if not input_genes:
raise RuntimeError("GeneToTissueBiclusters ERROR: missing mandatory input_genes parameter")
input_gene_set = self.get_simple_input_identifier_list(input_genes)
most_common_tissues = asyncio.run(self.module.gene_to_tissue_biclusters_async(input_gene_set))
self.results = pd.DataFrame.from_records(most_common_tissues)
GeneToTissueBiclusters.set_metadata(
ModuleMetaData(
name="Mod9A - Gene-to-Tissue Bicluster",
source='RNAseqDB Biclustering',
association=GeneToExpressionSiteAssociation,
domain=ConceptSpace(Gene, ['ENSEMBL']),
relationship='related_to',
range=ConceptSpace(AnatomicalEntity, ['MONDO', 'DOID', 'UBERON']),
)
)
def metadata():
"""
Retrieve Module Metadata
"""
return GeneToTissueBiclusters.get_metadata()
def main():
fire.Fire(GeneToTissueBiclusters)
if not input_diseases:
raise RuntimeError("DiseaseToPhenotypeBiclusters ERROR: missing mandatory input_diseases parameter")
input_disease_ids = self.get_simple_input_identifier_list(input_diseases)
most_common_phenotype = asyncio.run(self.module.disease_to_phenotype_biclusters_async(input_disease_ids))
self.results = pd.DataFrame.from_records(most_common_phenotype, columns=["hit_id", "score"])
DiseaseToPhenotypeBiclusters.set_metadata(
ModuleMetaData(
name="Mod2.0 - Disease Associated Genes",
source='RNAseqDB Biclustering',
association=DiseaseToPhenotypicFeatureAssociation,
domain=ConceptSpace(Disease, ['MONDO']),
relationship='has_phenotype',
range=ConceptSpace(PhenotypicFeature, ['HP']),
)
)
def metadata():
"""
Retrieve Module Metadata
"""
return DiseaseToPhenotypeBiclusters.get_metadata()
def main():
fire.Fire(DiseaseToPhenotypeBiclusters)
input_gene_set = self.get_simple_input_identifier_list(input_genes)
asyncio.run(self.module.gene_to_gene_biclusters_async(input_gene_set))
sorted_list_of_output_genes = self.module.gene_to_gene_bicluster_summarize(
input_gene_set, keep_input_id)
self.results = pd.DataFrame.from_records(sorted_list_of_output_genes)
GeneToGeneDepMapBiclusters.set_metadata(
ModuleMetaData(name="Mod9B - Gene-to-Gene Bicluster",
source='DepMap Biclustering',
association=GeneToGeneAssociation,
domain=ConceptSpace(Gene, ['NCBI']),
relationship='related_to',
range=ConceptSpace(Gene, ['NCBI'])))
def metadata():
"""
Retrieve Module Metadata
"""
return GeneToGeneDepMapBiclusters.get_metadata()
def main():
fire.Fire(GeneToGeneDepMapBiclusters)
disease_identifier, disease_label, query_biolink)
if not self.results.empty:
self.disease_associated_genes = self.results[[
'hit_id', 'hit_symbol'
]].to_dict(orient='records')
else:
self.disease_associated_genes = []
DiseaseAssociatedGeneSet.set_metadata(
ModuleMetaData(
name="Mod2.0 - Disease Associated Genes",
source='Monarch Biolink',
association=GeneToDiseaseAssociation,
domain=ConceptSpace(Disease, ['MONDO']),
relationship='gene_associated_with_condition',
range=ConceptSpace(Gene, ['HGNC']),
))
def metadata():
"""
Retrieve Module Metadata
"""
return DiseaseAssociatedGeneSet.get_metadata()
def main():
fire.Fire(DiseaseAssociatedGeneSet)
raise RuntimeError(
"GeneToChemicalInteractionPayload ERROR: missing mandatory input_genes parameter"
)
input_gene_set = self.get_simple_input_identifier_list(
input_genes, object_id_only=True)
self.results = self.module.get_chemicals_interacting_with_genes(
input_gene_set, rows)
GeneToChemicalInteractionPayload.set_metadata(
ModuleMetaData(name="Module 1B: Gene to Chemical Interactions",
source='Chemical Toxicology Database (CTD)',
association=ChemicalToGeneAssociation,
domain=ConceptSpace(Gene, ['NCBIGene']),
relationship='interacts_with',
range=ConceptSpace(ChemicalSubstance, ['CTD'])))
def metadata():
"""
Retrieve Module Metadata
"""
return GeneToChemicalInteractionPayload.get_metadata()
def main():
fire.Fire(GeneToChemicalInteractionPayload)
input_gene_set = self.get_simple_input_identifier_list(input_genes)
asyncio.run(self.module.gene_to_gene_biclusters_async(input_gene_set))
sorted_list_of_output_genes = self.module.gene_to_gene_bicluster_summarize(
input_gene_set, keep_input_id)
self.results = pd.DataFrame.from_records(sorted_list_of_output_genes)
DepMapBiclusters.set_metadata(
ModuleMetaData(name="Mod9B - Gene-to-CellLine Bicluster",
source='DepMap Biclustering',
association=GeneToGeneAssociation,
domain=ConceptSpace(Gene, ['NCBI']),
relationship='related_to',
range=ConceptSpace(CellLine, ['ACH'])))
def metadata():
"""
Retrieve Module Metadata
"""
return DepMapBiclusters.get_metadata()
def main():
fire.Fire(DepMapBiclusters)
input_tissue_ids = self.get_simple_input_identifier_list(input_tissues)
most_common_tissues = asyncio.run(
self.module.tissue_to_tissue_biclusters_async(input_tissue_ids))
self.results = pd.DataFrame.from_records(most_common_tissues,
columns=["hit_id", "score"])
TissueToTissueBicluster.set_metadata(
ModuleMetaData(
name="Mod9A - Tissue-to-Tissue Bicluster",
source='RNAseqDB Biclustering',
association=AnatomicalEntityToAnatomicalEntityAssociation,
domain=ConceptSpace(AnatomicalEntity, ['UBERON']),
relationship='related_to',
range=ConceptSpace(AnatomicalEntity, ['UBERON']),
))
def metadata():
"""
Retrieve Module Metadata
"""
return TissueToTissueBicluster.get_metadata()
def main():
fire.Fire(TissueToTissueBicluster)
def mock_concept_space():
cs = ConceptSpace(
category=mock_concept_space_category,
id_prefixes=[mock_concept_space_id_prefixes]
)
return cs
super(GeneInteractionSet, self).__init__(module=GeneInteractions())
if not input_genes:
raise RuntimeError("GeneInteractionSet ERROR: missing mandatory input_genes parameter")
input_gene_data_frame = self.get_input_data_frame(input_genes)
self.results = self.module.get_interactions(input_gene_data_frame, threshold)
GeneInteractionSet.set_metadata(
ModuleMetaData(
name="Module 1E - Gene Interaction",
source='Monarch Biolink',
association=GeneToGeneAssociation,
domain=ConceptSpace(Gene, ['HGNC']),
relationship='interacts_with',
range=ConceptSpace(Gene, ['HGNC']),
)
)
def metadata():
"""
Retrieve Module Metadata
"""
return GeneInteractionSet.get_metadata()
def main():
fire.Fire(GeneInteractionSet)