBUG] check_path: dir_path=/Users/simonzetko/Users/simonzetko/goreverselookup/research_models/10oct_allsteps_ortho/IEAda/2IEA+indann8/results
2024-10-15 07:34:18,373 [DEBUG] check_path: Doesn't exist: '**/Users/simonzetko/Users/simonzetko**/goreverselookup/research_models/10oct_allsteps_ortho/IEAda/2IEA+indann8/results/data.json'
Model data was not found by auto-infer.
Report is True, but no model data (data.json) files were found. You need to keep both statistically_relevant_genes.json and data.json in the same folders wihtout deleting them!

Bugfix in response to:


2024-10-13 09:02:22,598 [INFO] create_products_from_goterms: Created 47 Product objects from GOTerm object definitions
2024-10-13 09:02:22,598 [INFO] create_products_from_goterms: Total Product objects in ReverseLookup model: 29809
2024-10-13 09:02:22,598 [INFO] print_elapsed_time: Elapsed: 0:00:10
2024-10-13 09:02:22,598 [INFO] save_data: Cacher is saving data. Please, be patient.
2024-10-13 09:02:22,598 [INFO] save_data: Successfully saved url, uniprot, ensembl, geneontology and gprofiler cache.
Traceback (most recent call last):
File "/Users/simonzetko/goreverselookup/bin/goreverselookup", line 5, in <module>
from goreverselookup.main_cli import main
File "/Users/simonzetko/goreverselookup/lib/python3.11/site-packages/goreverselookup/main_cli.py", line 276, in <module>
model = main(input_file=f, destination_dir=destination_dir, report=report, model_data_filepath=model_data_filepath, rescore_model=static_rescore_model)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/simonzetko/goreverselookup/lib/python3.11/site-packages/goreverselookup/main_cli.py", line 173, in main
model.fetch_orthologs_products_batch_gOrth(target_taxon_number=f"{model.model_settings.target_organism.ncbi_id}") TODO: change!
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/simonzetko/goreverselookup/lib/python3.11/site-packages/goreverselookup/Model.py", line 823, in fetch_orthologs_products_batch_gOrth
ortholog_query_dict[product_taxon_number].append(p_id)
~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^
KeyError: '101163'
2024-10-13 09:02:22,607 [INFO] save_data: Cacher is saving data. Please, be patient.
2024-10-13 09:02:22,607 [INFO] save_data: Successfully saved url, uniprot, ensembl, geneontology and gprofiler cache.

Code works on Windows but not on MacOS. Presumed error in the FileUtil.check_path function (returns True on Windows and False on MacOS for a filepath that exists).

Debug output after the previous commit:


(goreverselookup) simonzetkoSimons-Laptop ~ % goreverselookup "statistically_relevant_genes.json" --report True --full_directory_op "/Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne"

2024-10-03 09:11:11,952 [INFO] setup_logging_config: Setup log config using: config/logging_config.json
2024-10-03 09:11:11,952 [INFO] <module>: Starting GOReverseLookup analysis!
2024-10-03 09:11:11,952 [INFO] <module>: os.getcwd() = /Users/simonzetko

No model data filepath was specified, auto-inferring model data.

2024-10-03 09:11:11,953 [DEBUG] backtrace: filepath=statistically_relevant_genes.json, backtrace=1, file_separator=/
2024-10-03 09:11:11,953 [WARNING] backtrace: Backtrace 1 is greater than final element index 0 for filepath statistically_relevant_genes.json! Returning ''.
2024-10-03 09:11:11,953 [DEBUG] check_path: path=data.json, is_file=True, auto_create=False
2024-10-03 09:11:11,953 [DEBUG] check_path: dir_path=
2024-10-03 09:11:11,953 [DEBUG] check_path: Doesn't exist: 'data.json'
Model data not found. Attempted file search at None

Found the following input files:
- [0]: /Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/8IEA-noindann8/results/statistically_relevant_genes.json
- [1]: /Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/7IEA-noindann5/results/statistically_relevant_genes.json
- [2]: /Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/5IEA-indann5/results/statistically_relevant_genes.json
- [3]: /Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/6IEA-indann8/results/statistically_relevant_genes.json

2024-10-03 09:11:11,955 [INFO] main: Starting GOReverseLookup analysis with input params:
2024-10-03 09:11:11,955 [INFO] main: - input_file: /Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/8IEA-noindann8/results/statistically_relevant_genes.json
2024-10-03 09:11:11,955 [INFO] main: - destination_dir: None
2024-10-03 09:11:11,955 [INFO] main: - report: True
2024-10-03 09:11:11,955 [INFO] main: - model_data_filepath: None

2024-10-03 09:11:11,955 [INFO] main: Model data filepath was None. Attempting auto infer data.json from /Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/8IEA-noindann8/results/statistically_relevant_genes.json
2024-10-03 09:11:11,955 [DEBUG] backtrace: filepath=/Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/8IEA-noindann8/results/statistically_relevant_genes.json, backtrace=1, file_separator=/
2024-10-03 09:11:11,955 [DEBUG] backtrace: elements=['', 'Users', 'simonzetko', 'goreverselookup', 'research_models', '2oct_natural_amigo_ortho', 'IEAne', '8IEA-noindann8', 'results', 'statistically_relevant_genes.json']
2024-10-03 09:11:11,955 [DEBUG] backtrace: res_elements=['', 'Users', 'simonzetko', 'goreverselookup', 'research_models', '2oct_natural_amigo_ortho', 'IEAne', '8IEA-noindann8', 'results']
2024-10-03 09:11:11,955 [DEBUG] backtrace: _ building final path
2024-10-03 09:11:11,955 [DEBUG] backtrace: - final_path=
2024-10-03 09:11:11,955 [DEBUG] backtrace: - final_path=Users
2024-10-03 09:11:11,955 [DEBUG] backtrace: - final_path=Users/simonzetko
2024-10-03 09:11:11,955 [DEBUG] backtrace: - final_path=Users/simonzetko/goreverselookup
2024-10-03 09:11:11,955 [DEBUG] backtrace: - final_path=Users/simonzetko/goreverselookup/research_models
2024-10-03 09:11:11,955 [DEBUG] backtrace: - final_path=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho
2024-10-03 09:11:11,955 [DEBUG] backtrace: - final_path=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne
2024-10-03 09:11:11,955 [DEBUG] backtrace: - final_path=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/8IEA-noindann8
2024-10-03 09:11:11,955 [DEBUG] backtrace: - final_path=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/8IEA-noindann8/results
2024-10-03 09:11:11,955 [INFO] backtrace: backtrace final path: Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/8IEA-noindann8/results

2024-10-03 09:11:11,955 [DEBUG] main: m_data_filepath=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/8IEA-noindann8/results/data.json
2024-10-03 09:11:11,955 [DEBUG] check_path: path=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/8IEA-noindann8/results/data.json, is_file=True, auto_create=False
2024-10-03 09:11:11,955 [DEBUG] check_path: dir_path=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/8IEA-noindann8/results
2024-10-03 09:11:11,955 [DEBUG] check_path: Doesn't exist: 'Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/8IEA-noindann8/results/data.json'
Model data was not found by auto-infer.
Report is True, but no model data (data.json) files were found. You need to keep both statistically_relevant_genes.json and data.json in the same folders wihtout deleting them!



2024-10-03 09:11:11,955 [INFO] main: Starting GOReverseLookup analysis with input params:
2024-10-03 09:11:11,955 [INFO] main: - input_file: /Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/7IEA-noindann5/results/statistically_relevant_genes.json
2024-10-03 09:11:11,955 [INFO] main: - destination_dir: None
2024-10-03 09:11:11,955 [INFO] main: - report: True
2024-10-03 09:11:11,955 [INFO] main: - model_data_filepath: None
2024-10-03 09:11:11,955 [INFO] main: Model data filepath was None. Attempting auto infer data.json from /Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/7IEA-noindann5/results/statistically_relevant_genes.json
2024-10-03 09:11:11,955 [DEBUG] backtrace: filepath=/Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/7IEA-noindann5/results/statistically_relevant_genes.json, backtrace=1, file_separator=/
2024-10-03 09:11:11,955 [DEBUG] backtrace: elements=['', 'Users', 'simonzetko', 'goreverselookup', 'research_models', '2oct_natural_amigo_ortho', 'IEAne', '7IEA-noindann5', 'results', 'statistically_relevant_genes.json']
2024-10-03 09:11:11,956 [DEBUG] backtrace: res_elements=['', 'Users', 'simonzetko', 'goreverselookup', 'research_models', '2oct_natural_amigo_ortho', 'IEAne', '7IEA-noindann5', 'results']
2024-10-03 09:11:11,956 [DEBUG] backtrace: _ building final path
2024-10-03 09:11:11,956 [DEBUG] backtrace: - final_path=
2024-10-03 09:11:11,956 [DEBUG] backtrace: - final_path=Users
2024-10-03 09:11:11,956 [DEBUG] backtrace: - final_path=Users/simonzetko
2024-10-03 09:11:11,956 [DEBUG] backtrace: - final_path=Users/simonzetko/goreverselookup
2024-10-03 09:11:11,956 [DEBUG] backtrace: - final_path=Users/simonzetko/goreverselookup/research_models
2024-10-03 09:11:11,956 [DEBUG] backtrace: - final_path=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho
2024-10-03 09:11:11,956 [DEBUG] backtrace: - final_path=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne
2024-10-03 09:11:11,956 [DEBUG] backtrace: - final_path=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/7IEA-noindann5
2024-10-03 09:11:11,956 [DEBUG] backtrace: - final_path=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/7IEA-noindann5/results
2024-10-03 09:11:11,956 [INFO] backtrace: backtrace final path: Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/7IEA-noindann5/results
2024-10-03 09:11:11,956 [DEBUG] main: m_data_filepath=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/7IEA-noindann5/results/data.json
2024-10-03 09:11:11,956 [DEBUG] check_path: path=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/7IEA-noindann5/results/data.json, is_file=True, auto_create=False
2024-10-03 09:11:11,956 [DEBUG] check_path: dir_path=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/7IEA-noindann5/results
2024-10-03 09:11:11,956 [DEBUG] check_path: Doesn't exist: 'Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/7IEA-noindann5/results/data.json'
Model data was not found by auto-infer.
Report is True, but no model data (data.json) files were found. You need to keep both statistically_relevant_genes.json and data.json in the same folders wihtout deleting them!
2024-10-03 09:11:11,956 [INFO] main: Starting GOReverseLookup analysis with input params:
2024-10-03 09:11:11,956 [INFO] main: - input_file: /Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/5IEA-indann5/results/statistically_relevant_genes.json
2024-10-03 09:11:11,956 [INFO] main: - destination_dir: None
2024-10-03 09:11:11,956 [INFO] main: - report: True
2024-10-03 09:11:11,956 [INFO] main: - model_data_filepath: None
2024-10-03 09:11:11,956 [INFO] main: Model data filepath was None. Attempting auto infer data.json from /Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/5IEA-indann5/results/statistically_relevant_genes.json
2024-10-03 09:11:11,956 [DEBUG] backtrace: filepath=/Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/5IEA-indann5/results/statistically_relevant_genes.json, backtrace=1, file_separator=/
2024-10-03 09:11:11,956 [DEBUG] backtrace: elements=['', 'Users', 'simonzetko', 'goreverselookup', 'research_models', '2oct_natural_amigo_ortho', 'IEAne', '5IEA-indann5', 'results', 'statistically_relevant_genes.json']
2024-10-03 09:11:11,956 [DEBUG] backtrace: res_elements=['', 'Users', 'simonzetko', 'goreverselookup', 'research_models', '2oct_natural_amigo_ortho', 'IEAne', '5IEA-indann5', 'results']
2024-10-03 09:11:11,956 [DEBUG] backtrace: _ building final path
2024-10-03 09:11:11,956 [DEBUG] backtrace: - final_path=
2024-10-03 09:11:11,956 [DEBUG] backtrace: - final_path=Users
2024-10-03 09:11:11,956 [DEBUG] backtrace: - final_path=Users/simonzetko
2024-10-03 09:11:11,956 [DEBUG] backtrace: - final_path=Users/simonzetko/goreverselookup
2024-10-03 09:11:11,956 [DEBUG] backtrace: - final_path=Users/simonzetko/goreverselookup/research_models
2024-10-03 09:11:11,956 [DEBUG] backtrace: - final_path=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho
2024-10-03 09:11:11,956 [DEBUG] backtrace: - final_path=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne
2024-10-03 09:11:11,956 [DEBUG] backtrace: - final_path=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/5IEA-indann5
2024-10-03 09:11:11,956 [DEBUG] backtrace: - final_path=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/5IEA-indann5/results
2024-10-03 09:11:11,956 [INFO] backtrace: backtrace final path: Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/5IEA-indann5/results
2024-10-03 09:11:11,956 [DEBUG] main: m_data_filepath=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/5IEA-indann5/results/data.json
2024-10-03 09:11:11,956 [DEBUG] check_path: path=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/5IEA-indann5/results/data.json, is_file=True, auto_create=False
2024-10-03 09:11:11,956 [DEBUG] check_path: dir_path=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/5IEA-indann5/results
2024-10-03 09:11:11,956 [DEBUG] check_path: Doesn't exist: 'Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/5IEA-indann5/results/data.json'
Model data was not found by auto-infer.
Report is True, but no model data (data.json) files were found. You need to keep both statistically_relevant_genes.json and data.json in the same folders wihtout deleting them!
2024-10-03 09:11:11,956 [INFO] main: Starting GOReverseLookup analysis with input params:
2024-10-03 09:11:11,956 [INFO] main: - input_file: /Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/6IEA-indann8/results/statistically_relevant_genes.json
2024-10-03 09:11:11,956 [INFO] main: - destination_dir: None
2024-10-03 09:11:11,956 [INFO] main: - report: True
2024-10-03 09:11:11,956 [INFO] main: - model_data_filepath: None
2024-10-03 09:11:11,957 [INFO] main: Model data filepath was None. Attempting auto infer data.json from /Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/6IEA-indann8/results/statistically_relevant_genes.json
2024-10-03 09:11:11,957 [DEBUG] backtrace: filepath=/Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/6IEA-indann8/results/statistically_relevant_genes.json, backtrace=1, file_separator=/
2024-10-03 09:11:11,957 [DEBUG] backtrace: elements=['', 'Users', 'simonzetko', 'goreverselookup', 'research_models', '2oct_natural_amigo_ortho', 'IEAne', '6IEA-indann8', 'results', 'statistically_relevant_genes.json']
2024-10-03 09:11:11,957 [DEBUG] backtrace: res_elements=['', 'Users', 'simonzetko', 'goreverselookup', 'research_models', '2oct_natural_amigo_ortho', 'IEAne', '6IEA-indann8', 'results']
2024-10-03 09:11:11,957 [DEBUG] backtrace: _ building final path
2024-10-03 09:11:11,957 [DEBUG] backtrace: - final_path=
2024-10-03 09:11:11,957 [DEBUG] backtrace: - final_path=Users
2024-10-03 09:11:11,957 [DEBUG] backtrace: - final_path=Users/simonzetko
2024-10-03 09:11:11,957 [DEBUG] backtrace: - final_path=Users/simonzetko/goreverselookup
2024-10-03 09:11:11,957 [DEBUG] backtrace: - final_path=Users/simonzetko/goreverselookup/research_models
2024-10-03 09:11:11,957 [DEBUG] backtrace: - final_path=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho
2024-10-03 09:11:11,957 [DEBUG] backtrace: - final_path=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne
2024-10-03 09:11:11,957 [DEBUG] backtrace: - final_path=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/6IEA-indann8
2024-10-03 09:11:11,957 [DEBUG] backtrace: - final_path=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/6IEA-indann8/results
2024-10-03 09:11:11,957 [INFO] backtrace: backtrace final path: Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/6IEA-indann8/results
2024-10-03 09:11:11,957 [DEBUG] main: m_data_filepath=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/6IEA-indann8/results/data.json
2024-10-03 09:11:11,957 [DEBUG] check_path: path=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/6IEA-indann8/results/data.json, is_file=True, auto_create=False
2024-10-03 09:11:11,957 [DEBUG] check_path: dir_path=Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/6IEA-indann8/results
2024-10-03 09:11:11,957 [DEBUG] check_path: Doesn't exist: 'Users/simonzetko/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/6IEA-indann8/results/data.json'
Model data was not found by auto-infer.
Report is True, but no model data (data.json) files were found. You need to keep both statistically_relevant_genes.json and data.json in the same folders wihtout deleting them!
Traceback (most recent call last):
File "/Users/simonzetko/goreverselookup/bin/goreverselookup", line 8, in <module>
sys.exit(main())
^^^^^^
TypeError: main() missing 1 required positional argument: 'input_file'
(goreverselookup) simonzetkoSimons-Laptop ~ %

A MacOS user experienced the following bug:


(goreverselookup) simonSimons-Laptop ~ % goreverselookup "statistically_relevant_genes.json" --report True --full_directory_op "/Users/simon/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne"
2024-10-02 21:33:30,457 [INFO] setup_logging_config: Setup log config using: config/logging_config.json
2024-10-02 21:33:30,457 [INFO] <module>: Starting GOReverseLookup analysis!
2024-10-02 21:33:30,457 [INFO] <module>: os.getcwd() = /Users/simon
No model data filepath was specified, auto-inferring model data.
2024-10-02 21:33:30,458 [WARNING] backtrace: Backtrace 1 is greater than final element index 0 for filepath statistically_relevant_genes.json! Returning ''.
Model data not found. Attempted file search at None
Found the following input files:
- [0]: /Users/simon/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/8IEA-noindann8/results/statistically_relevant_genes.json
- [1]: /Users/simon/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/7IEA-noindann5/results/statistically_relevant_genes.json
- [2]: /Users/simon/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/5IEA-indann5/results/statistically_relevant_genes.json
- [3]: /Users/simon/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/6IEA-indann8/results/statistically_relevant_genes.json
2024-10-02 21:33:30,459 [INFO] main: Starting GOReverseLookup analysis with input params:
2024-10-02 21:33:30,459 [INFO] main: - input_file: /Users/simon/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/8IEA-noindann8/results/statistically_relevant_genes.json
2024-10-02 21:33:30,459 [INFO] main: - destination_dir: None
2024-10-02 21:33:30,459 [INFO] main: - report: True
2024-10-02 21:33:30,459 [INFO] main: - model_data_filepath: None
Model data was not found by auto-infer.
2024-10-02 21:33:30,459 [INFO] load_json: Load JSON received input filepath: cache/connection_cache.json
2024-10-02 21:33:33,420 [INFO] load_json: Load JSON received input filepath: cache/uniprot_cache.json
2024-10-02 21:33:33,421 [INFO] load_json: Load JSON received input filepath: cache/ensembl_cache.json
2024-10-02 21:33:33,423 [INFO] load_json: Load JSON received input filepath: cache/geneontology_cache.json
2024-10-02 21:33:33,426 [INFO] load_json: Load JSON received input filepath: cache/gprofiler_cache.json
2024-10-02 21:33:33,430 [INFO] init: Cacher load dictionary response counts:
2024-10-02 21:33:33,430 [INFO] init: - urls: 775
2024-10-02 21:33:33,430 [INFO] init: - uniprot: 15
2024-10-02 21:33:33,430 [INFO] init: - ensembl: 465
2024-10-02 21:33:33,430 [INFO] init: - geneontology: 234
2024-10-02 21:33:33,430 [INFO] init: Register at exit save data for Cacher.
2024-10-02 21:33:33,462 [DEBUG] _new_conn: Starting new HTTPS connection (1): www.ensembl.org:443
2024-10-02 21:33:33,698 [DEBUG] _make_request: https://www.ensembl.org:443 "GET /info/genome/stable_ids/prefixes.html HTTP/11" 200 14150
2024-10-02 21:33:33,748 [DEBUG] from_bytes: Encoding detection: ascii is most likely the one.
2024-10-02 21:33:33,773 [DEBUG] _new_conn: Starting new HTTPS connection (1): www.ensembl.org:443
2024-10-02 21:33:34,049 [DEBUG] _make_request: https://www.ensembl.org:443 "GET /info/genome/stable_ids/prefixes.html HTTP/11" 200 14102
2024-10-02 21:33:34,059 [DEBUG] from_bytes: Encoding detection: ascii is most likely the one.
2024-10-02 21:33:34,087 [INFO] load_json: Load JSON received input filepath: data_files/ens_spec_ids_taxa.json
2024-10-02 21:33:34,089 [INFO] from_input_file: Computing defined SOIs:
2024-10-02 21:33:34,089 [INFO] from_input_file: Creating model from input file with:
2024-10-02 21:33:34,089 [INFO] from_input_file: - input file filepath: /Users/simon/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/8IEA-noindann8/results/statistically_relevant_genes.json
2024-10-02 21:33:34,089 [INFO] from_input_file: - destination dir: /Users/simon/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/8IEA-noindann8/results
2024-10-02 21:33:34,089 [INFO] from_input_file: - input file line count: 3
2024-10-02 21:33:34,089 [INFO] from_input_file: - count GO Terms: 0
2024-10-02 21:33:34,089 [INFO] from_input_file: - target_SOIs: []
2024-10-02 21:33:34,089 [INFO] from_input_file: - GO categories: []
2024-10-02 21:33:34,089 [INFO] from_input_file: - model settings: {'fisher_test_use_online_query': False, 'include_indirect_annotations': False, 'uniprotkb_genename_online_query': False, 'multiple_correction_method': 'fdr_bh', 'two_tailed': False, 'pvalue': 0.05, 'goterms_set': [], 'datafile_paths': {}, 'ortholog_organisms_ncbi_full_ids': [], 'gorth_ortholog_refetch': False, 'gorth_ortholog_fetch_for_indefinitive_orthologs': True, 'all_evidence_codes': {}, 'evidence_codes_to_ecoids': {}, 'valid_evidence_codes': [], 'goterm_gene_query_timeout': 20, 'goterm_gene_query_max_retries': 3, 'exclude_opposite_regulation_direction_check': False, 'destination_dir': '/Users/simon/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/8IEA-noindann8/results', '_valid_multiple_correction_methods': ['bonferroni', 'sidak', 'holm-sidak', 'holm', 'simes-hochberg', 'hommel', 'fdr_bh', 'fdr_by', 'fdr_tsbh', 'fdr_tsbky']}
2024-10-02 21:33:34,089 [INFO] from_input_file: - obo_parser: None
2024-10-02 21:33:34,089 [WARNING] get_datafile_path: datafile_name goa_human not found in (ModelSettings).datafile_paths
2024-10-02 21:33:34,089 [INFO] _init_: Attempting to create GOAF using: data_files/goa_human.gaf
2024-10-02 21:33:34,089 [INFO] _init_: - GOAF filepath exists.
2024-10-02 21:33:35,262 [INFO] _init_: - GOAF created with 0 annotations.
2024-10-02 21:33:35,340 [DEBUG] _new_conn: Starting new HTTPS connection (1): www.ebi.ac.uk:443
2024-10-02 21:33:35,514 [DEBUG] _make_request: https://www.ebi.ac.uk:443 "GET /QuickGO/services/ontology/go/about HTTP/11" 200 None
2024-10-02 21:33:35,515 [INFO] download_file: File data_files/go.obo exists and isn't empty.
2024-10-02 21:33:36,699 [INFO] _init_: Obo parser init completed.
2024-10-02 21:33:36,701 [DEBUG] _new_conn: Starting new HTTPS connection (1): www.ensembl.org:443
2024-10-02 21:33:36,936 [DEBUG] _make_request: https://www.ensembl.org:443 "GET /info/genome/stable_ids/prefixes.html HTTP/11" 200 14118
2024-10-02 21:33:36,982 [DEBUG] from_bytes: Encoding detection: ascii is most likely the one.
2024-10-02 21:33:37,007 [INFO] load_json: Load JSON received input filepath: data_files/ens_spec_ids_taxa.json
Model was created from input file: /Users/simon/goreverselookup/research_models/2oct_natural_amigo_ortho/IEAne/8IEA-noindann8/results/statistically_relevant_genes.json
2024-10-02 21:33:37,008 [DEBUG] _init_: Using selector: KqueueSelector
2024-10-02 21:33:37,008 [INFO] print_elapsed_time: Elapsed: 0:00:00
2024-10-02 21:33:37,008 [INFO] fetch_all_go_term_products: Started fetching all GO Term products.
2024-10-02 21:33:37,009 [DEBUG] _init_: Using selector: KqueueSelector
2024-10-02 21:33:37,009 [INFO] print_elapsed_time: Elapsed: 0:00:00
2024-10-02 21:33:37,009 [INFO] save_data: Cacher is saving data. Please, be patient.
2024-10-02 21:33:37,009 [INFO] save_data: Successfully saved url, uniprot, ensembl, geneontology and gprofiler cache.
2024-10-02 21:33:37,009 [INFO] create_products_from_goterms: Creating products from GO Terms. Num goterms = 0
Traceback (most recent call last):
File "/Users/simon/goreverselookup/bin/goreverselookup", line 5, in <module>
from goreverselookup.main_cli import main
File "/Users/simon/goreverselookup/lib/python3.11/site-packages/goreverselookup/main_cli.py", line 271, in <module>
model = main(input_file=f, destination_dir=destination_dir, report=report, model_data_filepath=model_data_filepath, rescore_model=static_rescore_model)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/simon/goreverselookup/lib/python3.11/site-packages/goreverselookup/main_cli.py", line 165, in main
model.create_products_from_goterms()
File "/Users/simon/goreverselookup/lib/python3.11/site-packages/goreverselookup/Model.py", line 512, in create_products_from_goterms
target_taxon = self.model_settings.target_organism.ncbi_id_full
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'ncbi_id_full'
2024-10-02 21:33:37,011 [INFO] save_data: Cacher is saving data. Please, be patient.
2024-10-02 21:33:37,011 [INFO] save_data: Successfully saved url, uniprot, ensembl, geneontology and gprofiler cache.


Added more debugging lines with an aim to capture the bug better.

Added a setting called `two_tailed`. If set to True, the program will analyze the following:

- if only a target SOI is defined (e.g. _stimulation of rheumatoid arthritis_) without its corresponding reverse SOI (e.g. _inhibition of rheumatoid arthritis_), the first tail of analysis discovers genes significant for the defined target SOI (`p < 0.05`), whereas the second tail of the analysis discovers gene statistically insignificant for the defined target SOI (`p > 0.95`) and adds them to an artifically created reverse SOI.
- if both target and reverse SOIs are defined in the input file, then two_tailed will evaluate the opposite condition of the specified target SOIs. Suppose that both _stimulation_ and _inhibition of rheumatoid arthritis_ are defined, and _stimulation of rh. art._ is defined as the target SOI. The first tail of significance comprises of genes, for which `p < 0.05` for _stimulation of rh. art_ and `p >= 0.05` for _inhibition of rh.art_. The second tail of significance comprises of genes, for which `p < 0.05` for _inhibition of rh. art_ and `p >= 0.05` for _stimulation of rh.art._.