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v0.4.0 #35

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Jun 16, 2024
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v0.4.0 #35

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cbbdde6
Documentation of ms2query functionality removal
mmzdouc Jun 15, 2024
5fb5b9b
Removed ms2query de novo calculation implementation
mmzdouc Jun 15, 2024
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5 changes: 5 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -10,6 +10,11 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm

N/A

## [0.4.0] 15-06-2024

### Removed
- [Breaking change] Removed MS2Query de novo annotation after observation of process instability (unforeseen process termination by system with SIGKILL (9))

## [0.3.3] 06-06-2024

### Fixed
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5 changes: 0 additions & 5 deletions example_data/case_study_parameters.json
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Expand Up @@ -121,11 +121,6 @@
"maximum_runtime": 200
}
},
"ms2query_annotation": {
"activate_module": true,
"score_cutoff": 0.7,
"maximum_runtime": 600
},
"as_kcb_matching": {
"modified_cosine": {
"activate_module": true,
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51 changes: 0 additions & 51 deletions fermo_core/config/class_default_settings.py
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Expand Up @@ -33,11 +33,6 @@ class DefaultPaths(BaseModel):
Attributes:
dirpath_ms2deepscore_pos: points towards default ms2deepscore dir
url_ms2deepscore_pos: the url to download the default ms2deepscore file
dirpath_ms2query_base: points towards default ms2query dir
dirpath_ms2query_pos: points towards default ms2query dir positive mode
dirpath_ms2query_neg: points towards default ms2query dir negative mode
url_ms2query_pos: urls to default ms2query files for positive ion mode
url_ms2query_neg: urls to default ms2query files for negative ion mode
dirpath_losses: point towards neutral loss dir
dirpath_frags: point towards fragment dir
library_mibig_pos: points towards mibig spectral library for positive ion mode
Expand All @@ -50,52 +45,6 @@ class DefaultPaths(BaseModel):
"https://zenodo.org/records/8274763/files/"
"ms2deepscore_positive_10k_1000_1000_1000_500.hdf5?download=1"
)
dirpath_ms2query_base: DirectoryPath = Path(__file__).parent.parent.joinpath(
"libraries/ms2query/"
)
dirpath_ms2query_pos: DirectoryPath = Path(__file__).parent.parent.joinpath(
"libraries/ms2query/pos"
)
dirpath_ms2query_neg: DirectoryPath = Path(__file__).parent.parent.joinpath(
"libraries/ms2query/neg"
)
url_ms2query_pos: tuple = (
"https://zenodo.org/records/10527997/files"
"/ALL_GNPS_210409_positive_processed_annotated_CF_NPC_classes.txt?download=1",
"https://zenodo.org/records/10527997/files"
"/library_GNPS_15_12_2021_ms2ds_embeddings.parquet?download=1",
"https://zenodo.org/records/10527997/files"
"/library_GNPS_15_12_2021_s2v_embeddings.parquet?download=1",
"https://zenodo.org/records/10527997/files/ms2ds_model_GNPS_15_12_2021.hdf5"
"?download=1",
"https://zenodo.org/records/10527997/files/ms2query_library.sqlite?download=1",
"https://zenodo.org/records/10527997/files/ms2query_random_forest_model.onnx"
"?download=1",
"https://zenodo.org/records/10527997/files/spec2vec_model_GNPS_15_12_2021"
".model?download=1",
"https://zenodo.org/records/10527997/files/spec2vec_model_GNPS_15_12_2021"
".model.syn1neg.npy?download=1",
"https://zenodo.org/records/10527997/files/spec2vec_model_GNPS_15_12_2021"
".model.wv.vectors.npy?download=1",
)
url_ms2query_neg: tuple = (
"https://zenodo.org/records/10528030/files/neg_GNPS_15_12_2021_ms2ds_model"
".hdf5?download=1",
"https://zenodo.org/records/10528030/files"
"/neg_GNPS_15_12_2021_ms2query_random_forest_model.onnx?download=1",
"https://zenodo.org/records/10528030/files"
"/neg_mode_GNPS_15_12_2021_ms2ds_embeddings.parquet?download=1",
"https://zenodo.org/records/10528030/files"
"/neg_mode_GNPS_15_12_2021_s2v_embeddings.parquet?download=1",
"https://zenodo.org/records/10528030/files"
"/neg_mode_spec2vec_model_GNPS_15_12_2021.model?download=1",
"https://zenodo.org/records/10528030/files"
"/neg_mode_spec2vec_model_GNPS_15_12_2021.model.syn1neg.npy?download=1",
"https://zenodo.org/records/10528030/files"
"/neg_mode_spec2vec_model_GNPS_15_12_2021.model.wv.vectors.npy?download=1",
"https://zenodo.org/records/10528030/files/negative_mode_15_12_2021.sqlite"
"?download=1",
)
dirpath_losses: DirectoryPath = Path(__file__).parent.parent.joinpath(
"libraries/loss_libs/"
)
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25 changes: 0 additions & 25 deletions fermo_core/config/schema.json
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Expand Up @@ -655,31 +655,6 @@
}
}
},
"ms2query_annotation": {
"title": "(Optional): settings for MS2Query annotation module. For non-specified parameters, default parameters will be used.",
"additionalProperties": false,
"type": "object",
"required": [
"activate_module"
],
"properties": {
"activate_module": {
"title": "Specifies whether this module should be run.",
"type": "boolean"
},
"maximum_runtime": {
"title": "(Optional): maximum running time of module, in seconds. A value of 0 (zero) indicates unlimited running time.",
"type": "integer",
"minimum": 0
},
"score_cutoff": {
"title": "(Optional): minimum score that must be reached to consider two MS/MS fragmentation spectra to be related.",
"type": "number",
"minimum": 0.1,
"maximum": 1.0
}
}
},
"as_kcb_matching": {
"title": "(Optional): settings for antiSMASH KnownClusterBlast results matching. Will be only executed if a 'as_results' directory was provided.",
"additionalProperties": false,
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46 changes: 0 additions & 46 deletions fermo_core/data_analysis/annotation_manager/class_annotation_manager.py
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Expand Up @@ -113,10 +113,6 @@ def _eval_as_results_file() -> bool:
_eval_ms2query_results_file(),
self.run_ms2query_results_assignment,
),
(
self.params.Ms2QueryAnnotationParameters.activate_module,
self.run_ms2query_annotation,
),
(
_eval_as_results_file(),
self.run_as_kcb_cosine_annotation,
Expand Down Expand Up @@ -304,14 +300,6 @@ def run_fragment_annotation(self: Self):

def run_ms2query_results_assignment(self: Self):
"""Annotate Features from existing MS2Query results"""
if self.params.Ms2QueryAnnotationParameters.activate_module is True:
logger.warning(
f"'AnnotationManager': both an MS2Query result file and instructions "
f"for running the MS2Query algorithm were provided. In this case, "
f"the existing MS2Query results file "
f"'{self.params.MS2QueryResultsParameters.filepath.name}' takes "
f"precedence. "
)

logger.info(
"'AnnotationManager': started annotation from existing MS2Query results."
Expand Down Expand Up @@ -340,40 +328,6 @@ def run_ms2query_results_assignment(self: Self):
"'AnnotationManager': completed annotation from existing MS2Query results."
)

def run_ms2query_annotation(self: Self):
"""Perform annotation of feature MS2 using ms2query - run algorithm"""
if self.params.MS2QueryResultsParameters is not None:
logger.warning(
f"'AnnotationManager': both an MS2Query result file and instructions "
f"for running the MS2Query algorithm were provided. In this case, "
f"the existing MS2Query results file "
f"'{self.params.MS2QueryResultsParameters.filepath.name}' takes "
f"precedence. "
)
logger.warning("'AnnotationManager': MS2QueryAnnotator - SKIP ")
return

logger.info("'AnnotationManager': started annotation using MS2Query")

try:
ms2query_annotator = MS2QueryAnnotator(
params=self.params,
features=self.features,
active_features=self.stats.active_features,
cutoff=self.params.Ms2QueryAnnotationParameters.score_cutoff,
)
ms2query_annotator.run_ms2query()
self.features = ms2query_annotator.return_features()
self.params.Ms2QueryAnnotationParameters.module_passed = True
except Exception as e:
logger.error(str(e))
logger.error(
"'AnnotationManager': Error during running of MS2QueryAnnotator - SKIP"
)
return

logger.info("'AnnotationManager': completed annotation using MS2Query")

def run_as_kcb_cosine_annotation(self: Self):
"""Match features against a antiSMASH knownclusterblast-derived library.

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