tooluniverse 1.0.9.1__py3-none-any.whl → 1.0.11__py3-none-any.whl

tooluniverse/tools/{gnomAD_query_variant.py → clinvar_get_clinical_significance.py}

@@ -1,30 +1,27 @@
 """
-gnomAD_query_variant
+clinvar_get_clinical_significance
 
-Query gnomAD GraphQL for a variant in a dataset (returns ID and genome allele counts/frequency).
+Get clinical significance information for a variant from ClinVar. Returns pathogenicity classific...
 """
 
 from typing import Any, Optional, Callable
 from ._shared_client import get_shared_client
 
 
-def gnomAD_query_variant(
+def clinvar_get_clinical_significance(
     variant_id: str,
-    dataset: Optional[str] = "gnomad_r4",
     *,
     stream_callback: Optional[Callable[[str], None]] = None,
     use_cache: bool = False,
     validate: bool = True,
 ) -> dict[str, Any]:
     """
-    Query gnomAD GraphQL for a variant in a dataset (returns ID and genome allele counts/frequency).
+    Get clinical significance information for a variant from ClinVar. Returns pathogenicity classific...
 
     Parameters
     ----------
     variant_id : str
-        Variant ID like '1-230710048-A-G'.
-    dataset : str
-        Dataset ID (e.g., gnomad_r4).
+        ClinVar variant ID (e.g., '12345', '123456')
     stream_callback : Callable, optional
         Callback for streaming output
     use_cache : bool, default False
@@ -40,8 +37,8 @@ def gnomAD_query_variant(
 
     return get_shared_client().run_one_function(
         {
-            "name": "gnomAD_query_variant",
-            "arguments": {"variant_id": variant_id, "dataset": dataset},
+            "name": "clinvar_get_clinical_significance",
+            "arguments": {"variant_id": variant_id},
         },
         stream_callback=stream_callback,
         use_cache=use_cache,
@@ -49,4 +46,4 @@ def gnomAD_query_variant(
     )
 
 
-__all__ = ["gnomAD_query_variant"]
+__all__ = ["clinvar_get_clinical_significance"]

tooluniverse/tools/clinvar_get_variant_details.py

@@ -0,0 +1,49 @@
+"""
+clinvar_get_variant_details
+
+Get detailed variant information from ClinVar by variant ID. Returns comprehensive variant data i...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def clinvar_get_variant_details(
+    variant_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Get detailed variant information from ClinVar by variant ID. Returns comprehensive variant data i...
+
+    Parameters
+    ----------
+    variant_id : str
+        ClinVar variant ID (e.g., '12345', '123456')
+    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": "clinvar_get_variant_details",
+            "arguments": {"variant_id": variant_id},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["clinvar_get_variant_details"]

tooluniverse/tools/dbSNP_get_variant_by_rsid.py

@@ -1,14 +1,14 @@
 """
-dbSNP_get_variant_by_rsid
+dbsnp_get_variant_by_rsid
 
-Fetch dbSNP variant by rsID using NCBI Variation Services (refsnp endpoint).
+Get variant information from dbSNP by rsID. Returns genomic coordinates, alleles, and basic varia...
 """
 
 from typing import Any, Optional, Callable
 from ._shared_client import get_shared_client
 
 
-def dbSNP_get_variant_by_rsid(
+def dbsnp_get_variant_by_rsid(
     rsid: str,
     *,
     stream_callback: Optional[Callable[[str], None]] = None,
@@ -16,12 +16,12 @@ def dbSNP_get_variant_by_rsid(
     validate: bool = True,
 ) -> dict[str, Any]:
     """
-    Fetch dbSNP variant by rsID using NCBI Variation Services (refsnp endpoint).
+    Get variant information from dbSNP by rsID. Returns genomic coordinates, alleles, and basic varia...
 
     Parameters
     ----------
     rsid : str
-        rsID without 'rs' prefix or with (e.g., rs699 or 699).
+        dbSNP rsID (e.g., 'rs12345', '12345')
     stream_callback : Callable, optional
         Callback for streaming output
     use_cache : bool, default False
@@ -36,11 +36,11 @@ def dbSNP_get_variant_by_rsid(
     # Handle mutable defaults to avoid B006 linting error
 
     return get_shared_client().run_one_function(
-        {"name": "dbSNP_get_variant_by_rsid", "arguments": {"rsid": rsid}},
+        {"name": "dbsnp_get_variant_by_rsid", "arguments": {"rsid": rsid}},
         stream_callback=stream_callback,
         use_cache=use_cache,
         validate=validate,
     )
 
 
-__all__ = ["dbSNP_get_variant_by_rsid"]
+__all__ = ["dbsnp_get_variant_by_rsid"]

tooluniverse/tools/dbsnp_get_frequencies.py

@@ -0,0 +1,46 @@
+"""
+dbsnp_get_frequencies
+
+Get allele frequencies for a variant from dbSNP. Returns population-specific allele frequency data.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def dbsnp_get_frequencies(
+    rsid: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Get allele frequencies for a variant from dbSNP. Returns population-specific allele frequency data.
+
+    Parameters
+    ----------
+    rsid : str
+        dbSNP rsID (e.g., 'rs12345', '12345')
+    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": "dbsnp_get_frequencies", "arguments": {"rsid": rsid}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["dbsnp_get_frequencies"]

tooluniverse/tools/dbsnp_search_by_gene.py

@@ -0,0 +1,52 @@
+"""
+dbsnp_search_by_gene
+
+Search for variants in a specific gene. Returns variants associated with the gene symbol.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def dbsnp_search_by_gene(
+    gene_symbol: str,
+    limit: Optional[int] = 20,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Search for variants in a specific gene. Returns variants associated with the gene symbol.
+
+    Parameters
+    ----------
+    gene_symbol : str
+        Gene symbol (e.g., 'BRCA1', 'TP53', 'APOE')
+    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": "dbsnp_search_by_gene",
+            "arguments": {"gene_symbol": gene_symbol, "limit": limit},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["dbsnp_search_by_gene"]

tooluniverse/tools/download_binary_file.py

@@ -0,0 +1,66 @@
+"""
+download_binary_file
+
+Download binary files (images, videos, executables) with chunked
+streaming for better memory management.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def download_binary_file(
+    url: str,
+    output_path: str,
+    chunk_size: Optional[int] = 1048576,
+    timeout: Optional[int] = 30,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Download binary files (images, videos, executables) with chunked
+    streaming for better memory management.
+
+    Parameters
+    ----------
+    url : str
+        HTTP or HTTPS URL to download from
+    output_path : str
+        Full path where to save the binary file
+        (e.g., /tmp/image.jpg or C:/Users/Downloads/file.pdf)
+    chunk_size : int
+        Download chunk size in bytes (default: 1MB for binary files)
+    timeout : int
+        Request timeout in seconds
+    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": "download_binary_file",
+            "arguments": {
+                "url": url,
+                "output_path": output_path,
+                "chunk_size": chunk_size,
+                "timeout": timeout,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["download_binary_file"]

tooluniverse/tools/download_file.py

@@ -0,0 +1,71 @@
+"""
+download_file
+
+Download files from HTTP/HTTPS URLs with cross-platform support (Windows, Mac, Linux). Similar to...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def download_file(
+    url: str,
+    output_path: Optional[str] = None,
+    timeout: Optional[int] = 30,
+    return_content: Optional[bool] = False,
+    chunk_size: Optional[int] = 8192,
+    follow_redirects: Optional[bool] = True,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Download files from HTTP/HTTPS URLs with cross-platform support (Windows, Mac, Linux). Similar to...
+
+    Parameters
+    ----------
+    url : str
+        HTTP or HTTPS URL to download from (e.g., https://example.com/file.txt)
+    output_path : str
+        Optional path to save the file. If not specified, file will be saved to syste...
+    timeout : int
+        Request timeout in seconds
+    return_content : bool
+        If true, return file content as text instead of saving to disk (default: false)
+    chunk_size : int
+        Download chunk size in bytes (default: 8192)
+    follow_redirects : bool
+        Follow HTTP redirects (default: true)
+    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": "download_file",
+            "arguments": {
+                "url": url,
+                "output_path": output_path,
+                "timeout": timeout,
+                "return_content": return_content,
+                "chunk_size": chunk_size,
+                "follow_redirects": follow_redirects,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["download_file"]

tooluniverse/tools/download_text_content.py

@@ -0,0 +1,55 @@
+"""
+download_text_content
+
+Download and return text content from URLs. Optimized for text files with automatic encoding dete...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def download_text_content(
+    url: str,
+    encoding: Optional[str] = None,
+    timeout: Optional[int] = 30,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Download and return text content from URLs. Optimized for text files with automatic encoding dete...
+
+    Parameters
+    ----------
+    url : str
+        HTTP or HTTPS URL to download text from
+    encoding : str
+        Text encoding (e.g., utf-8, latin1). Auto-detected if not specified.
+    timeout : int
+        Request timeout in seconds
+    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": "download_text_content",
+            "arguments": {"url": url, "encoding": encoding, "timeout": timeout},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["download_text_content"]

tooluniverse/tools/dynamic_package_discovery.py

@@ -0,0 +1,59 @@
+"""
+dynamic_package_discovery
+
+Dynamically searches PyPI and evaluates packages based on requirements
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def dynamic_package_discovery(
+    requirements: str,
+    functionality: Optional[str] = None,
+    constraints: Optional[dict[str, Any]] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Dynamically searches PyPI and evaluates packages based on requirements
+
+    Parameters
+    ----------
+    requirements : str
+        Description of what the package should do
+    functionality : str
+        Specific functionality needed
+    constraints : dict[str, Any]
+        Constraints (python version, license, etc.)
+    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": "dynamic_package_discovery",
+            "arguments": {
+                "requirements": requirements,
+                "functionality": functionality,
+                "constraints": constraints,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["dynamic_package_discovery"]

tooluniverse/tools/ensembl_get_sequence.py

@@ -0,0 +1,52 @@
+"""
+ensembl_get_sequence
+
+Get DNA sequence for a gene, transcript, or genomic region. Returns sequence in FASTA format.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ensembl_get_sequence(
+    sequence_id: str,
+    type: Optional[str] = "genomic",
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Get DNA sequence for a gene, transcript, or genomic region. Returns sequence in FASTA format.
+
+    Parameters
+    ----------
+    sequence_id : str
+        Ensembl gene/transcript ID or genomic region (e.g., 'ENSG00000139618' or '1:1...
+    type : str
+        Sequence type: 'genomic', 'cds', 'cdna', 'peptide'
+    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": "ensembl_get_sequence",
+            "arguments": {"sequence_id": sequence_id, "type": type},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ensembl_get_sequence"]

tooluniverse/tools/{Ensembl_lookup_gene_by_symbol.py → ensembl_get_variants.py}

@@ -1,15 +1,15 @@
 """
-Ensembl_lookup_gene_by_symbol
+ensembl_get_variants
 
-Lookup Ensembl gene by species and gene symbol, returning core metadata and coordinates (uses /xr...
+Get genetic variants in a genomic region. Returns SNP and indel information.
 """
 
 from typing import Any, Optional, Callable
 from ._shared_client import get_shared_client
 
 
-def Ensembl_lookup_gene_by_symbol(
-    symbol: str,
+def ensembl_get_variants(
+    region: str,
     species: Optional[str] = "homo_sapiens",
     *,
     stream_callback: Optional[Callable[[str], None]] = None,
@@ -17,14 +17,14 @@ def Ensembl_lookup_gene_by_symbol(
     validate: bool = True,
 ) -> dict[str, Any]:
     """
-    Lookup Ensembl gene by species and gene symbol, returning core metadata and coordinates (uses /xr...
+    Get genetic variants in a genomic region. Returns SNP and indel information.
 
     Parameters
     ----------
+    region : str
+        Genomic region in format 'chromosome:start-end' (e.g., '13:32315086-32400268')
     species : str
-        Species name (e.g., 'homo_sapiens').
-    symbol : str
-        Gene symbol (e.g., BRCA1).
+        Species name
     stream_callback : Callable, optional
         Callback for streaming output
     use_cache : bool, default False
@@ -40,8 +40,8 @@ def Ensembl_lookup_gene_by_symbol(
 
     return get_shared_client().run_one_function(
         {
-            "name": "Ensembl_lookup_gene_by_symbol",
-            "arguments": {"species": species, "symbol": symbol},
+            "name": "ensembl_get_variants",
+            "arguments": {"region": region, "species": species},
         },
         stream_callback=stream_callback,
         use_cache=use_cache,
@@ -49,4 +49,4 @@ def Ensembl_lookup_gene_by_symbol(
     )
 
 
-__all__ = ["Ensembl_lookup_gene_by_symbol"]
+__all__ = ["ensembl_get_variants"]

tooluniverse/tools/ensembl_lookup_gene.py

@@ -0,0 +1,46 @@
+"""
+ensembl_lookup_gene
+
+Lookup gene information by Ensembl gene ID or symbol. Returns gene details including location, de...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ensembl_lookup_gene(
+    gene_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Lookup gene information by Ensembl gene ID or symbol. Returns gene details including location, de...
+
+    Parameters
+    ----------
+    gene_id : str
+        Ensembl gene ID or symbol (e.g., 'ENSG00000139618' or 'BRCA1')
+    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": "ensembl_lookup_gene", "arguments": {"gene_id": gene_id}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ensembl_lookup_gene"]