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

tooluniverse/tools/get_protein_classification_by_pdb_id.py

@@ -0,0 +1,49 @@
+"""
+get_protein_classification_by_pdb_id
+
+Get the classification of the protein structure (e.g., transferase, oxidoreductase).
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_protein_classification_by_pdb_id(
+    pdb_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get the classification of the protein structure (e.g., transferase, oxidoreductase).
+
+    Parameters
+    ----------
+    pdb_id : str
+        PDB ID of the entry
+    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": "get_protein_classification_by_pdb_id",
+            "arguments": {"pdb_id": pdb_id},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_protein_classification_by_pdb_id"]

tooluniverse/tools/get_protein_metadata_by_pdb_id.py

@@ -0,0 +1,46 @@
+"""
+get_protein_metadata_by_pdb_id
+
+Retrieve basic protein structure metadata, including structure title, experimental method, resolu...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_protein_metadata_by_pdb_id(
+    pdb_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Retrieve basic protein structure metadata, including structure title, experimental method, resolu...
+
+    Parameters
+    ----------
+    pdb_id : str
+        4-character RCSB PDB ID of the protein
+    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": "get_protein_metadata_by_pdb_id", "arguments": {"pdb_id": pdb_id}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_protein_metadata_by_pdb_id"]

tooluniverse/tools/get_pubchempy_info.py

@@ -0,0 +1,44 @@
+"""
+get_pubchempy_info
+
+Get information about the pubchempy package. Python interface for PubChem REST API
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_pubchempy_info(
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get information about the pubchempy package. Python interface for PubChem REST API
+
+    Parameters
+    ----------
+    No parameters
+    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": "get_pubchempy_info", "arguments": {}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_pubchempy_info"]

tooluniverse/tools/get_pybedtools_info.py

@@ -0,0 +1,49 @@
+"""
+get_pybedtools_info
+
+Get comprehensive information about pybedtools – Python wrapper for BEDTools
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_pybedtools_info(
+    include_examples: bool,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get comprehensive information about pybedtools – Python wrapper for BEDTools
+
+    Parameters
+    ----------
+    include_examples : bool
+        Whether to include usage examples and quick start guide
+    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": "get_pybedtools_info",
+            "arguments": {"include_examples": include_examples},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_pybedtools_info"]

tooluniverse/tools/get_pybigwig_info.py

@@ -0,0 +1,46 @@
+"""
+get_pybigwig_info
+
+Get comprehensive information about pyBigWig – BigWig file access in Python
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_pybigwig_info(
+    info_type: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get comprehensive information about pyBigWig – BigWig file access in Python
+
+    Parameters
+    ----------
+    info_type : str
+        Type of information to retrieve about pyBigWig
+    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": "get_pybigwig_info", "arguments": {"info_type": info_type}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_pybigwig_info"]

tooluniverse/tools/get_pydeseq2_info.py

@@ -0,0 +1,46 @@
+"""
+get_pydeseq2_info
+
+Get comprehensive information about PyDESeq2 – RNA-seq differential expression analysis
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_pydeseq2_info(
+    info_type: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get comprehensive information about PyDESeq2 – RNA-seq differential expression analysis
+
+    Parameters
+    ----------
+    info_type : str
+        Type of information to retrieve about PyDESeq2
+    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": "get_pydeseq2_info", "arguments": {"info_type": info_type}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_pydeseq2_info"]

tooluniverse/tools/get_pyensembl_info.py

@@ -0,0 +1,44 @@
+"""
+get_pyensembl_info
+
+Get information about the pyensembl package. Python interface to Ensembl reference genome metadata
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_pyensembl_info(
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get information about the pyensembl package. Python interface to Ensembl reference genome metadata
+
+    Parameters
+    ----------
+    No parameters
+    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": "get_pyensembl_info", "arguments": {}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_pyensembl_info"]

tooluniverse/tools/get_pyephem_info.py

@@ -0,0 +1,44 @@
+"""
+get_pyephem_info
+
+Get information about the pyephem package. Astronomical computations for Python
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_pyephem_info(
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get information about the pyephem package. Astronomical computations for Python
+
+    Parameters
+    ----------
+    No parameters
+    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": "get_pyephem_info", "arguments": {}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_pyephem_info"]

tooluniverse/tools/get_pyfaidx_info.py

@@ -0,0 +1,49 @@
+"""
+get_pyfaidx_info
+
+Get comprehensive information about pyfaidx – efficient FASTA file indexing and random access
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_pyfaidx_info(
+    include_examples: bool,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get comprehensive information about pyfaidx – efficient FASTA file indexing and random access
+
+    Parameters
+    ----------
+    include_examples : bool
+        Whether to include usage examples and quick start guide
+    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": "get_pyfaidx_info",
+            "arguments": {"include_examples": include_examples},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_pyfaidx_info"]

tooluniverse/tools/get_pyfasta_info.py

@@ -0,0 +1,44 @@
+"""
+get_pyfasta_info
+
+Get information about the pyfasta package. Python library for efficient random access to fasta su...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_pyfasta_info(
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get information about the pyfasta package. Python library for efficient random access to fasta su...
+
+    Parameters
+    ----------
+    No parameters
+    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": "get_pyfasta_info", "arguments": {}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_pyfasta_info"]

tooluniverse/tools/get_pykalman_info.py

@@ -0,0 +1,46 @@
+"""
+get_pykalman_info
+
+Get comprehensive information about PyKalman – Kalman filtering and smoothing
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_pykalman_info(
+    info_type: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get comprehensive information about PyKalman – Kalman filtering and smoothing
+
+    Parameters
+    ----------
+    info_type : str
+        Type of information to retrieve about PyKalman
+    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": "get_pykalman_info", "arguments": {"info_type": info_type}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_pykalman_info"]

tooluniverse/tools/get_pyliftover_info.py

@@ -0,0 +1,49 @@
+"""
+get_pyliftover_info
+
+Get comprehensive information about PyLiftover – genomic coordinate conversion between assemblies
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_pyliftover_info(
+    include_examples: bool,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get comprehensive information about PyLiftover – genomic coordinate conversion between assemblies
+
+    Parameters
+    ----------
+    include_examples : bool
+        Whether to include usage examples and quick start guide
+    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": "get_pyliftover_info",
+            "arguments": {"include_examples": include_examples},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_pyliftover_info"]

tooluniverse/tools/get_pymassspec_info.py

@@ -0,0 +1,46 @@
+"""
+get_pymassspec_info
+
+Get comprehensive information about PyMassSpec – mass spectrometry data analysis
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_pymassspec_info(
+    info_type: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get comprehensive information about PyMassSpec – mass spectrometry data analysis
+
+    Parameters
+    ----------
+    info_type : str
+        Type of information to retrieve about PyMassSpec
+    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": "get_pymassspec_info", "arguments": {"info_type": info_type}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_pymassspec_info"]

tooluniverse/tools/get_pymed_info.py

@@ -0,0 +1,46 @@
+"""
+get_pymed_info
+
+Get comprehensive information about PyMed – PubMed access in Python
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_pymed_info(
+    include_examples: bool,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get comprehensive information about PyMed – PubMed access in Python
+
+    Parameters
+    ----------
+    include_examples : bool
+        Whether to include usage examples and quick start guide
+    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": "get_pymed_info", "arguments": {"include_examples": include_examples}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_pymed_info"]