macsypy.error.MacsypyError: 'defense-finder-models/Rst_Hydrolase-Tm__Hydrolase-Tm': No such profile

[ezherman]

Since updating defensefinder and the associated models, I am receiving the error pasted at the bottom of this issue. The profile seems inaccessible to defensefinder, despite being present under /home/elh605/.macsyfinder/models/defense-finder-models/profiles/Rst_Hydrolase-Tm__Hydrolase-Tm.hmm.

I installed and ran defensefinder as follows:

mamba create -c bioconda -c conda-forge -n defensefinder_test pip hmmer -y
mamba activate defensefinder_test
pip install mdmparis-defense-finder
defense-finder update
defense-finder run GCF_900143905.1.faa.gz

The input file is available here.

I'm not sure, but this issue may be related to this comment in another issue.

If there is anything I can do to help, please let me know.

Traceback (most recent call last):
  File "/home/elh605/mambaforge/envs/defensefinder_test/lib/python3.12/site-packages/macsypy/profile.py", line 70, in get_profile
    path = model_location.get_profile(gene.name)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/elh605/mambaforge/envs/defensefinder_test/lib/python3.12/site-packages/macsypy/registries.py", line 344, in get_profile
    return self._profiles[name]
           ~~~~~~~~~~~~~~^^^^^^
KeyError: 'Rst_Hydrolase-Tm__Hydrolase-Tm'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/elh605/mambaforge/envs/defensefinder_test/bin/defense-finder", line 8, in <module>
    sys.exit(cli())
             ^^^^^
  File "/home/elh605/mambaforge/envs/defensefinder_test/lib/python3.12/site-packages/click/core.py", line 1128, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/elh605/mambaforge/envs/defensefinder_test/lib/python3.12/site-packages/click/core.py", line 1053, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/home/elh605/mambaforge/envs/defensefinder_test/lib/python3.12/site-packages/click/core.py", line 1659, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/elh605/mambaforge/envs/defensefinder_test/lib/python3.12/site-packages/click/core.py", line 1395, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/elh605/mambaforge/envs/defensefinder_test/lib/python3.12/site-packages/click/core.py", line 754, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/elh605/mambaforge/envs/defensefinder_test/lib/python3.12/site-packages/defense_finder_cli/main.py", line 143, in run
    defense_finder.run(protein_file_name, dbtype, workers, coverage, tmp_dir, models_dir, no_cut_ga, loglevel)
  File "/home/elh605/mambaforge/envs/defensefinder_test/lib/python3.12/site-packages/defense_finder/__init__.py", line 29, in run
    macsyfinder.main(args=msf_cmd)
  File "/home/elh605/mambaforge/envs/defensefinder_test/lib/python3.12/site-packages/macsypy/scripts/macsyfinder.py", line 1193, in main
    all_systems, rejected_candidates = search_systems(config, model_registry, models_def_to_detect, logger)
                                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/elh605/mambaforge/envs/defensefinder_test/lib/python3.12/site-packages/macsypy/scripts/macsyfinder.py", line 529, in search_systems
    parser.parse(models_def_to_detect)
  File "/home/elh605/mambaforge/envs/defensefinder_test/lib/python3.12/site-packages/macsypy/definition_parser.py", line 85, in parse
    self._fill_gene_bank(model_node, model_location, def_loc)
  File "/home/elh605/mambaforge/envs/defensefinder_test/lib/python3.12/site-packages/macsypy/definition_parser.py", line 287, in _fill_gene_bank
    self.gene_bank.add_new_gene(model_location, gene_name, self.profile_factory)
  File "/home/elh605/mambaforge/envs/defensefinder_test/lib/python3.12/site-packages/macsypy/gene.py", line 102, in add_new_gene
    gene = CoreGene(model_location, name, profile_factory)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/elh605/mambaforge/envs/defensefinder_test/lib/python3.12/site-packages/macsypy/gene.py", line 114, in __init__
    self._profile = profile_factory.get_profile(self, model_location)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/elh605/mambaforge/envs/defensefinder_test/lib/python3.12/site-packages/macsypy/profile.py", line 72, in get_profile
    raise MacsypyError(f"'{model_location.name}/{gene.name}': No such profile")
macsypy.error.MacsypyError: 'defense-finder-models/Rst_Hydrolase-Tm__Hydrolase-Tm': No such profile

[ZarulHanifah]

I got this too. I had free time to look into the problem. Actually, it was because of some python string substitution went wrong:

>>> "Rst_RT-Tm__RT-Tm.hmm".strip(".hmm")
'Rst_RT-Tm__RT-T'

Still trying to figure out how to correct this.

[ZarulHanifah]

A quick cheat is to find the lib/python3.11/site-packages/macsypy/registries.py file, go to line 232, replace line
base = profile.strip(profile_suffix)
to
base = profile[:-4]

[ezherman]

Ah! Thanks for contributing @ZarulHanifah. I'll open an issue in the Macsyfinder repo and reference our discussion here.

[mmolari]

I'm having the same exact issue, looking forward to a non-hacky fix. Thank you guys for the info!

[China-LHY]

Thank you for your help. It helps me a lot!

A quick cheat is to find the lib/python3.11/site-packages/macsypy/registries.py file, go to line 232, replace line base = profile.strip(profile_suffix) to base = profile[:-4]

[jeanrjc]

This is fixed in version 1.2.2 (you can update on pip, soon on conda)