geney 1.4.40__py3-none-any.whl → 1.4.41__py3-none-any.whl

geney/utils.py

@@ -1,254 +0,0 @@
-__all__ = ['is_monotonic', 'contains', 'unload_json', 'unload_pickle', 'dump_json', 'dump_pickle', 'generate_random_nucleotide_sequences', 'generate_random_sequence', 'short_hash_of_list']
-
-import pickle
-import json
-from pathlib import Path
-from bisect import bisect_left
-import hashlib
-import random
-from typing import Any, List, Sequence, Union
-
-# def is_monotonic(A):
-#     x, y = [], []
-#     x.extend(A)
-#     y.extend(A)
-#     x.sort()
-#     y.sort(reverse=True)
-#     if (x == A or y == A):
-#         return True
-#     return False
-
-
-# def available_genes(organism='hg38'):
-#     from geney import config
-#     annotation_path = config[organism]['MRNA_PATH'] / 'protein_coding'
-#     return sorted(list(set([m.stem.split('_')[-1] for m in annotation_path.glob('*')])))
-
-
-def contains(a: Sequence[Any], x: Any) -> bool:
-    """Check if sorted sequence contains value using binary search.
-    
-    Args:
-        a: Sorted sequence to search in
-        x: Value to search for
-        
-    Returns:
-        True if value is found, False otherwise
-        
-    Raises:
-        TypeError: If sequence is not sortable
-    """
-    if not hasattr(a, '__len__') or not hasattr(a, '__getitem__'):
-        raise TypeError("First argument must be a sequence")
-        
-    try:
-        i = bisect_left(a, x)
-        return i != len(a) and a[i] == x
-    except TypeError as e:
-        raise TypeError(f"Cannot compare types in sequence: {e}") from e
-
-
-def unload_json(file_path: Union[str, Path]) -> Any:
-    """Load data from JSON file.
-    
-    Args:
-        file_path: Path to JSON file
-        
-    Returns:
-        Loaded data structure
-        
-    Raises:
-        FileNotFoundError: If file doesn't exist
-        JSONDecodeError: If file contains invalid JSON
-    """
-    file_path = Path(file_path)
-    
-    if not file_path.exists():
-        raise FileNotFoundError(f"JSON file not found: {file_path}")
-        
-    try:
-        with open(file_path, 'r', encoding='utf-8') as f:
-            data = json.load(f)
-        return data
-    except json.JSONDecodeError as e:
-        raise json.JSONDecodeError(f"Invalid JSON in file {file_path}: {e.msg}", e.doc, e.pos) from e
-
-
-def dump_json(file_path: Union[str, Path], payload: Any, indent: int = 2) -> None:
-    """Save data to JSON file.
-    
-    Args:
-        file_path: Path to output JSON file
-        payload: Data to save
-        indent: JSON indentation level
-        
-    Raises:
-        TypeError: If payload is not JSON serializable
-        PermissionError: If cannot write to file
-    """
-    file_path = Path(file_path)
-    
-    # Create parent directory if it doesn't exist
-    file_path.parent.mkdir(parents=True, exist_ok=True)
-    
-    try:
-        with open(file_path, 'w', encoding='utf-8') as f:
-            json.dump(payload, f, indent=indent, ensure_ascii=False)
-    except TypeError as e:
-        raise TypeError(f"Cannot serialize data to JSON: {e}") from e
-
-
-def unload_pickle(file_path: Union[str, Path]) -> Any:
-    """Load data from pickle file.
-    
-    Args:
-        file_path: Path to pickle file
-        
-    Returns:
-        Loaded data structure
-        
-    Raises:
-        FileNotFoundError: If file doesn't exist
-        pickle.UnpicklingError: If file contains invalid pickle data
-    """
-    file_path = Path(file_path)
-    
-    if not file_path.exists():
-        raise FileNotFoundError(f"Pickle file not found: {file_path}")
-        
-    try:
-        with open(file_path, 'rb') as f:
-            data = pickle.load(f)
-        return data
-    except pickle.UnpicklingError as e:
-        raise pickle.UnpicklingError(f"Invalid pickle data in file {file_path}: {e}") from e
-
-
-def dump_pickle(file_path: Union[str, Path], payload: Any) -> None:
-    """Save data to pickle file.
-    
-    Args:
-        file_path: Path to output pickle file
-        payload: Data to save
-        
-    Raises:
-        PermissionError: If cannot write to file
-    """
-    file_path = Path(file_path)
-    
-    # Create parent directory if it doesn't exist
-    file_path.parent.mkdir(parents=True, exist_ok=True)
-    
-    try:
-        with open(file_path, 'wb') as f:
-            pickle.dump(payload, f)
-    except Exception as e:
-        raise RuntimeError(f"Failed to save pickle file {file_path}: {e}") from e
-
-
-
-def is_monotonic(A: Sequence[Any]) -> bool:
-    """Check if sequence is monotonic (non-decreasing or non-increasing).
-    
-    Args:
-        A: Sequence to check
-        
-    Returns:
-        True if sequence is monotonic, False otherwise
-        
-    Raises:
-        TypeError: If sequence elements are not comparable
-    """
-    if not hasattr(A, '__len__') or len(A) < 2:
-        return True
-        
-    try:
-        return (all(x <= y for x, y in zip(A, A[1:])) or 
-                all(x >= y for x, y in zip(A, A[1:])))
-    except TypeError as e:
-        raise TypeError(f"Cannot compare sequence elements: {e}") from e
-
-
-def generate_random_sequence(length: int) -> str:
-    """Generate a random DNA sequence of given length.
-    
-    Args:
-        length: Length of sequence to generate
-        
-    Returns:
-        Random DNA sequence containing only A, C, G, T
-        
-    Raises:
-        ValueError: If length is not positive
-    """
-    if not isinstance(length, int):
-        raise TypeError(f"Length must be integer, got {type(length).__name__}")
-        
-    if length <= 0:
-        raise ValueError(f"Length must be positive, got {length}")
-        
-    return ''.join(random.choices('ACGT', k=length))
-
-def generate_random_nucleotide_sequences(num_sequences: int, min_len: int = 3, max_len: int = 10) -> List[str]:
-    """
-    Generate random DNA sequences of variable lengths.
-
-    Args:
-        num_sequences: Number of sequences to generate
-        min_len: Minimum sequence length
-        max_len: Maximum sequence length
-
-    Returns:
-        List of random nucleotide sequences
-        
-    Raises:
-        ValueError: If parameters are invalid
-    """
-    if not isinstance(num_sequences, int) or num_sequences <= 0:
-        raise ValueError(f"num_sequences must be positive integer, got {num_sequences}")
-        
-    if not isinstance(min_len, int) or min_len <= 0:
-        raise ValueError(f"min_len must be positive integer, got {min_len}")
-        
-    if not isinstance(max_len, int) or max_len <= 0:
-        raise ValueError(f"max_len must be positive integer, got {max_len}")
-        
-    if min_len > max_len:
-        raise ValueError(f"min_len ({min_len}) cannot be greater than max_len ({max_len})")
-    
-    nucleotides = ['A', 'C', 'G', 'T']
-    lengths = list(range(min_len, max_len + 1))
-    
-    sequences = [
-        ''.join(random.choices(nucleotides, k=random.choice(lengths)))
-        for _ in range(num_sequences)
-    ]
-    return sequences
-
-
-
-def short_hash_of_list(numbers: List[Any], length: int = 5) -> str:
-    """Generate a short hash string from a list of numbers.
-    
-    Args:
-        numbers: List of values to hash
-        length: Length of output hash string
-        
-    Returns:
-        Short hash string
-        
-    Raises:
-        ValueError: If length is not positive
-    """
-    if not isinstance(length, int) or length <= 0:
-        raise ValueError(f"Length must be positive integer, got {length}")
-        
-    if length > 64:  # SHA256 hex digest is 64 characters
-        raise ValueError(f"Length cannot exceed 64, got {length}")
-    
-    try:
-        encoded = repr(numbers).encode('utf-8')
-        full_hash = hashlib.sha256(encoded).hexdigest()
-        return full_hash[:length]
-    except Exception as e:
-        raise RuntimeError(f"Failed to generate hash: {e}") from e

geney-1.4.40.dist-info/RECORD

@@ -1,14 +0,0 @@
-geney/__init__.py,sha256=1V1SxqcLFPxRJOqr4VmGillv1r4_azJtbmNtf0pZ18I,684
-geney/engines.py,sha256=ZK6x0YdY8_yPRTUmhwL8GWcuS3U5OotqMJBKPE-z7cE,10548
-geney/oncosplice.py,sha256=eGQQl9ftmoFENMYBWoJtenKWmzyxR9N1of5cZst_bHQ,18014
-geney/pipelines.py,sha256=zK1zDFFAxElnxgXWeM_xZqEZtwxyF7CwmtQLCkKOq2w,3356
-geney/samples.py,sha256=3KrWNILHYql-vPC_TidkzqDuFaLx3JSJZbUoVW2RTlo,92
-geney/splice_graph.py,sha256=wCStApnnrwbej_yhk_s39p5sQatRtqg9Ve8GqH2ZfGA,14849
-geney/splicing_table.py,sha256=mXDXUr4h_q7grYQpmXO5Ex15Mt7BchieWF9lawd6src,5412
-geney/transcripts.py,sha256=I6NmBcW9QG5XtRumn6i0TeT8tKECHQycsbSSZ7e8LZo,2601
-geney/utils.py,sha256=pv4_LPIzjYAxwUgmufZJL6UhVVq2SllpF90ix_uH_-Q,7627
-geney/variants.py,sha256=vjbiBH-duZ4TJZyXwXbQ_VmJxCFafjeDwLNTZg3ubSc,11832
-geney-1.4.40.dist-info/METADATA,sha256=BiZJ2yQaYrHybVewBIQ2Cdw_qKNENiHoIEiFPp29xs8,952
-geney-1.4.40.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-geney-1.4.40.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.4.40.dist-info/RECORD,,