Filesystem API Reference

This page contains the API reference for the filesystem module.

find_files

def find_files(
    root_dir: str,
    file_type: str = 'f',
    min_depth: int = None,
    max_depth: int = None,
    name_pattern: str = None,
    exclude_dirs: List[str] = None,
    custom_filter: Callable[[str], bool] = None
) -> Generator[str, None, None]:
    """
    Find files or directories recursively from root_dir.

    Args:
        root_dir: Root directory to start the search from
        file_type: Type of files to find ('f' for files, 'd' for directories, 'l' for symlinks)
        min_depth: Minimum depth to search (0 = root_dir)
        max_depth: Maximum depth to search
        name_pattern: Glob pattern to match filenames
        exclude_dirs: List of directory names to exclude from search
        custom_filter: Custom filter function that takes a path and returns a boolean

    Returns:
        Generator yielding paths to files or directories that match the criteria
    """

This function finds files or directories recursively from a root directory, with various filtering options.

Parameters

• root_dir: Root directory to start the search from
• file_type: Type of files to find ('f' for files, 'd' for directories, 'l' for symlinks)
• min_depth: Minimum depth to search (0 = root_dir)
• max_depth: Maximum depth to search
• name_pattern: Glob pattern to match filenames
• exclude_dirs: List of directory names to exclude from search
• custom_filter: Custom filter function that takes a path and returns a boolean

Returns

Generator yielding paths to files or directories that match the criteria.

Example

# Find all Python files in the current directory and its subdirectories
for file_path in find_files(".", name_pattern="*.py"):
    print(file_path)

# Find all directories at depth 1
for dir_path in find_files(".", file_type='d', min_depth=1, max_depth=1):
    print(dir_path)

# Find all files larger than 1 MB
def is_large_file(path):
    return os.path.getsize(path) > 1_000_000

for file_path in find_files(".", custom_filter=is_large_file):
    print(file_path)

find_sequencer_runs

def find_sequencer_runs(
    root_dir: str,
    sequencer_type: str,
    completion_indicator: str = "RTAComplete.txt"
) -> Generator[str, None, None]:
    """
    Find sequencer runs of a specific type.

    Args:
        root_dir: Root directory to search for sequencer runs
        sequencer_type: Type of sequencer (miseq, nextseq, novaseq, etc.)
        completion_indicator: File that indicates a completed run

    Returns:
        Generator yielding paths to sequencer run directories
    """

This function finds sequencer runs of a specific type in a directory.

Parameters

• root_dir: Root directory to search for sequencer runs
• sequencer_type: Type of sequencer (miseq, nextseq, novaseq, etc.)
• completion_indicator: File that indicates a completed run

Returns

Generator yielding paths to sequencer run directories.

Example

# Find all completed MiSeq runs
for run_dir in find_sequencer_runs("/path/to/sequencer/data", "miseq"):
    print(run_dir)

# Find all completed NovaSeq runs with a custom completion indicator
for run_dir in find_sequencer_runs("/path/to/sequencer/data", "novaseq", completion_indicator="CopyComplete.txt"):
    print(run_dir)

_validate_sequencer_run

def _validate_sequencer_run(
    run_dir: str,
    sequencer_type: str
) -> bool:
    """
    Validate that a directory is a valid sequencer run.

    Args:
        run_dir: Path to the run directory
        sequencer_type: Type of sequencer (miseq, nextseq, novaseq, etc.)

    Returns:
        True if the directory is a valid sequencer run, False otherwise
    """

This function validates that a directory is a valid sequencer run of a specific type.

Parameters

• run_dir: Path to the run directory
• sequencer_type: Type of sequencer (miseq, nextseq, novaseq, etc.)

Returns

True if the directory is a valid sequencer run, False otherwise.

Example

# Check if a directory is a valid MiSeq run
is_valid = _validate_sequencer_run("/path/to/run/directory", "miseq")

Notes

• The find_files function uses generators to yield results one at a time, which makes it memory-efficient even when searching large directory trees.
• The find_sequencer_runs function uses _validate_sequencer_run to validate that a directory is a valid sequencer run.
• The _validate_sequencer_run function checks for required files and naming patterns specific to each sequencer type.