wellshuffled 0.1.0

A command line utility for shuffling biological sample positions in microwell plates.

WellShuffled 🎲

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Installation

There are two ways to install wellshuffled:

Option 1: Install from GitLab using pip

You can install the latest version of wellshuffled directly from GitLab by running the following command:

pip install git+https://github.com/exfab/wellshuffled.git

Option 2: Install from a local clone

1. Clone the repository:

   git clone https://github.com/exfab/wellshuffled.git
   cd wellshuffled
   

2. Install using pip:

   pip install .
   

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Usage

The main command is wellshuffled. It has two subcommands: shuffle and trace.

After installation, you can run the tool from your terminal like this:

wellshuffled --help

shuffle Command

The shuffle command generates randomized plate maps from a list of sample IDs.

wellshuffled shuffle <sample_file> <output_path> [OPTIONS]

Options:

• --plates, -n: Number of plates to generate. Default is 1.
• --size: Well plate size (96 or 384). Default is 96.
• --simple: Use simple randomization (disables neighbor-awareness).
• --separate-files: Save each plate map to a separate CSV file.
• --seed: Set the random seed for reproducible results.
• --control-prefix: Prefix used to identify control samples.
• --fixed-map: Manually specify fixed control locations (e.g., "A1:control-85,H12:control-96").
• --fixed-map-file: Manually specify fixed control locations from a CSV file.
• --nonstandard: Allow for the use of non-standard plate dimensions.
• --nonstandard_dims: The dimensions (x, y) for the nonstandard plate.

trace Command

The trace command traces the locations of samples across multiple plates.

wellshuffled trace <input_path> [OPTIONS]

Options:

• --output-csv: Optional path to save the full trajectory map as a CSV file.
• --numeric: Return the plate positions as 1-based column major numeric values.

Examples

1. Generate a single 96-well plate with neighbor-awareness:

wellshuffled shuffle example_files/samples.csv single_plate.csv --size 96

2. Generate 5 plates and save to a single combined file:

wellshuffled shuffle example_files/samples.csv combined_layouts.csv --plates 5

3. Generate 3 plates and save them to separate files in a directory: The output path my_layouts will be created if it doesn't exist.

wellshuffled shuffle example_files/samples.csv my_layouts --plates 3 --separate-files

4. Generate a reproducible layout using a seed: Running this command multiple times with --seed 123 will always produce the exact same output file.

wellshuffled shuffle example_files/samples.csv reproducible_run.csv --plates 4 --seed 123

5. Use the simple randomization logic (disabling neighbor-awareness):

wellshuffled shuffle example_files/samples.csv simple_run.csv --simple

6. Generate a plate with a predefined layout for the first plate: The samples_with_positions.csv file contains a second column with the initial well positions.

wellshuffled shuffle example_files/samples_with_positions.csv predefined_layout.csv

7. Provide Nonstandard plate dimensions: We use the --nonstandard flag to ensure you are explicitly meaning to pass in nonstandard plate dimensions along with the --nonstandard_dims=[RowsxColumns] or [Rows,Columns]

wellshuffled shuffle example_files/60_samples_w_controls_initial_pos.csv nonstandard_layout.csv --nonstandard --nonstandard_dims=6,10

8. View all available options and help:

wellshuffled --help

Development Installation

If you want to contribute to the development of wellshuffled, you can set up a development environment by following these steps:

1. Clone the repository:

   git clone https://github.com/exfab/wellshuffled.git
   cd wellshuffled
   

2. Sync the project using uv:

   This project is managed with uv, a fast Python package installer and resolver.

   uv sync
   

3. Installing without uv sync or using venv

   If you encounter errors with uv sync, you can install the project manually in editable mode:

   Using uv:

   uv run python -m pip install -e .
   

   Using venv:

   python -m venv .venv
   source .venv/bin/activate
   python -m pip install -e .