Merge pull request #244 from monarch-initiative/remove-obsoleted-anal…

…ysis-code

Remove obsolete analysis code

README.md

@@ -5,46 +5,11 @@
 
 GPSEA is a Python library for discovery of genotype-phenotype associations.
 
-An example of simple genotype-phenotype association analysis
+See the [Tutorial](https://monarch-initiative.github.io/gpsea/stable/tutorial.html) 
+and a comprehensive [User guide](https://monarch-initiative.github.io/gpsea/stable/user-guide/index.html)
+for more information.
 
-```python
-# Load HPO
-import hpotk
-
-store = hpotk.configure_ontology_store()
-hpo = store.load_minimal_hpo()
-
-# Load a cohort of phenopackets
-from gpsea.data import get_toy_cohort
-
-cohort = get_toy_cohort()
-
-# Analyze genotype-phenotype associations
-from gpsea.analysis import configure_cohort_analysis
-from gpsea.analysis.predicate import PatientCategories
-
-from gpsea.model import VariantEffect
-
-cohort_analysis = configure_cohort_analysis(cohort, hpo)
-frameshift = cohort_analysis.compare_by_variant_effect(VariantEffect.FRAMESHIFT_VARIANT, tx_id='NM_1234.5')
-
-frameshift.summarize(hpo, category=PatientCategories.YES)
-```
-
-provides a pandas data frame with genotype-phenotype correlations:
-
-```text
-FRAMESHIFT_VARIANT on NM_1234.5                                    No                Yes
-                                                                Count   Percent    Count   Percent    p value    Corrected p value
-    Arachnodactyly [HP:0001166]                                  1/10       10%    13/16       81%   0.000781             0.020299
-    Abnormality of the musculature [HP:0003011]                   6/6      100%    11/11      100%   1.000000             1.000000
-    Abnormal nervous system physiology [HP:0012638]               9/9      100%    15/15      100%   1.000000             1.000000
-    ...                                                           ...       ...      ...       ...        ...                  ...
-```
-
-## Documentation
-
-Check out the User guide and the API reference for more info:
+The documentation comes in two flavors:
 
 - [Stable documentation](https://monarch-initiative.github.io/gpsea/stable/) (last release on `main` branch)
 - [Latest documentation](https://monarch-initiative.github.io/gpsea/latest) (bleeding edge, latest commit on `develop` branch)

src/gpsea/analysis/__init__.py

@@ -1,15 +0,0 @@
-from ._api import CohortAnalysis, GenotypePhenotypeAnalysisResult, HpoMtcReport
-# TODO This should go away
-from ._config import CohortAnalysisConfiguration, configure_cohort_analysis, configure_default_protein_metadata_service, MtcStrategy
-from ._gp_analysis import apply_predicates_on_patients
-from ._util import prepare_hpo_terms_of_interest
-
-__all__ = [
-    'configure_cohort_analysis',
-    'CohortAnalysis', 'GenotypePhenotypeAnalysisResult',
-    'CohortAnalysisConfiguration', 'MtcStrategy',
-    'HpoMtcReport',
-    'apply_predicates_on_patients',
-    'configure_default_protein_metadata_service',
-    'prepare_hpo_terms_of_interest',
-]