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I wanted to use anvi-inspect to visualise a specific split, but the split cannot be visualised because the code relies on the genes_in_splits table. The split I want to see has no genes so cannot be visualised because it relies on the gene table info from the contigs.db. I wanted to see the split jsut to see what was happening and didn't realise it didn't have any genes on it until the debug error
Files / commands to reproduce the issue
anvi-inspect -c /fs/dss/groups/agecodatasci/RESOURCES/PUBLIC/METAGENOMES/OCEAN/TARA/03_CONTIGS/SAMEA2620505-contigs.db -p ../06_MERGED/SAMEA2620505/PROFILE.db --split-name SAMEA2620505_000000001329_split_00001 --debug
/fs/dss/groups/agecodatasci/PEOPLE/Katy/anvio-katy/lib/python3.10/site-packages/sklearn/base.py:318: UserWarning: Trying to unpickle estimator DecisionTreeClassifier from version 0.24.0 when using version 1.2.2. This might lead to breaking code or invalid results. Use at your own risk. For more info please refer to:
https://scikit-learn.org/stable/model_persistence.html#security-maintainability-limitations
warnings.warn(
/fs/dss/groups/agecodatasci/PEOPLE/Katy/anvio-katy/lib/python3.10/site-packages/sklearn/base.py:318: UserWarning: Trying to unpickle estimator RandomForestClassifier from version 0.24.0 when using version 1.2.2. This might lead to breaking code or invalid results. Use at your own risk. For more info please refer to:
https://scikit-learn.org/stable/model_persistence.html#security-maintainability-limitations
warnings.warn(
[28 Jan 25 10:45:18 Loading the contigs DB] Reading **SOME** data from `genes in splits` table :)
Traceback for debugging
================================================================================
File "/fs/dss/groups/agecodatasci/PEOPLE/Katy/github/anvio/bin/anvi-inspect", line 60, in <module>
d = interactive.Interactive(args)
File "/fs/dss/groups/agecodatasci/PEOPLE/Katy/github/anvio/anvio/interactive.py", line 234, in __init__
ContigsSuperclass.__init__(self, self.args)
File "/fs/dss/groups/agecodatasci/PEOPLE/Katy/github/anvio/anvio/dbops.py", line 178, in __init__
self.genes_in_splits = contigs_db.db.smart_get(t.genes_in_splits_table_name, 'split', self.split_names_of_interest, progress=self.progress)
File "/fs/dss/groups/agecodatasci/PEOPLE/Katy/github/anvio/anvio/db.py", line 868, in smart_get
return self.get_some_rows_from_table_as_dict(table_name, where_clause=f"{column} IN ({items})", string_the_key=string_the_key, error_if_no_data=error_if_no_data)
File "/fs/dss/groups/agecodatasci/PEOPLE/Katy/github/anvio/anvio/db.py", line 1152, in get_some_rows_from_table_as_dict
raise ConfigError("Query on %s with the where clause of '%s' did not return anything." % (table_name, where_clause))
================================================================================
Config Error: Query on genes_in_splits with the where clause of 'split IN
('SAMEA2620505_000000001329_split_00001')' did not return anything.
The files are available on ROSA :)
The text was updated successfully, but these errors were encountered:
Short description of the problem
anvi-inspect
does not show splits without genesanvi'o version
development version
Detailed description of the issue
I wanted to use anvi-inspect to visualise a specific split, but the split cannot be visualised because the code relies on the genes_in_splits table. The split I want to see has no genes so cannot be visualised because it relies on the gene table info from the contigs.db. I wanted to see the split jsut to see what was happening and didn't realise it didn't have any genes on it until the debug error
Files / commands to reproduce the issue
The files are available on ROSA :)
The text was updated successfully, but these errors were encountered: