tooluniverse 1.0.11.1__py3-none-any.whl → 1.0.12__py3-none-any.whl

tooluniverse/tools/ENCODE_search_experiments.py

@@ -0,0 +1,67 @@
+"""
+ENCODE_search_experiments
+
+Search ENCODE functional genomics experiments (e.g., ChIP-seq, ATAC-seq) by assay/target/organism...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ENCODE_search_experiments(
+    assay_title: Optional[str] = None,
+    target: Optional[str] = None,
+    organism: Optional[str] = None,
+    status: Optional[str] = "released",
+    limit: Optional[int] = 10,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Search ENCODE functional genomics experiments (e.g., ChIP-seq, ATAC-seq) by assay/target/organism...
+
+    Parameters
+    ----------
+    assay_title : str
+        Assay name filter (e.g., 'ChIP-seq', 'ATAC-seq').
+    target : str
+        Target filter (e.g., 'CTCF').
+    organism : str
+        Organism filter (e.g., 'Homo sapiens', 'Mus musculus').
+    status : str
+        Record status filter (default 'released').
+    limit : int
+        Max number of results (1–100).
+    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": "ENCODE_search_experiments",
+            "arguments": {
+                "assay_title": assay_title,
+                "target": target,
+                "organism": organism,
+                "status": status,
+                "limit": limit,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ENCODE_search_experiments"]

tooluniverse/tools/GBIF_search_occurrences.py

@@ -0,0 +1,67 @@
+"""
+GBIF_search_occurrences
+
+Retrieve species occurrence records from GBIF with optional filters (taxonKey, country, coordinat...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def GBIF_search_occurrences(
+    taxonKey: Optional[int] = None,
+    country: Optional[str] = None,
+    hasCoordinate: Optional[bool] = True,
+    limit: Optional[int] = 10,
+    offset: Optional[int] = 0,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Retrieve species occurrence records from GBIF with optional filters (taxonKey, country, coordinat...
+
+    Parameters
+    ----------
+    taxonKey : int
+        GBIF taxon key to filter occurrences by a specific taxon (from species search).
+    country : str
+        ISO 3166-1 alpha-2 country code filter (e.g., 'US', 'CN').
+    hasCoordinate : bool
+        Only return records with valid latitude/longitude coordinates when true.
+    limit : int
+        Maximum number of results to return (1–300).
+    offset : int
+        Result offset for pagination (0-based).
+    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": "GBIF_search_occurrences",
+            "arguments": {
+                "taxonKey": taxonKey,
+                "country": country,
+                "hasCoordinate": hasCoordinate,
+                "limit": limit,
+                "offset": offset,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["GBIF_search_occurrences"]

tooluniverse/tools/GBIF_search_species.py

@@ -0,0 +1,55 @@
+"""
+GBIF_search_species
+
+Find taxa by keyword (scientific/common names) in GBIF. Use to resolve organism names to stable t...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def GBIF_search_species(
+    query: str,
+    limit: Optional[int] = 10,
+    offset: Optional[int] = 0,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Find taxa by keyword (scientific/common names) in GBIF. Use to resolve organism names to stable t...
+
+    Parameters
+    ----------
+    query : str
+        Search string for species/taxa (supports scientific/common names), e.g., 'Hom...
+    limit : int
+        Maximum number of results to return (1–300).
+    offset : int
+        Result offset for pagination (0-based).
+    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": "GBIF_search_species",
+            "arguments": {"query": query, "limit": limit, "offset": offset},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["GBIF_search_species"]

tooluniverse/tools/GDC_list_files.py

@@ -0,0 +1,55 @@
+"""
+GDC_list_files
+
+List GDC files filtered by data_type and other fields. Use to identify downloadable artifacts (e....
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def GDC_list_files(
+    data_type: Optional[str] = None,
+    size: Optional[int] = 10,
+    offset: Optional[int] = 0,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    List GDC files filtered by data_type and other fields. Use to identify downloadable artifacts (e....
+
+    Parameters
+    ----------
+    data_type : str
+        Data type filter (e.g., 'Gene Expression Quantification').
+    size : int
+        Number of results (1–100).
+    offset : int
+        Offset for pagination (0-based).
+    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": "GDC_list_files",
+            "arguments": {"data_type": data_type, "size": size, "offset": offset},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["GDC_list_files"]

tooluniverse/tools/GDC_search_cases.py

@@ -0,0 +1,55 @@
+"""
+GDC_search_cases
+
+Search cancer cohort cases in NCI GDC by project and filters. Use to retrieve case-level metadata...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def GDC_search_cases(
+    project_id: Optional[str] = None,
+    size: Optional[int] = 10,
+    offset: Optional[int] = 0,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Search cancer cohort cases in NCI GDC by project and filters. Use to retrieve case-level metadata...
+
+    Parameters
+    ----------
+    project_id : str
+        GDC project identifier (e.g., 'TCGA-BRCA').
+    size : int
+        Number of results (1–100).
+    offset : int
+        Offset for pagination (0-based).
+    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": "GDC_search_cases",
+            "arguments": {"project_id": project_id, "size": size, "offset": offset},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["GDC_search_cases"]

tooluniverse/tools/GTEx_get_expression_summary.py

@@ -0,0 +1,49 @@
+"""
+GTEx_get_expression_summary
+
+Summarize tissue-specific expression (e.g., median TPM) for a gene across GTEx tissues. Use to pr...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def GTEx_get_expression_summary(
+    ensembl_gene_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Summarize tissue-specific expression (e.g., median TPM) for a gene across GTEx tissues. Use to pr...
+
+    Parameters
+    ----------
+    ensembl_gene_id : str
+        Ensembl gene identifier (e.g., 'ENSG00000141510' for TP53).
+    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": "GTEx_get_expression_summary",
+            "arguments": {"ensembl_gene_id": ensembl_gene_id},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["GTEx_get_expression_summary"]

tooluniverse/tools/GTEx_query_eqtl.py

@@ -0,0 +1,59 @@
+"""
+GTEx_query_eqtl
+
+Query GTEx single-tissue eQTL associations for a gene. Use to identify regulatory variants (varia...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def GTEx_query_eqtl(
+    ensembl_gene_id: str,
+    page: Optional[int] = 1,
+    size: Optional[int] = 10,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Query GTEx single-tissue eQTL associations for a gene. Use to identify regulatory variants (varia...
+
+    Parameters
+    ----------
+    ensembl_gene_id : str
+        Ensembl gene identifier (e.g., 'ENSG00000141510').
+    page : int
+        Page number (1-based).
+    size : int
+        Number of records per page (1–100).
+    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": "GTEx_query_eqtl",
+            "arguments": {
+                "ensembl_gene_id": ensembl_gene_id,
+                "page": page,
+                "size": size,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["GTEx_query_eqtl"]

tooluniverse/tools/MGnify_list_analyses.py

@@ -0,0 +1,52 @@
+"""
+MGnify_list_analyses
+
+List analyses associated with a study accession (taxonomic/functional outputs). Use to enumerate ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def MGnify_list_analyses(
+    study_accession: str,
+    size: Optional[int] = 10,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    List analyses associated with a study accession (taxonomic/functional outputs). Use to enumerate ...
+
+    Parameters
+    ----------
+    study_accession : str
+        MGnify study accession (e.g., 'MGYS00000001').
+    size : int
+        Number of records per page (1–100).
+    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": "MGnify_list_analyses",
+            "arguments": {"study_accession": study_accession, "size": size},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["MGnify_list_analyses"]

tooluniverse/tools/MGnify_search_studies.py

@@ -0,0 +1,55 @@
+"""
+MGnify_search_studies
+
+Search MGnify metagenomics/microbiome studies by biome/keyword. Use to discover study accessions ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def MGnify_search_studies(
+    biome: Optional[str] = None,
+    search: Optional[str] = None,
+    size: Optional[int] = 10,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Search MGnify metagenomics/microbiome studies by biome/keyword. Use to discover study accessions ...
+
+    Parameters
+    ----------
+    biome : str
+        Biome identifier (e.g., 'root:Host-associated').
+    search : str
+        Keyword to search in study titles/descriptions.
+    size : int
+        Number of records per page (1–100).
+    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": "MGnify_search_studies",
+            "arguments": {"biome": biome, "search": search, "size": size},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["MGnify_search_studies"]

tooluniverse/tools/OBIS_search_occurrences.py

@@ -0,0 +1,59 @@
+"""
+OBIS_search_occurrences
+
+Retrieve marine species occurrence records (with coordinates/time) from OBIS using flexible filte...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def OBIS_search_occurrences(
+    scientificname: Optional[str] = None,
+    areaid: Optional[str] = None,
+    size: Optional[int] = 10,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Retrieve marine species occurrence records (with coordinates/time) from OBIS using flexible filte...
+
+    Parameters
+    ----------
+    scientificname : str
+        Scientific name filter to restrict occurrences.
+    areaid : str
+        Area identifier filter (per OBIS API).
+    size : int
+        Number of records to return (1–100).
+    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": "OBIS_search_occurrences",
+            "arguments": {
+                "scientificname": scientificname,
+                "areaid": areaid,
+                "size": size,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["OBIS_search_occurrences"]

tooluniverse/tools/OBIS_search_taxa.py

@@ -0,0 +1,52 @@
+"""
+OBIS_search_taxa
+
+Resolve marine taxa in OBIS by scientific name to obtain standardized identifiers (AphiaID), rank...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def OBIS_search_taxa(
+    scientificname: str,
+    size: Optional[int] = 10,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Resolve marine taxa in OBIS by scientific name to obtain standardized identifiers (AphiaID), rank...
+
+    Parameters
+    ----------
+    scientificname : str
+        Scientific name query (e.g., 'Gadus').
+    size : int
+        Number of records to return (1–100).
+    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": "OBIS_search_taxa",
+            "arguments": {"scientificname": scientificname, "size": size},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["OBIS_search_taxa"]

tooluniverse/tools/RNAcentral_get_by_accession.py

@@ -0,0 +1,46 @@
+"""
+RNAcentral_get_by_accession
+
+Retrieve a single RNAcentral entry by accession for detailed annotations and source cross-referen...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def RNAcentral_get_by_accession(
+    accession: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Retrieve a single RNAcentral entry by accession for detailed annotations and source cross-referen...
+
+    Parameters
+    ----------
+    accession : str
+        RNAcentral accession (e.g., 'URS000075C808').
+    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": "RNAcentral_get_by_accession", "arguments": {"accession": accession}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["RNAcentral_get_by_accession"]