tooluniverse 1.0.6__py3-none-any.whl → 1.0.7__py3-none-any.whl

tooluniverse/tools/HPA_get_cancer_prognostics_by_gene.py

@@ -0,0 +1,49 @@
+"""
+HPA_get_cancer_prognostics_by_gene
+
+Retrieve prognostic value of a gene across various cancer types, indicating if its expression lev...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def HPA_get_cancer_prognostics_by_gene(
+    ensembl_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieve prognostic value of a gene across various cancer types, indicating if its expression lev...
+
+    Parameters
+    ----------
+    ensembl_id : str
+        Ensembl Gene ID of the gene to check, e.g., 'ENSG00000141510' for TP53, 'ENSG...
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "HPA_get_cancer_prognostics_by_gene",
+            "arguments": {"ensembl_id": ensembl_id},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["HPA_get_cancer_prognostics_by_gene"]

tooluniverse/tools/HPA_get_comparative_expression_by_gene_and_cellline.py

@@ -0,0 +1,52 @@
+"""
+HPA_get_comparative_expression_by_gene_and_cellline
+
+Compare the expression level differences of a gene between a specific cell line and healthy tissu...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def HPA_get_comparative_expression_by_gene_and_cellline(
+    gene_name: str,
+    cell_line: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Compare the expression level differences of a gene between a specific cell line and healthy tissu...
+
+    Parameters
+    ----------
+    gene_name : str
+        Gene name or gene symbol, e.g., 'TP53', 'BRCA1', 'EGFR', etc.
+    cell_line : str
+        Cell line name, supported cell lines include: ishikawa, hela, mcf7, a549, hep...
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "HPA_get_comparative_expression_by_gene_and_cellline",
+            "arguments": {"gene_name": gene_name, "cell_line": cell_line},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["HPA_get_comparative_expression_by_gene_and_cellline"]

tooluniverse/tools/HPA_get_comprehensive_gene_details_by_ensembl_id.py

@@ -0,0 +1,63 @@
+"""
+HPA_get_comprehensive_gene_details_by_ensembl_id
+
+Get detailed in-depth information from gene page using Ensembl Gene ID, including image URLs, ant...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def HPA_get_comprehensive_gene_details_by_ensembl_id(
+    ensembl_id: str,
+    include_images: bool,
+    include_antibodies: bool,
+    include_expression: bool,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get detailed in-depth information from gene page using Ensembl Gene ID, including image URLs, ant...
+
+    Parameters
+    ----------
+    ensembl_id : str
+        Ensembl Gene ID, e.g., 'ENSG00000064787' (BCAS1), 'ENSG00000141510' (TP53), e...
+    include_images : bool
+        Whether to include image URL information (immunofluorescence, cell line image...
+    include_antibodies : bool
+        Whether to include detailed antibody information (validation status, Western ...
+    include_expression : bool
+        Whether to include detailed expression data (tissue specificity, subcellular ...
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "HPA_get_comprehensive_gene_details_by_ensembl_id",
+            "arguments": {
+                "ensembl_id": ensembl_id,
+                "include_images": include_images,
+                "include_antibodies": include_antibodies,
+                "include_expression": include_expression,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["HPA_get_comprehensive_gene_details_by_ensembl_id"]

tooluniverse/tools/HPA_get_contextual_biological_process_analysis.py

@@ -0,0 +1,52 @@
+"""
+HPA_get_contextual_biological_process_analysis
+
+Analyze a gene's biological processes in the context of a specific tissue or cell line by integra...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def HPA_get_contextual_biological_process_analysis(
+    gene_name: str,
+    context_name: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Analyze a gene's biological processes in the context of a specific tissue or cell line by integra...
+
+    Parameters
+    ----------
+    gene_name : str
+        Gene name or symbol, e.g., 'TP53', 'EGFR', 'BRCA1'.
+    context_name : str
+        Name of the tissue or cell line to provide context, e.g., 'brain', 'liver', '...
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "HPA_get_contextual_biological_process_analysis",
+            "arguments": {"gene_name": gene_name, "context_name": context_name},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["HPA_get_contextual_biological_process_analysis"]

tooluniverse/tools/HPA_get_disease_expression_by_gene_tissue_disease.py

@@ -0,0 +1,59 @@
+"""
+HPA_get_disease_expression_by_gene_tissue_disease
+
+Compare the expression level of a gene in specific disease state versus healthy state using gene ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def HPA_get_disease_expression_by_gene_tissue_disease(
+    gene_name: str,
+    tissue_type: str,
+    disease_name: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Compare the expression level of a gene in specific disease state versus healthy state using gene ...
+
+    Parameters
+    ----------
+    gene_name : str
+        Gene name or gene symbol, e.g., 'TP53', 'BRCA1', 'KRAS', etc.
+    tissue_type : str
+        Tissue type, e.g., 'brain', 'breast', 'colon', 'lung', etc., optional parameter.
+    disease_name : str
+        Disease name, supported diseases include: brain_cancer, breast_cancer, colon_...
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "HPA_get_disease_expression_by_gene_tissue_disease",
+            "arguments": {
+                "gene_name": gene_name,
+                "tissue_type": tissue_type,
+                "disease_name": disease_name,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["HPA_get_disease_expression_by_gene_tissue_disease"]

tooluniverse/tools/HPA_get_gene_basic_info_by_ensembl_id.py

@@ -0,0 +1,49 @@
+"""
+HPA_get_gene_basic_info_by_ensembl_id
+
+Get gene basic information and expression data from Human Protein Atlas using Ensembl Gene ID. En...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def HPA_get_gene_basic_info_by_ensembl_id(
+    ensembl_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get gene basic information and expression data from Human Protein Atlas using Ensembl Gene ID. En...
+
+    Parameters
+    ----------
+    ensembl_id : str
+        Ensembl Gene ID, e.g., 'ENSG00000134057', 'ENSG00000141510', etc.
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "HPA_get_gene_basic_info_by_ensembl_id",
+            "arguments": {"ensembl_id": ensembl_id},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["HPA_get_gene_basic_info_by_ensembl_id"]

tooluniverse/tools/HPA_get_gene_tsv_data_by_ensembl_id.py

@@ -0,0 +1,49 @@
+"""
+HPA_get_gene_tsv_data_by_ensembl_id
+
+Get detailed gene data in TSV format from Human Protein Atlas using Ensembl Gene ID (backward com...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def HPA_get_gene_tsv_data_by_ensembl_id(
+    ensembl_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get detailed gene data in TSV format from Human Protein Atlas using Ensembl Gene ID (backward com...
+
+    Parameters
+    ----------
+    ensembl_id : str
+        Ensembl Gene ID, e.g., 'ENSG00000134057', 'ENSG00000141510', etc.
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "HPA_get_gene_tsv_data_by_ensembl_id",
+            "arguments": {"ensembl_id": ensembl_id},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["HPA_get_gene_tsv_data_by_ensembl_id"]

tooluniverse/tools/HPA_get_protein_interactions_by_gene.py

@@ -0,0 +1,49 @@
+"""
+HPA_get_protein_interactions_by_gene
+
+Fetch known protein-protein interaction partners for a given gene from Human Protein Atlas database.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def HPA_get_protein_interactions_by_gene(
+    gene_name: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Fetch known protein-protein interaction partners for a given gene from Human Protein Atlas database.
+
+    Parameters
+    ----------
+    gene_name : str
+        Official gene symbol, e.g., 'EGFR', 'TP53', 'BRCA1', etc.
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "HPA_get_protein_interactions_by_gene",
+            "arguments": {"gene_name": gene_name},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["HPA_get_protein_interactions_by_gene"]

tooluniverse/tools/HPA_get_rna_expression_by_source.py

@@ -0,0 +1,59 @@
+"""
+HPA_get_rna_expression_by_source
+
+Get RNA expression level (nTPM) for a gene in a specific biological source using optimized column...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def HPA_get_rna_expression_by_source(
+    gene_name: str,
+    source_type: str,
+    source_name: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get RNA expression level (nTPM) for a gene in a specific biological source using optimized column...
+
+    Parameters
+    ----------
+    gene_name : str
+        Gene name or gene symbol, e.g., 'GFAP', 'TP53', 'BRCA1', etc.
+    source_type : str
+        The type of biological source. Choose from: 'tissue', 'blood', 'brain', 'sing...
+    source_name : str
+        The specific name of the biological source, e.g., 'liver', 'heart_muscle', 't...
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "HPA_get_rna_expression_by_source",
+            "arguments": {
+                "gene_name": gene_name,
+                "source_type": source_type,
+                "source_name": source_name,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["HPA_get_rna_expression_by_source"]

tooluniverse/tools/HPA_get_rna_expression_in_specific_tissues.py

@@ -0,0 +1,52 @@
+"""
+HPA_get_rna_expression_in_specific_tissues
+
+Query RNA expression levels (nTPM) for a specific gene in one or more user-specified tissues with...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def HPA_get_rna_expression_in_specific_tissues(
+    ensembl_id: str,
+    tissue_names: list[Any],
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Query RNA expression levels (nTPM) for a specific gene in one or more user-specified tissues with...
+
+    Parameters
+    ----------
+    ensembl_id : str
+        Ensembl Gene ID for the gene, e.g., 'ENSG00000141510' for TP53.
+    tissue_names : list[Any]
+        List of tissue names to query, e.g., ['brain', 'liver', 'heart muscle', 'kidn...
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "HPA_get_rna_expression_in_specific_tissues",
+            "arguments": {"ensembl_id": ensembl_id, "tissue_names": tissue_names},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["HPA_get_rna_expression_in_specific_tissues"]

tooluniverse/tools/HPA_get_subcellular_location.py

@@ -0,0 +1,46 @@
+"""
+HPA_get_subcellular_location
+
+Get annotated subcellular locations for a protein using optimized columns parameter. Retrieves bo...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def HPA_get_subcellular_location(
+    gene_name: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get annotated subcellular locations for a protein using optimized columns parameter. Retrieves bo...
+
+    Parameters
+    ----------
+    gene_name : str
+        Gene name or gene symbol, e.g., 'CCNB1', 'TP53', 'EGFR', etc.
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {"name": "HPA_get_subcellular_location", "arguments": {"gene_name": gene_name}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["HPA_get_subcellular_location"]

tooluniverse/tools/HPA_search_genes_by_query.py

@@ -0,0 +1,49 @@
+"""
+HPA_search_genes_by_query
+
+Search for matching genes by gene name, keywords, or cell line names and return Ensembl ID list. ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def HPA_search_genes_by_query(
+    search_query: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Search for matching genes by gene name, keywords, or cell line names and return Ensembl ID list. ...
+
+    Parameters
+    ----------
+    search_query : str
+        Gene name, alias, keyword, or cell line name to search for, e.g., 'EGFR', 'TP...
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "HPA_search_genes_by_query",
+            "arguments": {"search_query": search_query},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["HPA_search_genes_by_query"]