tooluniverse 1.0.6__py3-none-any.whl → 1.0.8__py3-none-any.whl

tooluniverse/tools/gwas_get_snps_for_gene.py

@@ -0,0 +1,55 @@
+"""
+gwas_get_snps_for_gene
+
+Get all SNPs mapped to a specific gene.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def gwas_get_snps_for_gene(
+    mapped_gene: str,
+    size: Optional[int] = None,
+    page: Optional[int] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Get all SNPs mapped to a specific gene.
+
+    Parameters
+    ----------
+    mapped_gene : str
+        Gene name or symbol
+    size : int
+        Number of results to return per page
+    page : int
+        Page number for pagination
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "gwas_get_snps_for_gene",
+            "arguments": {"mapped_gene": mapped_gene, "size": size, "page": page},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["gwas_get_snps_for_gene"]

tooluniverse/tools/gwas_get_studies_for_trait.py

@@ -0,0 +1,75 @@
+"""
+gwas_get_studies_for_trait
+
+Get studies for a specific trait with optional filters for cohort, GxE interactions, and summary ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def gwas_get_studies_for_trait(
+    efo_trait: Optional[str] = None,
+    disease_trait: Optional[str] = None,
+    cohort: Optional[str] = None,
+    gxe: Optional[bool] = None,
+    full_pvalue_set: Optional[bool] = None,
+    size: Optional[int] = None,
+    page: Optional[int] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Get studies for a specific trait with optional filters for cohort, GxE interactions, and summary ...
+
+    Parameters
+    ----------
+    efo_trait : str
+        EFO trait identifier or name
+    disease_trait : str
+        Disease trait name
+    cohort : str
+        Cohort name (e.g., 'UKB' for UK Biobank)
+    gxe : bool
+        Filter for Gene-by-Environment interaction studies
+    full_pvalue_set : bool
+        Filter for studies with full summary statistics
+    size : int
+        Number of results to return per page
+    page : int
+        Page number for pagination
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "gwas_get_studies_for_trait",
+            "arguments": {
+                "efo_trait": efo_trait,
+                "disease_trait": disease_trait,
+                "cohort": cohort,
+                "gxe": gxe,
+                "full_pvalue_set": full_pvalue_set,
+                "size": size,
+                "page": page,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["gwas_get_studies_for_trait"]

tooluniverse/tools/gwas_get_study_by_id.py

@@ -0,0 +1,46 @@
+"""
+gwas_get_study_by_id
+
+Get a specific GWAS study by its unique identifier.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def gwas_get_study_by_id(
+    study_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Get a specific GWAS study by its unique identifier.
+
+    Parameters
+    ----------
+    study_id : str
+        GWAS study identifier
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {"name": "gwas_get_study_by_id", "arguments": {"study_id": study_id}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["gwas_get_study_by_id"]

tooluniverse/tools/gwas_get_variants_for_trait.py

@@ -0,0 +1,55 @@
+"""
+gwas_get_variants_for_trait
+
+Get all variants associated with a specific trait with pagination support.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def gwas_get_variants_for_trait(
+    efo_trait: str,
+    size: Optional[int] = None,
+    page: Optional[int] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Get all variants associated with a specific trait with pagination support.
+
+    Parameters
+    ----------
+    efo_trait : str
+        EFO trait identifier or name
+    size : int
+        Number of results to return per page
+    page : int
+        Page number for pagination
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "gwas_get_variants_for_trait",
+            "arguments": {"efo_trait": efo_trait, "size": size, "page": page},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["gwas_get_variants_for_trait"]

tooluniverse/tools/gwas_search_associations.py

@@ -0,0 +1,75 @@
+"""
+gwas_search_associations
+
+Search for GWAS associations by various criteria including EFO trait, rs ID, accession ID, with s...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def gwas_search_associations(
+    efo_trait: Optional[str] = None,
+    rs_id: Optional[str] = None,
+    accession_id: Optional[str] = None,
+    sort: Optional[str] = None,
+    direction: Optional[str] = None,
+    size: Optional[int] = None,
+    page: Optional[int] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Search for GWAS associations by various criteria including EFO trait, rs ID, accession ID, with s...
+
+    Parameters
+    ----------
+    efo_trait : str
+        EFO trait identifier or name
+    rs_id : str
+        dbSNP rs identifier
+    accession_id : str
+        Study accession identifier
+    sort : str
+        Sort field (e.g., 'p_value', 'or_value')
+    direction : str
+        Sort direction ('asc' or 'desc')
+    size : int
+        Number of results to return
+    page : int
+        Page number for pagination
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "gwas_search_associations",
+            "arguments": {
+                "efo_trait": efo_trait,
+                "rs_id": rs_id,
+                "accession_id": accession_id,
+                "sort": sort,
+                "direction": direction,
+                "size": size,
+                "page": page,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["gwas_search_associations"]

tooluniverse/tools/gwas_search_snps.py

@@ -0,0 +1,63 @@
+"""
+gwas_search_snps
+
+Search for GWAS single nucleotide polymorphisms (SNPs) by rs ID or mapped gene.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def gwas_search_snps(
+    rs_id: Optional[str] = None,
+    mapped_gene: Optional[str] = None,
+    size: Optional[int] = None,
+    page: Optional[int] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Search for GWAS single nucleotide polymorphisms (SNPs) by rs ID or mapped gene.
+
+    Parameters
+    ----------
+    rs_id : str
+        dbSNP rs identifier
+    mapped_gene : str
+        Gene name or symbol
+    size : int
+        Number of results to return
+    page : int
+        Page number for pagination
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "gwas_search_snps",
+            "arguments": {
+                "rs_id": rs_id,
+                "mapped_gene": mapped_gene,
+                "size": size,
+                "page": page,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["gwas_search_snps"]

tooluniverse/tools/gwas_search_studies.py

@@ -0,0 +1,75 @@
+"""
+gwas_search_studies
+
+Search for GWAS studies by various criteria including EFO trait, disease trait, cohort, GxE inter...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def gwas_search_studies(
+    efo_trait: Optional[str] = None,
+    disease_trait: Optional[str] = None,
+    cohort: Optional[str] = None,
+    gxe: Optional[bool] = None,
+    full_pvalue_set: Optional[bool] = None,
+    size: Optional[int] = None,
+    page: Optional[int] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Search for GWAS studies by various criteria including EFO trait, disease trait, cohort, GxE inter...
+
+    Parameters
+    ----------
+    efo_trait : str
+        EFO trait identifier or name
+    disease_trait : str
+        Disease trait name
+    cohort : str
+        Cohort name (e.g., 'UKB' for UK Biobank)
+    gxe : bool
+        Filter for Gene-by-Environment interaction studies
+    full_pvalue_set : bool
+        Filter for studies with full summary statistics
+    size : int
+        Number of results to return
+    page : int
+        Page number for pagination
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "gwas_search_studies",
+            "arguments": {
+                "efo_trait": efo_trait,
+                "disease_trait": disease_trait,
+                "cohort": cohort,
+                "gxe": gxe,
+                "full_pvalue_set": full_pvalue_set,
+                "size": size,
+                "page": page,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["gwas_search_studies"]

tooluniverse/tools/humanbase_ppi_analysis.py

@@ -0,0 +1,67 @@
+"""
+humanbase_ppi_analysis
+
+Retrieve tissue-specific protein-protein interactions and biological processes from HumanBase. Re...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def humanbase_ppi_analysis(
+    gene_list: list[Any],
+    tissue: str,
+    max_node: int,
+    interaction: str,
+    string_mode: bool,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieve tissue-specific protein-protein interactions and biological processes from HumanBase. Re...
+
+    Parameters
+    ----------
+    gene_list : list[Any]
+        List of gene names or symbols to analyze for protein-protein interactions. Th...
+    tissue : str
+        Tissue type for tissue-specific interactions. Examples: 'brain', 'heart', 'li...
+    max_node : int
+        Maximum number of nodes to retrieve in the interaction network. Warning: the ...
+    interaction : str
+        Specific interaction type to filter by. Available types: 'co-expression', 'in...
+    string_mode : bool
+        Whether to return the result in string mode. If True, the result will be a st...
+    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": "humanbase_ppi_analysis",
+            "arguments": {
+                "gene_list": gene_list,
+                "tissue": tissue,
+                "max_node": max_node,
+                "interaction": interaction,
+                "string_mode": string_mode,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["humanbase_ppi_analysis"]

tooluniverse/tools/mesh_get_subjects_by_pharmacological_action.py

@@ -0,0 +1,63 @@
+"""
+mesh_get_subjects_by_pharmacological_action
+
+Find MeSH (Medical Subject Heading) subjects with matching pharmacological actions.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def mesh_get_subjects_by_pharmacological_action(
+    query: str,
+    case_sensitive: bool,
+    exact_match: bool,
+    limit: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Find MeSH (Medical Subject Heading) subjects with matching pharmacological actions.
+
+    Parameters
+    ----------
+    query : str
+        Pharmacological action to search for in MeSH subjects
+    case_sensitive : bool
+        Select True to perform a case-sensitive search for the pharmacological action...
+    exact_match : bool
+        Select True to require an exact match for the pharmacological action query
+    limit : int
+        Maximum number of results to return
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "mesh_get_subjects_by_pharmacological_action",
+            "arguments": {
+                "query": query,
+                "case_sensitive": case_sensitive,
+                "exact_match": exact_match,
+                "limit": limit,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["mesh_get_subjects_by_pharmacological_action"]

tooluniverse/tools/mesh_get_subjects_by_subject_id.py

@@ -0,0 +1,63 @@
+"""
+mesh_get_subjects_by_subject_id
+
+Find MeSH (Medical Subject Heading) subjects with a matching subject ID (also called Descriptor UI).
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def mesh_get_subjects_by_subject_id(
+    query: str,
+    case_sensitive: bool,
+    exact_match: bool,
+    limit: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Find MeSH (Medical Subject Heading) subjects with a matching subject ID (also called Descriptor UI).
+
+    Parameters
+    ----------
+    query : str
+        Query ID to search for among the MeSH subject IDs
+    case_sensitive : bool
+        Select True to perform a case-sensitive search for the query
+    exact_match : bool
+        Select True to require an exact match for the query
+    limit : int
+        Maximum number of results to return
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "mesh_get_subjects_by_subject_id",
+            "arguments": {
+                "query": query,
+                "case_sensitive": case_sensitive,
+                "exact_match": exact_match,
+                "limit": limit,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["mesh_get_subjects_by_subject_id"]

tooluniverse/tools/mesh_get_subjects_by_subject_name.py

@@ -0,0 +1,63 @@
+"""
+mesh_get_subjects_by_subject_name
+
+Find MeSH (Medical Subject Heading) subjects with matching names.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def mesh_get_subjects_by_subject_name(
+    query: str,
+    case_sensitive: bool,
+    exact_match: bool,
+    limit: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Find MeSH (Medical Subject Heading) subjects with matching names.
+
+    Parameters
+    ----------
+    query : str
+        Query string to search for in the name of each MeSH subject and the names of ...
+    case_sensitive : bool
+        Select True to perform a case-sensitive search for the query
+    exact_match : bool
+        Select True to require an exact match for the query
+    limit : int
+        Maximum number of results to return
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "mesh_get_subjects_by_subject_name",
+            "arguments": {
+                "query": query,
+                "case_sensitive": case_sensitive,
+                "exact_match": exact_match,
+                "limit": limit,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["mesh_get_subjects_by_subject_name"]