cytosnake.utils package#

Submodules#

cytosnake.utils.config_utils module#

cytosnake.utils.config_utils.load_configs(config_path: str | Path) → dict#

Returns a dictionary of given configurations

Parameters:: config_path (str | Path) – path to config file
Returns:: configuration dictionary
Return type:: dict
Raises:: FileNotFoundError – raised if provided config file paths is invalid

cytosnake.utils.config_utils.load_cytosnake_configs() → dict#

Loads in CytoSnake’s general configuration

Returns:: CytoSnake configs
Return type:: dict

cytosnake.utils.config_utils.load_data_path_configs()#

Returns path pointing where the data folder is

Returns:: Path to data folder in project directory
Return type:: Path

cytosnake.utils.config_utils.load_general_configs() → dict#

Loads cytosnake’s general configurations

Returns:#

dict: dictionary containing the cytosnake general configs

cytosnake.utils.config_utils.load_meta_path_configs() → dict#

Loads the metadata path from .cytosnake/_paths.yaml file

Returns:: meta path contents from the _paths.yaml file
Return type:: dict

cytosnake.utils.config_utils.load_workflow_path(wf_name: str) → Path#

Loads in configurations and returns path pointing to workflow

Parameters:: wf_name (str) – workflow name
Returns:: Path to workflow
Return type:: pathlib.PosixPath
Raises:: WorkFlowNotFound – Raised if the desired workflow is not found.

cytosnake.utils.config_utils.load_workflow_paths_config() → dict#

cytosnake.utils.cyto_paths module#

module: cyto_paths.py

This module will contain functions that handles cytosnake’s pathing

cytosnake.utils.cyto_paths.get_config_dir_path() → Path#

Returns path to configuration folder

Returns:: Path to config directory
Return type:: Path

cytosnake.utils.cyto_paths.get_config_fpaths() → dict#

Obtains all file paths located in the configs folder as a dictionary.

Returns:: structured dictionary with directory name and file paths as key value pairs
Return type:: dict

cytosnake.utils.cyto_paths.get_cytosnake_config_path() → Path#

Returns absolute path to CytoSnake’s general config file .

Returns:: path to cytosnake general config file
Return type:: pathlib.Path

cytosnake.utils.cyto_paths.get_cytosnake_package_path() → Path#

Returns paths where the package is installed

Returns:: Returns absolute path of where the package is installed
Return type:: Path
Raises:: FileNotFoundError – Raised if CytoSnake Package is not found

cytosnake.utils.cyto_paths.get_meta_path() → Path#

returns meta path configurational file path.

Returns:: Path object pointing to _paths.yaml config file
Return type:: Path

cytosnake.utils.cyto_paths.get_project_dirpaths(args: Namespace) → dict#

returns a dictionary containing directory name and path as key value pairs.

Parameters:: args (Namespace) – Uses argparse’s Namespace object to add additional information into the data section in _path.yaml
Returns:: directory name and path as key value pairs.
Return type:: dict

cytosnake.utils.cyto_paths.get_project_root() → Path#

Returns complete path where cytosnake performs the analysis. The function will check if .cytosnake folder exists, if not an error will be raised.

Returns:: Returns absolute path of the project folder
Return type:: Path
Raises:: FileNotFoundError – Raised with the current directory is not a project folder

cytosnake.utils.cyto_paths.get_results_dir_path() → Path#

Returns path to results directory. This is where all the outputs generated from the workflow will be placed.

Returns:: absolute path to results directory
Return type:: pathlib.Path

cytosnake.utils.cyto_paths.get_workflow_fpaths() → dict#

Obtains all file paths located in the workflows folder as a dictionary.

Returns:: Structured dictionary containing directory names and paths are key value pairs
Return type:: dict
Raises:: FileNotFoundError – Raised if the file workflows directory is not found

cytosnake.utils.cyto_paths.is_cytosnake_dir(dir_path: str | Path | None = None) → bool#

Checks if the current directory has been set up for cytosnake. Searches for the .cytosnake file in current or specified directory.

Parameters:: dir_path (Optional[str | Path]) – Path to directory. If None, current directory will be used. [Default=None]
Returns:: True if directory has been initialized for cytosnake, else False
Return type:: bool

cytosnake.utils.cytosnake_setup module#

Module: cytosnake_setup.py

This modules sets up the current directory as a project directory. Project directories are dictated by the presence of .cytosnake, which contains meta data for cytosnake to use.

cytosnake.utils.cytosnake_setup.create_cytosnake_dir() → None#

Sets up a .cytosnake folder that contains meta information that helps cytosnake’s cli functionality. This will include configurations that contains states, paths and settings.

Returns:

None – Generates a .cytosnake file in current directory
Raises
FileExistsError – Raised by pathlib.Path if `.cytosnake’ already exists

cytosnake.utils.cytosnake_setup.generate_meta_path_configs(args: Namespace) → None#

constructs a _paths.yaml file that contains the necessary path information for file handling. this allows cytosnake to know which folders to look for when performing tasks.

Returns:: creates a _paths.yaml file in the .cytosnake project directory
Return type:: none

cytosnake.utils.cytosnake_setup.setup_cytosnake_env(args: Namespace) → None#: main wrapper function that sets up current directory into a cytosnake project directory. this means that all the analysis being conducted within the current directory will allow

cytosnake.utils.cytosnake_setup.transport_project_files() → None#: obtains the necessary files from software package and transport them into current working directory

cytosnake.utils.feature_utils module#

cytosnake.utils.feature_utils.infer_dp_features(dp_profile) → list[str]#

Returns a list of Deep profiler features found within the single cell dataframe

Parameters:: dp_profile (pd.DataFrame) – dataframe features captured from deep profiler
Returns:: list of deep profiler features
Return type:: list[str]
Raises:: ValueError – Raised if no Deep profiler features are found within the given DataFrame

cytosnake.utils.file_utils module#

Module: file_utils.py

Contains functions that involves file manipulations like:

searching
transferring
creating symbolic links
creating and deleting files

cytosnake.utils.file_utils.file_search(fpath: str | Path) → dict#

Returns a list of all the files inside a directory

Parameters:: fpath (str | Path) – path to specific directory
Returns:: Returns a list of dir names and file paths as key value pairs
Return type:: dict

cytosnake.utils.file_utils.find_project_dir(steps: int | None = 10) → Path | None#

Recursively searches for project directory`.cytosnake` directory. If the directory is not found, None is returned.

steps: Optional[int]: number of recursive steps for searching. [default=10]